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-- Table structure for table `categories`
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CREATE TABLE `categories` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;

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-- Dumping data for table `categories`
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INSERT INTO `categories` VALUES (1,'Advanced Sampling'),(2,'Configuration Manipulation'),(3,'File Input and Output'),(4,'Parallel'),(5,'Parser'),(6,'Properties'),(7,'Simulation and Control'),(8,'Visualization'),(9,'Miscellaneous');

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-- Table structure for table `entries`
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CREATE TABLE `entries` (
  `name` varchar(255) DEFAULT NULL,
  `data_type` varchar(255) DEFAULT NULL,
  `default_value` varchar(250) DEFAULT NULL,
  `source` varchar(50) NOT NULL,
  `description` text,
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `category_id` int(11) DEFAULT NULL,
  PRIMARY KEY (`id`)
) ENGINE=MyISAM AUTO_INCREMENT=927 DEFAULT CHARSET=latin1;

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-- Dumping data for table `entries`
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INSERT INTO `entries` VALUES ('dope_Yttria','COMMAND','N/A','bmb','If <tt>input = [ <i>yttriaconc</i> ]</tt> is set before calling the command, then\n\n<p>\nrelabel certain (randomly chosen) Zr atoms as Y atoms and remove certain (randomly\nchosen) Oxygen atoms (creating vacancies) to achieve the specified Yttria doping\nconcentration (<tt>yttriaconc</tt>).\n',1,2),('eamgrid','INT','6000\n','eam','The length of the table to be read for the arrays\n<tt>rho</tt>, <tt>rhop</tt>, <tt>phi</tt>, <tt>phip</tt>, &hellip;.\n',2,3),('pottype','INT','1\n','eam','1 for EAM, 2 for MEAM (not implemented in this program).\n',3,3),('eamfiletype','INT','0\n','eam','If <tt>eamfiletype = 2</tt> then the EAM potential file also \ncontains the cross potential data (<tt>phix</tt> and <tt>phipx</tt>)\nbetween two elements.\n',4,3),('readeam','COMMAND','N/A','eam','Read parameters for the EAM potential contained in the <tt>potfile</tt>.\n\n<p>\nUsage:\n <tt>potfile = <i>filename</i> eamgrid = <i>n</i> readeam </tt>\n\n<p>\nExample: <tt>MD++/scripts/Examples/example05-au.tcl</tt>\n\n',5,3),('readMEAM','COMMAND','N/A','eam','Empty function.  Do not use.\n',6,3),('Broadcast_EAM_Param','COMMAND','N/A','eam','CPU 0 (master) broadcast EAM potential parameters to other CPUs (slaves).\n\n<p>\nNeeded before <tt>eval_parallel</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',7,4),('F_Ewald','DOUBLE','N/A','ewald','Array containing Ewald contribution to the force on each atom.\n',8,6),('F_Ewald_Real','DOUBLE','N/A','ewald','Array containing the real space part of the Ewald contribution to the force on each atom.\n',9,6),('F_Ewald_Rec','DOUBLE','N/A','ewald','Array containing the reciprocal space part of the Ewald contribution to the force on each atom.\n',10,6),('EPOT_IND_Ewald','DOUBLE','N/A','ewald','Array containing Ewald contribution to the local energy of each atom.\n',11,6),('EPOT_IND_Ewald_Real','DOUBLE','N/A','ewald','Array containing the real space part of the Ewald contribution to the local energy of each atom.\n',12,6),('EPOT_IND_Ewald_Rec','DOUBLE','N/A','ewald','Array containing the reciprocal space part of the Ewald contribution to the local energy of each atom.\n',13,6),('A','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',14,6),('d','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',15,6),('beta','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',16,6),('c','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',17,6),('c0','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',18,6),('c1','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',19,6),('c2','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',20,6),('alpha','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',21,6),('b0','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',22,6),('B','DOUBLE','N/A','fs','Parameters in the FS potential.\n\n<p>\nIt will be specified by the <tt>readpot</tt> command.\n',23,6),('readpot','COMMAND','N/A','fs','Read parameters for the FS potential specified in the <tt>potfile</tt>.\n',24,3),('Broadcast_FS_Param','COMMAND','N/A','fs','CPU 0 (master) broadcast FS potential parameters to other CPUs (slaves).\n\n<p>\nNeeded before <tt>eval_parallel</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',25,4),('rhoh','DOUBLE','N/A','fs','Array containing electron density at each atom.\n\n<p>\nFor diagnostic purposes.\n',26,6),('af','DOUBLE','N/A','fs','Array containing the square root of the electron density at each atom.\n\n<p>\nFor diagnostic purposes.\n',27,6),('myname','STRING','N/A','ising','Empty variable.  Do not use.\n',28,5),('command','STRING','N/A','ising','Has similar meaning as the same variable in md\n',29,5),('input','DOUBLE','N/A','ising','Has similar meaning as the same variable in md\n',30,5),('NX','INT','100\n','ising','<tt>NX</tt>, <tt>NY</tt>, <tt>NZ</tt> specify the size of the Ising model.\n',31,6),('NY','INT','100\n','ising','<tt>NX</tt>, <tt>NY</tt>, <tt>NZ</tt> specify the size of the Ising model.\n',32,6),('NZ','INT','1\n','ising','<tt>NX</tt>, <tt>NY</tt>, <tt>NZ</tt> specify the size of the Ising model.\n',33,6),('nsample','INT','100\n','ising','Number of samples (i.e. tests) for command <tt>ComputeSuccessRate</tt>.\n',34,6),('nsuccess','INT','0\n','ising','Number of successful outcomes in <tt>ComputeSuccessRate</tt>.\n\n<p>\nAlso see <tt>nsample</tt>.\n',35,6),('kBT','DOUBLE','N/A','ising','<tt>kBT</tt> is the temperature in the Ising model\n',36,6),('J','DOUBLE','N/A','ising','<tt>J</tt> and <tt>H</tt> are two parameters in the Hamiltonian of the Ising model\n',37,6),('H','DOUBLE','N/A','ising','<tt>J</tt> and <tt>H</tt> are two parameters in the Hamiltonian of the Ising model\n',38,6),('totalsteps','INT','N/A','ising','Has similar meaning as the same variable in md\n',39,7),('savepropfreq','INT','N/A','ising','Has similar meaning as the same variable in md\n',40,7),('randseed','INT','N/A','ising','Has similar meaning as the same variable in md\n',41,7),('curstep','INT','N/A','ising','Has similar meaning as the same variable in md\n',42,7),('continue_curstep','INT','N/A','ising','Has similar meaning as the same variable in md\n',43,7),('N_lgst_cluster','INT','N/A','ising','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',44,1),('N_lgst_avg','INT','N/A','ising','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',45,1),('saveFFScn','INT','N/A','ising','Has similar meaning as the same variable in md\n',46,1),('FFSoption','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',47,1),('FFSpruning','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',48,1),('FFScn_weight','DOUBLE','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',49,1),('FFS_Pp','DOUBLE','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',50,1),('FFS0_check','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',51,1),('lambda_A','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',52,1),('lambda_B','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',53,1),('FFScurstep','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',54,1),('FFSautoend','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',55,1),('YES_UMB','INT','N/A','ising','Umbrella Sampling parameter\n',56,1),('UMB_K','DOUBLE','N/A','ising','Umbrella Sampling parameter\n',57,1),('UMB_equilstep','INT','N/A','ising','Umbrella Sampling parameter\n',58,1),('UMB_curstep','INT','N/A','ising','Umbrella Sampling parameter\n',59,1),('n_center','INT','0\n','ising','Umbrella Sampling parameter\n',60,1),('delta_n','INT','0\n','ising','Umbrella Sampling parameter\n',61,1),('Kinetic','INT','N/A','ising','Has similar meaning as the same variable in md\n',62,1),('Kinetic_Time','DOUBLE','N/A','ising','Has similar meaning as the same variable in md\n',63,1),('Kinetic_Swip','INT','N/A','ising','Has similar meaning as the same variable in md\n',64,1),('savecn','INT','N/A','ising','Has similar meaning as the same variable in md\n',65,3),('saveprop','INT','N/A','ising','Has similar meaning as the same variable in md\n',66,3),('savecnfreq','INT','N/A','ising','Has similar meaning as the same variable in md\n',67,3),('savepropfreq','INT','N/A','ising','Has similar meaning as the same variable in md\n',68,3),('printfreq','INT','N/A','ising','Has similar meaning as the same variable in md\n',69,3),('calcryfreq','INT','100\n','ising','During Monte Carlo simulations, the command <tt>calcrystalorder</tt> is called\nwhen <tt>curstep</tt> is a multiple of <tt>calcryfreq</tt> and when\n<tt>iter</tt> is a multiple of <tt>calcryfreq1</tt>.\n\n<p>\nFor details, see Seunghwa Ryu.\n',70,3),('calcryfreq1','INT','1\n','ising','During Monte Carlo simulations, the command <tt>calcrystalorder</tt> is called\nwhen <tt>curstep</tt> is a multiple of <tt>calcryfreq</tt> and when\n<tt>iter</tt> is a multiple of <tt>calcryfreq1</tt>.\n\n<p>\nFor details, see Seunghwa Ryu.\n',71,3),('filecounter','INT','N/A','ising','Has similar meaning as the same variable in md\n',72,3),('FFSfilecounter','INT','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',73,3),('incnfile','STRING','N/A','ising','Has similar meaning as the same variable in md\n',74,3),('finalcnfile','STRING','N/A','ising','Has similar meaning as the same variable in md\n',75,3),('outpropfile','STRING','N/A','ising','Has similar meaning as the same variable in md\n',76,3),('intercnfile','STRING','N/A','ising','Has similar meaning as the same variable in md\n',77,3),('FFScnfile','STRING','N/A','ising','Parameter in Forward Flux Sampling (FFS) simulations\n',78,3),('zipfiles','INT','N/A','ising','Has similar meaning as the same variable in md\n',79,3),('win_width','INT','N/A','ising','Has similar meaning as the same variable in md\n',80,8),('win_height','INT','N/A','ising','Has similar meaning as the same variable in md\n',81,8),('plotfreq','INT','N/A','ising','Has similar meaning as the same variable in md\n',82,8),('atomradius','DOUBLE','N/A','ising','Has similar meaning as the same variable in md\n',83,8),('backgroundcolor','STRING','N/A','ising','Has similar meaning as the same variable in md\n',84,8),('rotateangles','DOUBLE','N/A','ising','Has similar meaning as the same variable in md\n',85,8),('rotateangles','STRING','N/A','ising','Has similar meaning as the same variable in md\n',86,8),('atomcolor','STRING','N/A','ising','Has similar meaning as the same variable in md\n',87,8),('atomcolor','STRING','N/A','ising','Has similar meaning as the same variable in md\n',88,8),('runcommand','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',89,5),('initspin','COMMAND','N/A','ising','Initialize the spin matrix <tt>S</tt>.\n\n<p>\nUsage: <tt> input = <i>style</i> initspin</tt>\n\n<p>\nIf <tt><i>style</i> = -1</tt>, then the entire matrix <tt>S</tt> is set to <tt>-1</tt>.\n<br>\nIf <tt><i>style</i> = 1</tt>, then the entire matrix <tt>S</tt> is set to <tt> 1</tt>.\n<br>\nIf <tt><i>style</i> = 0</tt>, then each entry in <tt>S</tt> is set to either\n<tt> 1</tt> or <tt>-1</tt> at random.\n',90,2),('initpath','COMMAND','N/A','ising','Usage: <tt>input = <i>pn</i> initpath</tt>\n\n<p>\nInitialize the path to be a random path going from all spin down (-1) to all spin up (+1).\nThe path will be used in future path sampling simulations.\nThere are three paths in the MD++/ising model: <tt>pathA</tt>, <tt>pathB</tt>, <tt>pathC</tt>.\nWhich one gets initialized by <tt>initpath</tt> depends on the value of <tt><i>pn</i></tt>\n(1 for <tt>pathA</tt>, 2 for <tt>pathB</tt>, 3 for <tt>pathC</tt>).\n\n<p>\nAlso see <tt>copyPathtoS</tt>.\n',91,2),('MCrun','COMMAND','N/A','ising','Perform Monte Carlo (MC) simulation.\n\n<p>\nVariables <tt>totalsteps</tt>, <tt>saveprop</tt>, <tt>savecn</tt>,\n&hellip; etc. should be set before calling this command.\n',92,7),('srand','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',93,7),('srand48','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',94,7),('srandbytime','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',95,7),('srand48bytime','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',96,7),('copyPathtoS','COMMAND','N/A','ising','Usage: <tt>input = [ <i>pn  id</i> ] copyPathtoS</tt>\n\n<p>\nCopy the spin configuration from the path to array <tt>S</tt>.\nThere are three paths in the MD++/ising model: <tt>pathA</tt>, <tt>pathB</tt>, <tt>pathC</tt>.\nWhich one gets chosen by <tt>copyPathtoS</tt> depends on the value of <tt><i>pn</i></tt>\n(1 for <tt>pathA</tt>, 2 for <tt>pathB</tt>, 3 for <tt>pathC</tt>).\n<tt><i>id</i></tt> specifies which configuration along the chosen path will be copied.\n\n<p>\nAlso see <tt>initpath</tt>, <tt>copyRchaintoCN</tt>.\n\n',97,2),('SampleMCpath','COMMAND','N/A','ising','Usage: <tt>input = [ <i>smin smax nmax pn</i> ] SampleMCpath</tt>\n\n<p>\nGenerate a new path by performing Monte Carlo simulation from an initial condition \nstored in array <tt>S</tt>.\nThe Monte Carlo simulation continues until the average spin value drops\nbelow <tt><i>smin</i></tt>, or exceeds <tt><i>smax</i></tt>, or if the average number of MC \nsteps exceeds <tt><i>nmax</i></tt>.\nThe resulting path is stored in one of the three paths: <tt>pathA</tt>, <tt>pathB</tt>, \n<tt>pathC</tt>, depending on the value of <tt><i>pn</i></tt>\n(1 for <tt>pathA</tt>, 2 for <tt>pathB</tt>, 3 for <tt>pathC</tt>).\n\n<p>\nAlso see <tt>ComputeSuccessRate</tt>.\n',98,1),('WalkonChain','COMMAND','N/A','ising','Usage: <tt>input = [ <i>smin smax nmax</i> ] WalkonChain</tt>\n\n<p>\nSample transition paths connecting two states (most spins down v.s. most spins up)\nby randomly picking a point on the existing path and generate a trajectory\n(by <tt>SampleMCpath</tt>) with this \npoint as the initial condition.  The trajectory is then used to replace half of the\noriginal path to generate a new path.\n\n<p>\nThe parameters <tt><i>smin smax nmax</i></tt> are passed to <tt>SampleMCpath</tt>.\n\n<p>\nAlso see <tt>ComputeSuccessRate</tt>.\n\n',99,1),('ComputeSuccessRate','COMMAND','N/A','ising','Usage: <tt>nsample = <i>NS</i> input = [ <i>smin smax nmax</i> ] ComputeSuccessRate</tt>\n\n<p>\nCompute the success rate of a given spin configuration stored in array <tt>S</tt>.\nby generating paths all starting from <tt>S</tt> via <tt>SampleMCpath</tt>.\n<br>\n<tt><i>NS</i></tt> is the number of path to be generated.\n<br>\nEach path is generated by a Monte Carlo simulation from configuration <tt>S</tt>, \nuntil the average spin value drops below <tt><i>smin</i></tt> (failure), \nor exceeds <tt><i>smax</i></tt> (success),\nor if the average number of MC steps exceeds <tt><i>nmax</i></tt>.\n\n<p>\nThe result is stored in the <tt>nsuccess</tt> variable.\n\n',100,1),('AnalyzeConfigs','COMMAND','N/A','ising','Usage: <tt>nsample = <i>NS</i> input = [ <i>nstart nend smin smax nmax</i> ] WalkonChain</tt>\n\n<p>\nRead in intermediate .cn files \"inter####.cn\" (in the current directory specified by\n<tt>dirname</tt>), whose numbers run from <tt><i>nstart</i></tt> to <tt><i>nend</i></tt>, \nand compute the energy, total spin, and success rate.\n\n<p>\nThe success rate is the probability of reaching state with most spins up in Monte Carlo\nsimulations starting from this configuration as the initical condition.  It is computed \nby calling <tt>ComputeSuccessRate</tt>.\n\n\n\n',101,1),('FFSprocess','COMMAND','N/A','ising','Implements the Forward Flux Sampling (FFS) algorithm.  Called within <tt>MCrun</tt>.\n',102,1),('calcrystalorder','COMMAND','N/A','ising','Group spins into clusters and determine the size of the largest cluster.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',103,1),('allocDFS','COMMAND','N/A','ising','Allocate arrays needed to analyze the size distribution of clusters (islands of opposite spin)\nin the spin configuration <tt>S</tt> generated by the Monte Carlo simulation.\n',104,1),('assign_Lam','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',105,1),('writecn','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',106,3),('readcn','COMMAND','N/A','ising','Read spin configurations from <tt>incnfile</tt>.\n',107,3),('openintercnfile','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',108,3),('openFFScnfile','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',109,3),('writeintercn','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',110,3),('writeFFScn','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',111,3),('setfilecounter','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',112,3),('setFFSfilecounter','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',113,3),('openpropfile','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',114,3),('writepath','COMMAND','N/A','ising','Usage: <tt>input = <i>pn</i> finalcnfile = <i>fname</i> writepath</tt>\n\n<p>\nWrite the path into file.\nThere are three paths in the MD++/ising model: <tt>pathA</tt>, <tt>pathB</tt>, <tt>pathC</tt>.\nWhich one gets written depends on the value of <tt><i>pn</i></tt>\n(1 for <tt>pathA</tt>, 2 for <tt>pathB</tt>, 3 for <tt>pathC</tt>).\n\n<p>\nAlso see <tt>readpath</tt>.\n',115,3),('readpath','COMMAND','N/A','ising','Usage: <tt>input = <i>pn</i> incnfile = <i>fname</i> readpath</tt>\n\n<p>\nRead path from file.\nThere are three paths in the MD++/ising model: <tt>pathA</tt>, <tt>pathB</tt>, <tt>pathC</tt>.\nWhich one gets written depends on the value of <tt><i>pn</i></tt>\n(1 for <tt>pathA</tt>, 2 for <tt>pathB</tt>, 3 for <tt>pathC</tt>).\n\n<p>\nAlso see <tt>writepath</tt>.\n\n',116,3),('openwin','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',117,8),('plot','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',118,8),('alloccolors','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',119,8),('alloccolorsX','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',120,8),('rotate','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',121,8),('saverot','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',122,8),('reversergb','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',123,8),('wintogglepause','COMMAND','N/A','ising','Has similar meaning as the same command in md.\n',124,8),('C12_00','DOUBLE','N/A','lj2','Parameter in the LJ potential between species 0 and 0.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',125,6),('C6_00','DOUBLE','N/A','lj2','Parameter in the LJ potential between species 0 and 0.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',126,6),('C12_11','DOUBLE','N/A','lj2','Parameter in the LJ potential between species 1 and 1.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',127,6),('C6_11','DOUBLE','N/A','lj2','Parameter in the LJ potential between species 1 and 1.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',128,6),('C12_01','DOUBLE','N/A','lj2','Parameter in the LJ potential between species 0 and 1.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',129,6),('C6_01','DOUBLE','N/A','lj2','Parameter in the LJ potential between species 0 and 1.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',130,6),('initLJ','COMMAND','N/A','lj2','Initialize the parameters in the LJ potential.\n\n',131,7),('C12_ij','DOUBLE','N/A','ljbond','Parameter in the LJ potential between species i and j.\n\nThe actual parameters to set in MD++ are: <tt>C12_00</tt>, <tt>C12_01</tt>, &hellip;\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',132,6),('C6_ij','DOUBLE','N/A','ljbond','Parameter in the LJ potential between species i and j.\n\nThe actual parameters to set in MD++ are: <tt>C6_00</tt>, <tt>C6_01</tt>, &hellip;\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',133,6),('BOND_R0','DOUBLE','N/A','ljbond','Equilibrium length of the bonds between nearest neighbor atoms in a lipid molecule.\n\n<p>\nAlso see <tt>BOND_K</tt>.\n',134,6),('BOND_K','DOUBLE','0\n','ljbond','Stiffness of the bond between nearest neighbor atoms in a lipid molecule modeled as a harmonic spring.\n\n<p>\nAlso see <tt>BOND_R0</tt>.\n\n',135,6),('WALL_X0','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',136,6),('WALL_K','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',137,6),('ATTRAC_R0','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',138,6),('ATTRAC_K','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',139,6),('WALL2_X0','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',140,6),('WALL2_K','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',141,6),('ATTRAC2_Y0','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',142,6),('ATTRAC2_K','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',143,6),('LMAX','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',144,6),('LAMBDA','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',145,6),('dUdLAM_WALL','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',146,6),('dUdLAM_ATT','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',147,6),('dUdLAM_WALL2','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',148,6),('dUdLAM_ATT2','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',149,6),('dUdLAM_L','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',150,6),('dUdLAM','DOUBLE','N/A','ljbond','Parameter in wall potentials to compute free energy of lipid bilayer.  Still under development.\n',151,6),('Rcut','DOUBLE','N/A','ljbond','Cut-off radius of the LJ potential.\n',152,7),('usrfile','STRING','N/A','ljbond','Name of the atomic configuration file in Atomeye .usr format, which is created\nwhen command <tt>writeatomeyeusr</tt> is called.\n\n<p>\nThe .usr file instructs Atomeye to draw bonds between which atomic pairs, \nand may also contain information about the atom color/radius and bond color/radius.\n',153,3),('initLJ','COMMAND','N/A','ljbond','Initialize the parameters in the LJ potential.\n\n',154,7),('makelipids','COMMAND','N/A','ljbond','When the array <tt>input = [ nsolvent nlipid chainlen headid bond_len nalkane alkanelen ] </tt> is set before calling this command, then\n\n<p>\ncreate an initial configuration containing solvent, lipid and alkane molecules.  Lipid and alkane molecules are chain-like molecules formed by linking a series of atoms by covalent bonds.\n',155,2),('linklipids','COMMAND','N/A','ljbond','After a configuration has been read from a file, make covalent bonds between nearest neighbor atoms in lipid and alkane molecules.\n\n<p>\nRequires the <tt>input</tt> array to be set before calling this command, in the same way as <tt>makelipids</tt>.\n',156,2),('writeatomeyeusr','COMMAND','N/A','ljbond','Write Atomeye .usr file from the current atomic configuration.  \n\n<p>\nBefore calling this function, the filename must be specified in variable\n<tt>usrfile</tt>.\n',157,3),('myname','STRING','N/A','md','Empty variable.  Do not use.\n',158,5),('command','STRING','echo Hello World\n','md','A string containing a shell command for MD++ to call by <tt>runcommand</tt>.\n\n<p>\nFor example: <tt>command = \"ls\" runcommand</tt>\n',159,5),('input','DOUBLE','N/A','md','A generic input array that is used by many commands.  The corresponding input parameters\nneed to be set before the command is called.\n\n<p>\nAlso see <tt>makedipole</tt>, <tt>makedislpolygon</tt>, \n<tt>makecylinder</tt>, <tt>scaleVel</tt>, <tt>extendbox</tt>.\n',160,5),('output_dat','DOUBLE','N/A','md','(For debugging purposes.  Not for general use.)\n',161,3),('output_str','STRING','N/A','md','For debugging purposes.  <tt>output_str</tt> is the string that contains the numerical values \nof the variables specified in <tt>output_fmt</tt>.  During MD simulation (<tt>run</tt>), every\n<tt>savepropfreq</tt> steps the <tt>output_str</tt> string is evaluated and gets written\ninto the property file.\n\n<p>\nAlso see <tt>saveprop</tt>, <tt>outpropfile</tt>.\n',162,3),('output_fmt','STRING','N/A','md','A string instructing MD++ what variables to write to the property file.  Any variable\nrecognized by MD++ can included, e.g.<br> &nbsp;\n <tt>output_fmt = \"curstep EPOT KATOM Tinst\" </tt>\n\n<p>\nExample: <tt>MD++/scripts/Examples/example05-au.tcl</tt>\n\n<p>\nAlso see <tt>saveprop</tt>, <tt>outpropfile</tt>.\n',163,3),('NP','INT','0\n','md','Total number of atoms (particles).  This variable is usually not set manually \nby the user, but is set automatically when commands such as <tt>makecrystal</tt>\nand <tt>readcn</tt> is called.  In Tcl the value of this variable can be printed\nout by, e.g.\n\n<p>\n<tt>\n puts \"Number of atoms = [MD++_Get NP]\"\n</tt>\n\n',164,6),('NP0','INT','0\n','md','Empty variable.  Do not use.\n',165,6),('NIMAGES','INT','0\n','md','A parameter for the implementation of torsional Periodic Boundary Conditions (tPBC)\nor bending Periodic Boundary Conditions (bPBC).\n\n<p>\nAlso see <tt>bendspec</tt>.\n',166,6),('NPfree','INT','0\n','md','Number of atoms <tt>i</tt> whose <tt>fixed[i] == 0</tt>.\n\n<p>\nAlso see <tt>NP</tt>, <tt>NPfixed</tt>.\n',167,6),('NPfixed','INT','0\n','md','Number of atoms <tt>i</tt> whose <tt>fixed[i] == 1</tt>.\n\n<p>\nAlso see <tt>NP</tt>, <tt>NPfree</tt>.\n',168,6),('H','DOUBLE','0\n','md','The 3x3 matrix <b>H</b> consists of three column vectors\n[<b>c</b><sub>1</sub> | <b>c</b><sub>2</sub> | <b>c</b><sub>3</sub> ], \nwhich are the repeat vector of the simulation cell (under periodic boundary\nconditions).\n\n<p>\nSee <a href=\"http://micro.stanford.edu/wiki/Output_File_Formats_in_MD++#Configuration_.cn_File\">wiki\npage</a> for more details.\n',169,6),('H0','DOUBLE','0\n','md','A copy of the <tt><b>H</b></tt> matrix.\n\n<p>\nAlso see <tt>saveH</tt>, <tt>restoreH</tt>.\n',170,6),('OMEGA','DOUBLE','N/A','md','Volume of the simulation cell, <tt>OMEGA</tt> = det ( <b>H</b> ).\n',171,6),('VIRIAL','DOUBLE','N/A','md','<tt>VIRIAL</tt> (in unit of eV) is a Rank 2 tensor (force times distance),\nwhich is an intermediate result for computing the total Virial stress\n<tt>TSTRESS</tt> (in unit of eV/&Aring;<sup>3</sup>).\n\n<p>\n<tt>TSTRESS = (VIRIAL + PSTRESS) / OMEGA</tt>\n\n<p>\nAlso see <tt>PSTRESS</tt>, <tt>TSTRESS</tt>, <tt>TSTRESSinMPa</tt>.\n',172,6),('DVIRIALDexx','DOUBLE','N/A','md','A 3x3 matrix containing the derivative of the <tt>VIRIAL</tt> matrix\nwith respect to strain <tt>e_xx = e_11</tt>.\n\n<p>\n<tt>DVIRIALDexx_ij</tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_11</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n\n<p>\nAlso see <tt>Dexx</tt>.\n',173,6),('DVIRIAL_1111','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',174,6),('DVIRIAL_2222','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',175,6),('DVIRIAL_3333','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',176,6),('DVIRIAL_1122','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',177,6),('DVIRIAL_2211','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',178,6),('DVIRIAL_2233','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',179,6),('DVIRIAL_3322','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',180,6),('DVIRIAL_3311','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',181,6),('DVIRIAL_1133','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',182,6),('DVIRIAL_1112','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',183,6),('DVIRIAL_1121','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',184,6),('DVIRIAL_1123','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',185,6),('DVIRIAL_1132','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',186,6),('DVIRIAL_1131','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',187,6),('DVIRIAL_1113','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',188,6),('DVIRIAL_2212','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',189,6),('DVIRIAL_2221','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',190,6),('DVIRIAL_2223','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',191,6),('DVIRIAL_2232','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',192,6),('DVIRIAL_2231','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',193,6),('DVIRIAL_2213','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',194,6),('DVIRIAL_3312','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',195,6),('DVIRIAL_3321','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',196,6),('DVIRIAL_3323','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',197,6),('DVIRIAL_3332','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',198,6),('DVIRIAL_3331','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',199,6),('DVIRIAL_3313','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',200,6),('DVIRIAL_1211','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',201,6),('DVIRIAL_1222','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',202,6),('DVIRIAL_1233','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',203,6),('DVIRIAL_1212','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',204,6),('DVIRIAL_1221','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',205,6),('DVIRIAL_1223','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',206,6),('DVIRIAL_1232','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',207,6),('DVIRIAL_1231','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',208,6),('DVIRIAL_1213','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',209,6),('DVIRIAL_2111','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',210,6),('DVIRIAL_2122','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',211,6),('DVIRIAL_2133','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',212,6),('DVIRIAL_2112','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',213,6),('DVIRIAL_2121','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',214,6),('DVIRIAL_2123','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',215,6),('DVIRIAL_2132','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',216,6),('DVIRIAL_2131','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',217,6),('DVIRIAL_2113','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',218,6),('DVIRIAL_2311','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',219,6),('DVIRIAL_2322','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',220,6),('DVIRIAL_2333','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',221,6),('DVIRIAL_2312','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',222,6),('DVIRIAL_2321','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',223,6),('DVIRIAL_2323','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',224,6),('DVIRIAL_2332','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',225,6),('DVIRIAL_2331','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',226,6),('DVIRIAL_2313','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',227,6),('DVIRIAL_3211','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',228,6),('DVIRIAL_3222','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',229,6),('DVIRIAL_3233','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',230,6),('DVIRIAL_3212','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',231,6),('DVIRIAL_3221','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',232,6),('DVIRIAL_3223','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',233,6),('DVIRIAL_3232','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',234,6),('DVIRIAL_3231','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',235,6),('DVIRIAL_3213','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',236,6),('DVIRIAL_3111','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',237,6),('DVIRIAL_3122','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',238,6),('DVIRIAL_3133','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',239,6),('DVIRIAL_3112','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',240,6),('DVIRIAL_3121','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',241,6),('DVIRIAL_3123','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',242,6),('DVIRIAL_3132','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',243,6),('DVIRIAL_3131','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',244,6),('DVIRIAL_3113','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',245,6),('DVIRIAL_1311','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',246,6),('DVIRIAL_1322','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',247,6),('DVIRIAL_1333','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',248,6),('DVIRIAL_1312','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',249,6),('DVIRIAL_1321','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',250,6),('DVIRIAL_1323','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',251,6),('DVIRIAL_1332','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',252,6),('DVIRIAL_1331','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',253,6),('DVIRIAL_1313','DOUBLE','N/A','md','A component of the <tt>DVIRIAL</tt> (rank 4) tensor.\n\n<p>\n<tt>DVIRIAL_ijkl </tt> = d(<tt>VIRIAL_ij</tt>) / (d<tt>e_kl</tt>)\n\n<p>\n<tt>VIRIAL</tt> is the Virial stress tensor and <tt>e</tt> is the strain tensor.\n',254,6),('Dexx','DOUBLE','0\n','md','The step size used to compute the <tt>DVIRIAL</tt> tensor by centered finite difference.\n\n<p>\nAlso see <tt>DVIRIALDexx</tt>, <tt>DVIRIAL_<i>ijkl</i></tt>.\n',255,6),('VH','DOUBLE','N/A','md','A 3x3 matrix containing the velocity of the box matrix <b>H</b> times <tt>timestep</tt>.\n',256,6),('EPOT','DOUBLE','0\n','md','The potential energy of the simulation cell in eV.\n\n<p>\nAlso see <tt>EPOT_IND</tt>, <tt>KATOM</tt>, <tt>eval</tt>.\n',257,6),('EPBOX','DOUBLE','0\n','md','Potential energy of the box in Parrinello-Raman dynamics.\n\n<p>\nAlso see <tt>EPBOX</tt>.\n',258,6),('EPOT0','DOUBLE','0\n','md','The potential energy just before the trial move in Monte Carlo simulation.\n\n<p>\nAlso see <tt>EPOT</tt>, <tt>runMC</tt>.\n',259,6),('ESTRAIN','DOUBLE','N/A','md','Empty variable.  Do not use.\n',260,6),('KATOM','DOUBLE','0\n','md','The kinetic energy of the simulation cell in eV.\n\n<p>\nAlso see <tt>EPOT</tt>.\n',261,6),('KBOX','DOUBLE','0\n','md','Kinetic energy of the box in Parrinello-Raman dynamics.\n\n<p>\nAlso see <tt>EPBOX</tt>.\n',262,6),('Tinst','DOUBLE','0\n','md','The instantaneous temperature (in K) computed from the kinetic energy of all atoms.\n\n<p>\n<tt>Tinst = KATOM / (1.5 * KB * NPfree) </tt>\n\n<p>\nAlso see <tt>KATOM</tt>, <tt>NPfree</tt>.\n',263,6),('zeta','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',264,6),('zetav','DOUBLE','N/A','md','Parameter for the Nose-Hoover thermostat.\n',265,6),('zetaa','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',266,6),('zeta2','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',267,6),('zeta3','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',268,6),('zeta4','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',269,6),('zeta5','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',270,6),('zetaNHC','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',271,6),('zetaNHCv','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',272,6),('zetaNHCa','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',273,6),('zetaNHC2','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',274,6),('zetaNHC3','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',275,6),('zetaNHC4','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',276,6),('zetaNHC5','DOUBLE','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',277,6),('HELM','DOUBLE','N/A','md','<tt>HELM = EPOT + KATOM</tt> in <tt>NVE</tt> ensemble, where <tt>EPOT</tt> is\nthe potential energy and <tt>KATOM</tt> is the kinetic energy of the atoms.  In other ensembles,\nthe energies of the thermo-stat and bario-stat are added to <tt>HELM</tt> as well.\n\n<p>\nAlso see <tt>HELMP</tt>.\n',278,6),('HELMP','DOUBLE','N/A','md','<tt>HELMP</tt> equals <tt>HELM</tt> plus additional terms to make <tt>HELMP</tt>\na conserved quantity in various ensembles, including <tt>NVE</tt>, <tt>NVT</tt>, <tt>NPH</tt>,\n<tt>NPT</tt>, &hellip;  It is useful to include <tt>HELMP</tt> in <tt>output_fmt</tt>\nso that we can check whether this quantity is conserved in the property file.\n\n<p>\nAlso see <tt>HELM</tt>, <tt>saveprop</tt>.\n',279,6),('PSTRESS','DOUBLE','N/A','md','<tt>PSTRESS</tt> (in unit of eV) is a Rank 2 tensor (mass times velocity times velocity),\nwhich is an intermediate result for computing the total Virial stress\n<tt>TSTRESS</tt> (in unit of eV/&Aring;<sup>3</sup>).\n\n<p>\n<tt>TSTRESS = (VIRIAL + PSTRESS) / OMEGA</tt>\n\n<p>\nAlso see <tt>VIRIAL</tt>, <tt>TSTRESS</tt>, <tt>TSTRESSinMPa</tt>.\n',280,6),('TSTRESS','DOUBLE','N/A','md','Total stress in the simulation cell in unit of in eV/&Aring;<sup>3</sup>.\n\n<p>\nSign convention: a hydrostatic pressure corresponds to a positive \nvalue in <tt>TSTRESS</tt>.  \nA tensile stress corresponds to negative value in <tt>TSTRES</tt>.\n\nAlso see <tt>TSTRESSinMPa</tt>.\n\n\n\n',281,6),('TSTRESSinMPa','DOUBLE','N/A','md','Total stress in the simulation cell in MPa, converted from <tt>TSTRESS</tt> (in eV/&Aring;<sup>3</sup>).\n\n<p>\n<tt>TSTRESSinMPa = TSTRESS &lowast; 160.2e3</tt>\n\n<p>\nAlso see <tt>TSTRESS</tt>.\n',282,6),('PRESSURE','DOUBLE','N/A','md','Average of the diagnoal components of the total stress \n<tt>TSTRESS</tt> matrix (in unit of eV/&Aring;<sup>3</sup>).\n\n<p>\nAlso see <tt>TSTRESS</tt>, <tt>TSTRESSinMPa</tt>.\n',283,6),('SIGMA','DOUBLE','0\n','md','A 3x3 matrix (&Sigma;) that is needed to compute <tt>GH</tt> in Parrinello-Rahman barostat.\n\n<p>\nReference: Parrinello and Rahman, J. Appl. Phys. 52, 7182 (1981), Eq.(2.24).\n\n<p>\nAlso see <tt>GH</tt>, <tt>relax_freebox</tt>.\n',284,6),('GH','DOUBLE','N/A','md','A 3x3 matrix containing the gradient of the potential energy\nwith respect to the box matrix <b>H</b>.\n\n<p>\nAlso see <tt>relax_freebox</tt>.\n',285,6),('curstep','INT','N/A','md','Current step number in MD simulation <tt>run</tt>.\n\n<p>\nIt is used to determine when whether the X-window needs to be \nrefreshed, or intermediate .cn file needs to be saved, at the current \nsimulation step.\n\n<p>\nAlso see <tt>plotfreq</tt>, <tt>savecnfreq</tt>, <tt>continue_curstep</tt>, <tt>conj_step</tt>.\n',286,6),('conj_step','INT','0\n','md','Current step number in conjugate gradient relaxation <tt>relax</tt>, \nequivalent to <tt>curstep</tt> in MD simulation <tt>run</tt>.\n\n<p>\nIt is used to determine when whether the X-window needs to be \nrefreshed, or intermediate .cn file needs to be saved, at the current \nsimulation step.\n\n<p>\nAlso see <tt>plotfreq</tt>, <tt>savecnfreq</tt>.\n',287,7),('continue_curstep','INT','0\n','md','If <tt>continue_curstep</tt> = 1, then at the beginning of MD simulation by command\n<tt>run</tt>, the variable <tt>curstep</tt> will not be reset to zero.  Instead, it will keep \nits current value and the simulation will continue for another <tt>totalsteps</tt> number of\nsteps.  In this case, the <tt>curstep</tt> entry in the property file will be monotonically\nincreasing, when the command <tt>run</tt> is called several times in the input (script or tcl) \nfile.\n',288,7),('MC_accept_ratio','DOUBLE','0\n','md','The average acceptance ratio in Monte Carlo simulations.  For maximum efficiency\nthe <tt>timestep</tt> parameter should be adjusted so that <tt>MC_accept_ratio</tt>\nis around 0.5.\n',289,6),('MC_dr','DOUBLE','N/A','md','A vector containing the random trial displacement in the current Monte Carlo simulation step.\n\n<p>\nIn Monte Carlo simulation, the maximum displacement in x, y, z directions\nis specified by variable <tt>timestep</tt> (here in unit of &Aring;).\n',290,6),('dH','DOUBLE','N/A','md','A 3x3 matrix containing the change of <tt><b>H</b></tt> matrix introduced\nin <tt>makedipole</tt> to accomodate the plastic strain of the dislocation dipole.\n\n',291,6),('dEdlambda','DOUBLE','0\n','md','The derivative of the potential function with respect to the switching parameter &lambda;\n(that goes between <tt>lambda0</tt> and <tt>lambda1</tt>) in free energy calculations.\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n',292,6),('dlambdadt','DOUBLE','0\n','md','The switching rate (d&lambda;/dt) in free energy calculations.\n\n<p>\nAlso see <tt>dEdlambda</tt>, <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n',293,6),('Wtot','DOUBLE','0\n','md','The total work done during adiabatic switching simulation.\n<tt>Wtot += dEdlambda * dlambdadt * (lambda1 - lambda0)</tt> at each time step.\n\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',294,6),('Wavg','DOUBLE','0\n','md','The average work done per time step during adiabatic switching simulation.\n<tt>Wavg = Wtot / totalsteps</tt>.\n\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',295,6),('RLIST','DOUBLE','0\n','md','The cut-off radius of the Verlet neighbor list.  It equals the cut-off radius of the\npotential plus <tt>SKIN</tt>.   This variable is usually not set manually, but is\nset automatically by the command that reads and initializes the potential.\n\n<p>\nAlso see <tt>refreshnnlist</tt>, <tt>SKIN</tt>.\n',296,7),('SKIN','DOUBLE','0\n','md','The cut-off radius of the Verlet neighbor list <tt>RLIST</tt> minus the cut-off radius of the\npotential. <tt>SKIN</tt> is usually 0.1 times the cut-off radius of the potential.\nThis variable is usually not set manually, but is set automatically by the command that \nreads and initializes the potential.\n\n<p>\nAlso see <tt>refreshnnlist</tt>, <tt>RLIST</tt>.\n',297,7),('enable_Fext','INT','0\n','md','If <tt>enable_Fext = 1</tt>, then the external force vector \n<tt>Fext[i]</tt> is added to the total force <tt>F[i]</tt>\nfor every atom <tt>i</tt>.\n',298,7),('applyFext','INT','0\n','md','Same as <tt>enable_Fext</tt>.\n',299,7),('indentor_Z','DOUBLE','N/A','md','Empty variable.  Do not use.\n',300,7),('indentor_Z0','DOUBLE','N/A','md','Empty variable.  Do not use.\n',301,7),('indentor_Vz','DOUBLE','N/A','md','Empty variable.  Do not use.\n',302,7),('indentor_K','DOUBLE','N/A','md','Empty variable.  Do not use.\n',303,7),('indentor_Fz','DOUBLE','N/A','md','Empty variable.  Do not use.\n',304,7),('enable_FlatIndentor','INT','N/A','md','Empty variable.  Do not use.\n',305,7),('TSTRESS_xx','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',306,6),('TSTRESS_xy','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',307,6),('TSTRESS_xz','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',308,6),('TSTRESS_yx','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',309,6),('TSTRESS_yy','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',310,6),('TSTRESS_yz','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',311,6),('TSTRESS_zx','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',312,6),('TSTRESS_zy','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',313,6),('TSTRESS_zz','DOUBLE','N/A','md','A component of the <tt>TSTRESS</tt> (total stress) tensor (in eV/&Aring;<sup>3</sup>).\n',314,6),('TSTRESSinMPa_xx','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',315,6),('TSTRESSinMPa_xy','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',316,6),('TSTRESSinMPa_xz','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',317,6),('TSTRESSinMPa_yx','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',318,6),('TSTRESSinMPa_yy','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',319,6),('TSTRESSinMPa_yz','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',320,6),('TSTRESSinMPa_zx','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',321,6),('TSTRESSinMPa_zy','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',322,6),('TSTRESSinMPa_zz','DOUBLE','N/A','md','A component of the <tt>TSTRESSinMPa</tt> (total stress) tensor (in MPa).\n',323,6),('H_11','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',324,6),('H_12','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',325,6),('H_13','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',326,6),('H_21','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',327,6),('H_22','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',328,6),('H_23','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',329,6),('H_31','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',330,6),('H_32','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',331,6),('H_33','DOUBLE','N/A','md','A component of the <tt><b>H</b></tt> (3x3) matrix.\n',332,6),('relaxation_algorithm','STRING','ZXCGR\n','md','The name of the different variations of the conjugate gradient relaxation algorithms.\nThe options are <tt>ZXCGR</tt> and <tt>PRPLUS</tt>.\n\n<p>\nAlso see <tt>relax</tt>.\n',333,7),('conj_itmax','INT','1000\n','md','Maximum number of search iterations in conjugate gradient relaxation.\n\n<p>\nAlso see <tt>relax</tt>.\n',334,7),('conj_fevalmax','INT','10000\n','md','Maximum number of times the potential function can be called during\nconjugate gradient relaxation.\n\n<p>\nAlso see <tt>relax</tt>.\n',335,7),('conj_step','INT','0\n','md','Current step number in conjugate gradient relaxation <tt>relax</tt>, \nequivalent to <tt>curstep</tt> in MD simulation <tt>run</tt>.\n\n<p>\nIt is used to determine when whether the X-window needs to be \nrefreshed, or intermediate .cn file needs to be saved, at the current \nsimulation step.\n\n<p>\nAlso see <tt>plotfreq</tt>, <tt>savecnfreq</tt>.\n',336,7),('conj_fixbox','INT','1\n','md','If <tt>conj_fixbox = 1</tt> then in the conjugate gradient relaxation\n(invoked by the <tt>relax</tt> command), the box matrix <b>H</b> is not\nallowed to change.  \n\n<p>\nIf <tt>conj_fixbox = 0</tt> then the box matrix <b>H</b> is allowed to change\nduring relaxation.\n\n<p>\nAlso see <tt>conj_fixboxvec</tt>.\n\n',337,7),('conj_fixboxvec','DOUBLE','0\n','md','If <tt>conj_fixbox = 0</tt>, we may still fix individual components of\nthe box matrix <b>H</b> during the conjugate gradient relaxation\n(invoked by the <tt>relax</tt> command).\n\n<p>\nFormat: <tt>conj_fixboxvec = [  \n<br> &nbsp; &nbsp; &nbsp; <i>f</i><sub>11</sub>   <i>f</i><sub>12</sub> <i>f</i><sub>13</sub>\n<br> &nbsp; &nbsp; &nbsp; <i>f</i><sub>21</sub>   <i>f</i><sub>22</sub> <i>f</i><sub>23</sub>\n<br> &nbsp; &nbsp; &nbsp; <i>f</i><sub>31</sub>   <i>f</i><sub>32</sub> <i>f</i><sub>33</sub> ] </tt>\n\n<p>\nIf <tt><i>f</i><sub>ij</sub> == 1 </tt>, then H<sub>ij</sub> is fixed.\n\n',338,7),('conj_g2res','DOUBLE','0\n','md','Residual gradient in the conjugate gradient relaxation.  More precisely, it is\nthe sum of the square of the gradient for each degree of freedom.\n',339,7),('fixbox','INT','1\n','md','Same as <tt>conj_fix_box</tt>.\n\n<p>\nAlso see <tt>fixboxvec</tt>.\n\n',340,7),('fixboxvec','DOUBLE','0\n','md','Same as <tt>conj_fixboxvec</tt>.\n',341,7),('conj_fixdir','INT','0\n','md','Empty variable.  Do not use.\n',342,7),('conj_fixshape','INT','0\n','md','Option not yet working.\n\n',343,7),('conj_fixatoms','INT','0\n','md','If <tt>conj_fixatoms = 1</tt> then in the conjugate gradient relaxation\n(invoked by the <tt>relax</tt> command), all scaled coordinates of the atoms\nwill be fixed.  Only the box matrix <b>H</b> is allowed to change.  \n\n<p>\nAlso see <tt>conj_fixbox</tt>.\n\n\n',344,7),('conj_etol','DOUBLE','1e-8\n','md','The tolerance in the energy.  If the variation becomes lower than\nthis value, the conjugate gradient relaxation will declare convergence and exit.\nThis option is only used if <tt>relaxation_algorithm = PRPLUS</tt> (not the default).\n\n<p>\nAlso see <tt>relax</tt>.\n',345,7),('conj_ftol','DOUBLE','1e-8\n','md','The tolerance in the residual gradient.  If the residual gradient becomes lower than\nthis value, the conjugate gradient relaxation will declare convergence and exit.\n\n<p>\nAlso see <tt>relax</tt>.\n',346,7),('conj_dfpred','DOUBLE','1e-3\n','md','The anticipated reduction of potential energy in the first trial step of the\nconjugate gradient relaxation.  There is usually no need to change it from\nthe default value.\n',347,7),('H','DOUBLE','0\n','md','The 3x3 matrix <b>H</b> consists of three column vectors\n[<b>c</b><sub>1</sub> | <b>c</b><sub>2</sub> | <b>c</b><sub>3</sub> ], \nwhich are the repeat vector of the simulation cell (under periodic boundary\nconditions).\n\n<p>\nSee <a href=\"http://micro.stanford.edu/wiki/Output_File_Formats_in_MD++#Configuration_.cn_File\">wiki\npage</a> for more details.\n',348,6),('H0','DOUBLE','0\n','md','A copy of the <tt><b>H</b></tt> matrix.\n\n<p>\nAlso see <tt>saveH</tt>, <tt>restoreH</tt>.\n',349,6),('stress','DOUBLE','N/A','md','A 3x3 matrix specifying the external stress (in MPa) applied to the simulation cell.  This\naffects <tt>relax</tt> if <tt>conj_fixbox = 0</tt>, as well as <tt>run</tt> if\n<tt>ensemble_type = NPT</tt> or <tt>NPH</tt>.\n\n<p>\nThe sign convention of MD++ is such that a hydrostatic pressure corresponds to\na positive value in stress, while tensile loading corresponds to a negative value.\n\n<p>\nWe need to make sure <tt>stress</tt> is set to a symmetric matrix.\n',350,7),('stressmul','DOUBLE','1\n','md','A multiplicative factor in front of the <tt>stress</tt> matrix.  This allows\nus to easily vary the magnitude of stress without changing its orientation.\n',351,7),('extforce','DOUBLE','0\n','md','<tt>extforce = [ <i>n   &nbsp; f<sub>x1</sub> f<sub>y1</sub> f<sub>z1</sub>\n<br> &nbsp; &nbsp; &nbsp; &nbsp;  f<sub>x2</sub> f<sub>y2</sub> f<sub>z2</sub>\n<br> &nbsp; &nbsp; &nbsp; &nbsp;  &hellip;\n<br> &nbsp; &nbsp; &nbsp; &nbsp;  f<sub>xn</sub> f<sub>yn</sub> f<sub>zn</sub> </i> ] </tt>\n\n<p>\n<tt><i>n</i></tt> is the number of groups affected by this setting.\nIf <tt><i>n</i></tt> > 0, then atoms beloning to group <tt>k</tt> will experience\nan additional external force <tt><i> f<sub>xk</sub> f<sub>yk</sub> f<sub>zk</sub> </i></tt>.\n',352,7),('forcemul','DOUBLE','N/A','md','A multiplication factor to the external forces specified in the <tt>extforce</tt> array.\n',353,7),('pressureadd','DOUBLE','N/A','md','Empty variable.  Do not use.\n',354,7),('vacuumratio','DOUBLE','0\n','md','A value between 0 and 1 describing the fraction of the space in the simulation\ncell occupied by vacuum.  This instructs MD++ to subtract off the vacuum volume\nwhen computing the stress.\n\n<p> \n<tt>TSTRESS = (VIRIAL + PSTRESS) / (OMEGA * (1-vacuumratio)) </tt>\n',355,7),('hprecond','DOUBLE','1\n','md','Preconditioning parameters for conjugate gradient relaxation.  Perhaps useful when simulation box is highly different from a cube.\n',356,7),('xprecond','DOUBLE','1\n','md','Preconditioning parameters for conjugate gradient relaxation.  Perhaps useful when simulation box is highly different from a cube.\n',357,7),('yprecond','DOUBLE','1\n','md','Preconditioning parameters for conjugate gradient relaxation.  Perhaps useful when simulation box is highly different from a cube.\n',358,7),('zprecond','DOUBLE','1\n','md','Preconditioning parameters for conjugate gradient relaxation.  Perhaps useful when simulation box is highly different from a cube.\n',359,7),('constrainS','DOUBLE','N/A','md','The imposed constraint value during constrained relaxation.\n\n<p>\nAlso see <tt>constrainS_INST</tt>, <tt>constrainatoms</tt>.\n\n',360,7),('constrainS_INST','DOUBLE','N/A','md','The instantaneous (actual) value of the constraint, during constrained relaxation.  It is supposed to\nmatch the imposed constrain value <tt>constrainS</tt>.\n\n<p>\nAlso see <tt>constrainS</tt>.\n\n',361,7),('constrainF','DOUBLE','N/A','md','The force against the constraint in constrained relaxation.\n\n<p>\nAlso see <tt>constrainS</tt>, <tt>constrainatoms</tt>.\n',362,7),('constrainatoms','INT','0\n','md','<tt>constrainatoms = [ <i>n i<sub>1</sub> i<sub>2</sub> &hellip; i<sub>n</sub> </i> ]</tt>\n\n<p>\nWhen <tt><i>n</i></n></tt> > 0, \nthen atoms <tt>i<sub>1</sub> i<sub>2</sub> &hellip; i<sub>n</sub> </i></tt>\nwill be constrained in the hyperplane perpendicular to <tt>SR2 - SR1</tt>, which are two\nconfigurations set by <tt>setconfig1</tt> and <tt>setconfig2</tt>.\n\n<p>\nAlso see <tt>constrainedMD</tt>, <tt>constrainedrelax</tt>.\n',363,7),('ensemble_type','STRING','NVE\n','md','Specify the ensemble type of MD simulation, such as <tt>NVE</tt>,\n<tt>NVT</tt>, <tt>NPH</tt> or <tt>NPT</tt>.\n\n<p>\nMust be set before MD simulation (<tt>run</tt>).\n',364,7),('integrator_type','STRING','Gear6\n','md','The name of the integrator to be used in MD simulation (<tt>run</tt>).  Choices are:\n<tt>Gear6</tt> and <tt>VVerlet</tt>.\n\n<p>\nAlso see <tt>ensemble_type</tt>, <tt>implementation_type</tt>.\n',365,7),('implementation_type','INT','0\n','md','Select which implementation of the time integrator to use.  For certain\n<tt>ensemble_type</tt> and <tt>integrator_type</tt>, multiple versions of\nthe integrators have been implemented to choose from.\n\n<p>\nSee <tt>integrators.cpp</tt> to find how many implementations are available.\n',366,7),('initvelocity_type','STRING','Uniform\n','md','A string specifying the probability distribution of velocities to be assigned by command\n<tt>initvelocity</tt>.  Choices are <tt>Uniform</tt> and <tt>Gaussian</tt>.\n',367,7),('zerorot','STRING','none\n','md','A string specifying which component(s) of the angular momentum need to be zeroed out\nin <tt>initvelocity</tt>.\n\n<p>\nFor example, for a nanowire under PBC along z axis but subjected to\nfree surface boundary conditions in x and y directions, we need to set <tt>zerorot = z</tt>.\nFor a nanoparticle under free surface boundary conditions in x, y, and z directions, we\nneed to set <tt>zerorot = all</tt>.\n',368,7),('SAVEMEMORY','INT','0\n','md','A parameter instructing which arrays to allocate (or not) when creating a new configuration\n(e.g. <tt>makecrystal</tt>) or reading one from file (e.g. <tt>readcn</tt>).\n\n<p>\nWhen <tt>SAVEMEMORY = 9</tt>, only arrays <tt>SR</tt> and <tt>fixed</tt> are allocated.  This \nallows a crystal to be created and written to a file.\n\n<p>\nWhen <tt>SAVEMEMORY = 8</tt>, arrays <tt>R</tt> and <tt>R0</tt> are allocated, in addition to\nthe above.\n\n<p>\nWhen <tt>SAVEMEMORY = 7</tt>, arrays <tt>F</tt>, <tt>EPOT_IND</tt> and <tt>species</tt>\nare allocated, in addition to the above.  This allows the structure to be relaxed (e.g. <tt>relax</tt>).\n\n<p>\nWhen <tt>SAVEMEMORY = 6</tt>, arrays <tt>VR</tt> and <tt>VSR</tt>\nare allocated, in addition to the above.  This allows simple MD simulation (e.g. <tt>run</tt>).\n\n<p>\nWhen <tt>SAVEMEMORY = 5</tt>, arrays <tt>image</tt>, <tt>TOPOL</tt> and <tt>group</tt>\nare allocated, in addition to the above.  This allows the analysis and visualization of\nthe structure by central symmetry parameter (e.g. <tt>calcentralsymmetry</tt>).\n\n<p>\nWhen <tt>SAVEMEMORY = 4</tt>, arrays <tt>F0</tt> and <tt>Fext</tt>\nare allocated, in addition to the above.  This allows external forces to be applied\n (e.g. <tt>enable_Fext</tt>).\n\n<p>\nWhen <tt>SAVEMEMORY = 1</tt> (default), all the remaining arrays, <tt>EPOT_RMV</tt>,\n<tt>VIRIAL_IND</tt>, <tt>TORQUE_IND</tt> and <tt>BENDMOMENT_IND</tt>\nare allocated, in addition to the above. \n\n',369,7),('nspecies','INT','1\n','md','Total number of atomic species in the simulation.\n\n<p>\nAlso see <tt>species</tt>.\n',370,7),('totalsteps','INT','N/A','md','Total number of steps for Molecular dynamics simulation.\n\n<p>\nAlso see <tt>timestep</tt>, <tt>run</tt>.\n\n',371,7),('equilsteps','INT','0\n','md','The number of equilibration steps in MD simulation.  The property file only\ngets written to after the simulation has passed <tt>equilstep</tt> number of steps.\n\n<p>\nAlso see <tt>run</tt>, <tt>totalsteps</tt>, <tt>saveprop</tt>.\n',372,7),('atommass','DOUBLE','N/A','md','An array containing the atomic mass of each species (in g/mol).  \nMust be set before performing MD simulation (<tt>run</tt>).\n\n<p>\nExample: <tt>MD++/scripts/Example/example02a-si-md.script</tt>\n',373,7),('atomcharge','DOUBLE','N/A','md','An array storing the electric charge of each atomic species in unit of the fundamental\ncharge unit (e).\n\n<p>\nAlso see <tt>species</tt>, <tt>ewald</tt>.\n',374,7),('wallmass','DOUBLE','1\n','md','Effective mass of the box matrix <tt><b>H</b></tt> in Parrinello-Rahman dynamics.\n\nReference: Parrinello and Rahman, J. Appl. Phys. 52, 7182 (1981).\n\nAlso see <tt>KBOX</tt>.\n',375,7),('NHMass','DOUBLE','0\n','md','Parameter for the Nose-Hoover thermostat.\n',376,7),('NHChainLen','INT','N/A','md','Parameter for the Nose-Hoover chain thermostat.\n',377,7),('T_OBJ','DOUBLE','0\n','md','The target temperature (in K) used by <tt>initvelocity</tt>.\nIt is also used for the thermostat in MD simulation (<tt>run</tt>) when \n<tt>ensemble_type = NVT</tt> or <tt>NPT</tt>.\n\n<p>\nAlso see <tt>DOUBLE_T</tt>.\n',378,7),('DOUBLE_T','INT','0\n','md','If <tt>DOUBLE_T = 1</tt>, then <tt>initvelocity</tt> will set the instantaneous\ntemperature to twice the value specified in <tt>T_OBJ</tt> (in K).\n',379,7),('allocmultiple','INT','1\n','md','If <tt>allocmultiple = <i>n</i></tt> is set before <tt>\nreadcn</tt> or <tt>makecrystal</tt>, then the memory for <tt>NP</tt> &lowast; \n<i>n</i> atoms is allocated, where <tt>NP</tt> is the actual number of atoms.\n\n<p>\nUseful for <tt>extendbox</tt>.\n',380,7),('vt2','DOUBLE','0.25\n','md','Obsolete variable for controlling the Nose-Hoover thermostat.  Do not use.\nUse <tt>NHMass</tt> instead.\n\n',381,7),('boxdamp','DOUBLE','0\n','md','A damping coefficient on the box matrix <tt><b>H</b></tt> in MD simulations in the <tt>NPH</tt>\nor <tt>NPT</tt> ensemble to damp out the oscillations so that the box can be equilibrated\nfaster.\n\n<p>\n<tt>run</tt>, <tt>ensemble_type</tt>.\n',382,7),('timestep','DOUBLE','N/A','md','Molecular dynamics simulation time step in picoseconds.\n\n<p>\nAlso see <tt>totalsteps</tt>, <tt>run</tt>.\n',383,7),('RLIST','DOUBLE','0\n','md','The cut-off radius of the Verlet neighbor list.  It equals the cut-off radius of the\npotential plus <tt>SKIN</tt>.   This variable is usually not set manually, but is\nset automatically by the command that reads and initializes the potential.\n\n<p>\nAlso see <tt>refreshnnlist</tt>, <tt>SKIN</tt>.\n',384,7),('NIC','INT','N/A','md','Empty variable.  Do not use.\n',385,7),('NNM','INT','60\n','md','The maximum number of neighbors in the neighbor list.  You may need to enlarge this value if\nyou use a large cut off radius <tt>RLIST</tt>.\n',386,7),('nl_skip_pairs','INT','0\n','md','An array specifying the atom pairs that will be skipped when constructing the neighbor\nlist.  This effectively remove the interaction between the atom pairs, and is one way\nto prepare a crack.\n\n<p>\nFormat: <tt>nl_skip_pairs = [ <i>n  i<sub>1</sub> j<sub>1</sub> i<sub>2</sub> j<sub>2</sub> \n &hellip; i<sub>n</sub> j<sub>n</sub></i> ] </tt>\n<br>\nwhere <tt><i>n</i></tt> indicates the number of pairs, followed by the indices of the atom pairs.\n\n<p>\nThis array is usually not set manually, but is set automatically by commands <tt>cutbonds</tt>\nand <tt>cutbonds_by_ellipse</tt>.\n',387,7),('current_NIC','INT','0\n','md','The maximum number of atoms in one cell after the construction of the cell list.\n',388,7),('current_NNM','INT','0\n','md','The maximum number of neighbors in the neighbor list of all atoms after the construction of the cell list.\n',389,7),('shearrate','DOUBLE','N/A','md','<tt><b>shearrate</b></tt> is a 3x3 matrix.  When <tt>applyshear = 1</tt>, \nthen at every time step the simulation box matrix <tt><b>H</b></tt> is updated by,\n\n<p>\n<tt> <b>H</b> += <b>H</b> * <b>shearrate</b> * timestep </tt>.\n\n<p>\nAlso see <tt>applyshear</tt>.\n',390,7),('applyshear','INT','0\n','md','When <tt>applyshear = 1</tt>, \nthen at every time step the simulation box matrix <tt><b>H</b></tt> is updated by,\n\n<p>\n<tt> <b>H</b> += <b>H</b> * <b>shearrate</b> * timestep </tt>.\n\n<p>\nAlso see <tt>shearrate</tt>.\n',391,7),('constrainedMD','INT','0\n','md','If <tt>constrainedMD = 1</tt>, then during MD simulation, the scaled coordinates of the\natoms specified in array <tt>constrainatoms</tt> will be constrained in the hyperplane \nperpendicular to <tt>SR2 - SR1</tt>.\n',392,7),('runavgCN','INT','N/A','md','Empty variable.  Do not use.\n',393,7),('enable_DPD','INT','0\n','md','Dissipative Particle Dynamics (stochastic thermostat) parameter\n',394,7),('DPD_friction_const','DOUBLE','0\n','md','Dissipative Particle Dynamics (stochastic thermostat) parameter\n',395,7),('DPD_ratio','DOUBLE','1\n','md','Dissipative Particle Dynamics (stochastic thermostat) parameter\n',396,7),('DPD_rcut','DOUBLE','100\n','md','Dissipative Particle Dynamics (stochastic thermostat) parameter\n',397,7),('enable_ANDERSON','INT','N/A','md','If <tt>enable_ANDERSON</tt> = 1, then the Anderson thermostat is activated, so that the atomic\nvelocities will be randomly reassigned during MD simulations.\n\n<p>\nAlso see <tt>ANDERSON_ratio</tt>.\n',398,7),('ANDERSON_ratio','DOUBLE','N/A','md','A value between 0 and 1, specifying the probability of randomly reassigning the velocities\nfor each atom at every MD step.\n\n<p>\nAlso see <tt>enable_ANDERSON</tt>.\n',399,7),('mcatom','INT','0\n','md','If <tt>mcatom</tt> >= 0, then at each step of the Monte Carlo simulation, an atoms will be selected \nat random to be displaced by a small random vector (trial move).  <tt>mcatom</tt> then stores the\nindex of this selected atoms.\n\n<p>\nIf <tt>mcatom</tt> = -1, then all atoms will be displaced by random vectors in the trial move.  This\ngenerally leads to very low acceptance ratio unless the simulation cell is very small.\n',400,7),('lambda0','DOUBLE','0\n','md','The beginning value &lambda;<sub>0</sub> of thermodynamic integration (i.e. &lambda;-integration).\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n',401,7),('lambda1','DOUBLE','1\n','md','The final value &lambda;<sub>1</sub> of thermodynamic integration (i.e. &lambda;-integration).\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n',402,7),('Ecoh','DOUBLE','0\n','md','A parameter used to adjust the zero point of potential energy in free energy\ncalculations using the Adiabatic Switching method.\n',403,7),('switchfreq','INT','N/A','md','Parameter for adiabatic switching simulation for free energy calculation\n',404,7),('switchoffatoms','INT','N/A','md','Parameter for adiabatic switching simulation for free energy calculation\n\n<tt>switchoffatoms = [ <i>n i<sub>1</sub> i<sub>2</sub> &hellip; i<sub>n</sub> </i> ]</tt>\n\n<p>\nWhen <tt><i>n</i></n></tt> > 0, \nthen atoms <tt>i<sub>1</sub> i<sub>2</sub> &hellip; i<sub>n</sub> </i></tt>\nwill be gradually switched on or off during the adiabatic switching simulation.\n\n',405,7),('switchfunc','INT','N/A','md','Parameter for adiabatic switching simulation for free energy calculation\n',406,7),('refpotential','INT','0\n','md','Specifies the reference potential in adiabatic switching simulations to compute free energy.  Options are:\n\n<p>\n<tt>0</tt>: Einstein crystal (not implemented yet). <br>\n<tt>1</tt>: Harmonic potential. <br>\n<tt>2</tt>: Inverse-12 (I12) potential. <br>\n<tt>3</tt>: Inverse-12 (I12) potential * &lambda;. <br>\n<tt>4</tt>: Original potential * &lambda; (i.e. reversible scaling method). <br>\n<tt>5</tt>: Gaussian potential. <br>\n<tt>6</tt>: Gaussian potential * &lambda;. <br>\n<tt>10</tt>: User defined potential. <br>\n<tt>20</tt>: Calling VASP to evaluate potential. <br>\n\n<p>\nAlso see <tt>I12_epsilon</tt>, <tt>Gauss_epsilon</tt>, <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',407,7),('enableswitch','INT','N/A','md','Parameter for adiabatic switching simulation for free energy calculation\n',408,7),('ecspring','DOUBLE','0\n','md','Spring constant in the Einstein crystal model, which is a reference system for free energy calculations\nby adiabatic switching.\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n',409,7),('I12_rc','DOUBLE','0\n','md','Cut-off radius in the inverse-12 (I12) purely repulsive potential, which can be used\nas a reference model for adiabatic switching simulations.\n\n<p>\n&Phi;(r) = <tt>I12_epsilon</tt> &sdot; (<tt>I12_sigma</tt> / r)<sup>12</sup>\n &nbsp; (if r < <tt>I12_rc</tt>)\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',410,7),('I12_sigma','DOUBLE','0\n','md','A parameter in the inverse-12 (I12) purely repulsive potential, which can be used\nas a reference model for adiabatic switching simulations.\n\n<p>\n&Phi;(r) = <tt>I12_epsilon</tt> &sdot; (<tt>I12_sigma</tt> / r)<sup>12</sup>\n &nbsp; (if r < <tt>I12_rc</tt>)\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',411,7),('I12_epsilon','DOUBLE','0\n','md','A parameter in the inverse-12 (I12) purely repulsive potential, which can be used\nas a reference model for adiabatic switching simulations.\n\n<p>\n&Phi;(r) = <tt>I12_epsilon</tt> &sdot; (<tt>I12_sigma</tt> / r)<sup>12</sup>\n &nbsp; (if r < <tt>I12_rc</tt>)\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',412,7),('Gauss_rc','DOUBLE','0\n','md','Cut-off radius in the Gaussian potential, which can be used\nas a reference model for adiabatic switching simulations.\n\n<p>\n&Phi;(r) = <tt>Gauss_epsilon</tt> &sdot; exp(- r<sup>2</sup> / (2 * <tt>Gauss_sigma</tt><sup>2</sup> )\n&nbsp; (if r < <tt>Gauss_rc</tt>)\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',413,7),('Gauss_sigma','DOUBLE','0\n','md','A parameter in the Gaussian potential, which can be used\nas a reference model for adiabatic switching simulations.\n\n<p>\n&Phi;(r) = <tt>Gauss_epsilon</tt> &sdot; exp(- r<sup>2</sup> / (2 * <tt>Gauss_sigma</tt><sup>2</sup> )\n&nbsp; (if r < <tt>Gauss_rc</tt>)\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',414,7),('Gauss_epsilon','DOUBLE','0\n','md','A parameter in the Gaussian potential, which can be used\nas a reference model for adiabatic switching simulations.\n\n<p>\n&Phi;(r) = <tt>Gauss_epsilon</tt> &sdot; exp(- r<sup>2</sup> / (2 * <tt>Gauss_sigma</tt><sup>2</sup> )\n&nbsp; (if r < <tt>Gauss_rc</tt>)\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>.\n\n',415,7),('randseed','INT','12345\n','md','The seed to randomize the random number generator.  Must be set\nbefore calling <tt>srand48</tt> or <tt>srand</tt>.\n\n',416,7),('MC_dV_freq','INT','1\n','md','In Monte Carlo simulation under the <tt>NPT</tt> ensemble, a volume change is\nattempted every <tt>MC_dV_freq</tt> steps.\n\n\n<p>\nAlso see <tt>runMC</tt>, <tt>ensemble_type</tt>, <tt>MC_dVmax</tt>.\n',417,7),('MC_dN_freq','INT','1\n','md','In Monte Carlo simulation under the <tt>uVT</tt> ensemble, a change of number of atoms is\nattempted every <tt>MC_dN_freq</tt> steps.\n\n\n<p>\nAlso see <tt>runMC</tt>, <tt>ensemble_type</tt>.\n',418,7),('MC_dVmax','DOUBLE','0.1\n','md','The maximum allowed change of simulation cell volume in one trial step of MC simulation in\nthe NPT ensemble.  The actual trial volume change is <tt>MC_dVmax * (2*drand48() - 1)</tt>.\n\n<p>\nAlso see <tt>runMC</tt>.\n',419,7),('MC_dfrac','DOUBLE','0.1\n','md','In Monte Carlo simulations under the uVT ensemble, an atom is allowed to take\nfractional occupancy.  <tt>MC_dfrac</tt> is the change of the fractional\noccupancy of the atom in a trial move.\n\n<p>\nAlso see <tt>runMC</tt>.\n',420,7),('MC_P_ext','DOUBLE','0\n','md','The external pressure applied to the simulation cell Monte Carlo simulations\nin which the volume is allowed to fluctuate (when <tt>ensemble_type = NPT</tt>).\n',421,7),('MC_mu_ext','DOUBLE','N/A','md','The external chemical potential for an atom that will be gradually switched on or off during\nMonte Carlo switching simulations.\n\n<p>\nAlso see <tt>runMCSWITCH</tt>.\n',422,7),('nebspec','INT','N/A','md','Parameter for relaxation by the Nudged Elastic Band (NEB) method \n(<tt>nebrelax</tt>) or the string method (<tt>stringrelax</tt>).\n\n<p>\n<b><u>When used by</u></b>\n<tt>nebrelax</tt>, <tt>nebspec</tt> has the following meaning.\n\n<p>\n<tt>nebspec = [ <i>relax_surround k moveleftend moverightend yesclimbimage</i> ]</tt>\n\n<p>\nIf <tt><i>relax_surround</i> = 1</tt>, then relaxing the surrounding atoms\nof the constrained atoms during <tt>nebrelax</tt>.\nWe usually use <tt><i>relax_surround</i> = 0</tt>, then the surrounding atoms\nwill be a linear interpolation between <tt>SR1</tt> and <tt>SR2</tt>.\nWhen all atoms are included in <tt>constrainatoms</tt>, then this option has no effect.\n<tt><i>relax_surround</i> = 1</tt> does not work for parallel version of <tt>nebrelax</tt>.\n\n\n<p>\n<tt><i>k</i></tt> is the spring constant of the nudged elastic band. \nIf <tt><i>k</i> = 0</tt>, then the spring constant will be automatically chosen as the maximum force \nmagnitude times the number of chains.\n\n<p>\nIf <tt><i>moveleftend</i> = 0</tt>, then the left end replica of the chain does not move \nduring NEB relaxation. This is the correct setting if the left end is already at\nan energy minimum. <br>\nIf <tt><i>moveleftend</i> = 1</tt>, then the left end moves following spring force in the \nnormal to the real force direction.   This constrains the left end to a constant energy\nisosurface.  (We found that it is difficult to find the appropriate parameters to stablize\n<tt>nebrelax</tt> with this option.  Hence we prefer to use <tt>stringrelax</tt> when the end\nneeds to move.  For details, see T. Zhu, J. Li, et al. PNAS vol.104, pp.3031-3036, 2007. <br>\nIf <tt><i>moveleftend</i> = 2</tt>, then the left end is constrained to move along the chain \ntangential direction (constrained free fall). <br>\nIf <tt><i>moveleftend</i> = 3</tt>, the left end moves along the force direction (free fall).\n\n<p>\n<tt><i>moverightend</i></tt> has similar meaning for the right end.\n\n<p>\nIf <tt><i>yesclimbimage</i> = 1</tt>, then the image (or replica) of the highest energy starts \nto climb up the hill when <tt>curstep</tt> &gt; <tt>equilsteps</tt>.   This means that if \n<tt><i>yesclimbimage</i> = 1</tt>, <b>we need to set</b> <tt>equilsteps</tt> \n<b>to a non-zero value</b>, e.g.\n1000, and set <tt>totalsteps</tt> &gt; <tt>equilsteps</tt>.  \nOtherwise, <tt>equilstep = 0</tt> by default and running with <tt><i>yesclimbimage</i> = 1</tt>\nfrom the beginning makes <tt>nebrelax</tt> more unstable. \nTypically, we can set <tt>totalsteps</tt> to be <tt>equilsteps</tt> + 500, \nwhich means that the climbing image method will be applied to the last 500 steps of \n<tt>nebrelax</tt>.  \n\n(In the future, we may want to use a different variable to replace <tt>equilsteps</tt>.)\n\n\n<p>\n\n<b><u>When used by</u></b>\n<tt>stringrelax</tt>, <tt>nebspec</tt> (or, equivalently\n<tt>stringspec</tt>) has the following meaning.\n\n<p>\n<tt>nebspec = [ <i>relax_surround redistr_freq moveleftend moverightend yesclimbimage islengthconstant</i> ]</tt>\n\n<p>\nThe main difference from above is in <tt><i>redistrib_freq</i></tt> \n(instead of <tt><i>k</i></tt>) and in <tt><i>islengthconstant</i></tt>. \n\n<p>\nIn the string method, there is no need to specify a spring constant.  Instead,\n<tt><i>redistr_freq</i></tt> specifies how often the path gets reparameterized.\nWe recommend <tt><i>redistrib_freq</i> = 1</tt>, which means reparameterization\nat every step of <tt>stringrelax</tt>.\n\n<p>\nIf <tt><i>islengthconstant</i> = 1</tt>, the total length of the string will be kept \nconstant duringn <tt>stringrelax</tt>.  This option is neglected if both ends are fixed.\nThis option only works for parallel version of <tt>stringrelax</tt>.\n\n<p>\nNote that if <tt><i>yesclimbimage</i> = 1</tt>, <tt>equilsteps</tt> need to be set\nto a non-zero value (e.g. 1000) to avoid instability.\n\n<p>\nAlso see <tt>nebrelax</tt>, <tt>stringrelax</tt>.\n',423,7),('stringspec','INT','N/A','md','The same as (i.e. an alias of) <tt>nebspec</tt>.\n',424,7),('readrchainspec','INT','-1\n','md','Setting for command <tt>readRchain</tt>.\n',425,7),('annealspec','DOUBLE','N/A','md','Parameter for simulated annealing.\n',426,7),('chainlength','INT','0\n','md','The number of replicas in chain-of-state relaxation methods (<tt>nebrelax</tt>\nand <tt>stringrelax</tt>) to find the minimum energy path between two states.\n\n<p>\nAlso see <tt>nebrelax</tt>, <tt>stringrelax</tt>, <tt>allocchain</tt>.\n',427,7),('YES_SURFTEN','INT','0\n','md','Parameter for surface tension calculation\n',428,1),('surftensionspec','INT','N/A','md','Parameter for surface tension calculation\n',429,1),('YES_SURFTEN1','INT','N/A','md','Parameter for surface tension calculation\n',430,1),('ST_step','INT','N/A','md','Parameter for surface tension calculation\n',431,1),('ST_orien','INT','N/A','md','Parameter for surface tension calculation\n',432,1),('ST_Kmax','DOUBLE','0\n','md','Parameter for surface tension calculation\n',433,1),('ST_LAMBDA','DOUBLE','0\n','md','Parameter for surface tension calculation\n',434,1),('ST_LMAX','DOUBLE','0\n','md','Parameter for surface tension calculation\n',435,1),('ST_dUdLAM_L','DOUBLE','0\n','md','Parameter for surface tension calculation\n',436,1),('ST_dUdLAM_POT','DOUBLE','0\n','md','Parameter for surface tension calculation\n',437,1),('ST_dUdLAM_TOT','DOUBLE','0\n','md','Parameter for surface tension calculation\n',438,1),('YES_FFS','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',439,1),('L_for_QLM','INT','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',440,1),('l_for_qlm','INT','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',441,1),('N_solid_P','INT','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',442,1),('Principal_Inertia','DOUBLE','N/A','md','Variables describing the shape of a cluster of (defect) atoms identified by <tt>findcore</tt>.\n\n<p>\n<tt>Printcipal_Inertia = [ <i>I<sub>1</sub> I<sub>2</sub> I<sub>3</sub>  </i> ]</tt>\n',443,1),('N_lgst_index','DOUBLE','0\n','md','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',444,1),('N_lgst_skin','DOUBLE','0\n','md','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',445,1),('N_lgst_skin_index','DOUBLE','0\n','md','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',446,1),('qlm_type','STRING','N/A','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',447,1),('wSKIN','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',448,1),('DLxyz','INT','N/A','md','Empty variable.  Do not use.\n',449,1),('DLNdiv','INT','N/A','md','Empty variable.  Do not use.\n',450,1),('N_lgst_cluster','INT','0\n','md','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',451,1),('Rc_for_QLM','DOUBLE','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',452,1),('QLM_cutoff','DOUBLE','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',453,1),('saveFFScn','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',454,1),('FFSoption','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',455,1),('FFSpruning','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',456,1),('FFScn_weight','DOUBLE','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',457,1),('FFS_Pp','DOUBLE','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',458,1),('FFS0_check','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',459,1),('lambda_A','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',460,1),('lambda_B','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',461,1),('FFScurstep','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',462,1),('FFSautoend','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',463,1),('FFShist','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',464,1),('Delta_LAM','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',465,1),('MIN_LAM','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',466,1),('MAX_LAM','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',467,1),('FFSbackward','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',468,1),('B_lambda_cut','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',469,1),('B_lambda_B','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',470,1),('B_lambda_0','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',471,1),('FFScommitor','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',472,1),('YES_UMB','INT','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',473,1),('UMB_order_param','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',474,1),('UMB_order_group','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',475,1),('KinkDmax','DOUBLE','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',476,1),('printUMBorder','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',477,1),('UMB_noslipdirection','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',478,1),('HETERO_DN','INT','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',479,1),('MCequilstep','INT','N/A','md','Parameter in Umbrella Sampling by Monte Carlo simulation.\n\n<p>\nFor details, as Seunghwa Ryu.\n',480,1),('UMB_K','DOUBLE','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',481,1),('UMB_equilstep','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',482,1),('UMB_curstep','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',483,1),('UMB_tryrate','DOUBLE','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',484,1),('UMB_continue','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',485,1),('MC_UMB_cal_period','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',486,1),('MC_UMB_log_period','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',487,1),('MC_UMB_accept_tot','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',488,1),('MC_UMB_accept_ratio','DOUBLE','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',489,1),('MC_UMB_num_of_trials','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',490,1),('n_center','INT','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',491,1),('delta_n','INT','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',492,1),('acc_UMB','INT','N/A','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',493,1),('MC_RC_cal_period','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',494,1),('Kinetic','INT','N/A','md','A parameter controlling the Molecular Dynamics and Monte Carlo simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',495,1),('Kinetic_Time','DOUBLE','10\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',496,1),('Kinetic_Swip','INT','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',497,1),('N_lgst_temp','INT','0\n','md','Parameter for largest cluster sampled in Forward-Flus Sampling (FFS)\nand Umbrella Sampling (US) simulations.\n',498,1),('KN_Center','INT','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',499,1),('YES_HMC','INT','0\n','md','Parameter for Hybrid Monte Carlo\n\n<p>\nFor details, ask Seunghwa Ryu.\n',500,1),('Ns_HMC','INT','N/A','md','Parameter for Hybrid Monte Carlo\n\n<p>\nFor details, ask Seunghwa Ryu.\n',501,1),('YES_SEP','INT','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',502,1),('CLUSTER_CM','DOUBLE','N/A','md','Center of mass position of a cluster identified in the Forward Flux Sampling (FFS) simulation.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',503,1),('SEPA_ORDER','DOUBLE','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',504,1),('SEPA_TARGET','DOUBLE','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',505,1),('SEPA_RATIO','DOUBLE','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',506,1),('NORM_REACTION','DOUBLE','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',507,1),('NC_TIMES_SEPA','DOUBLE','0\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',508,1),('IMP_INDEX','INT','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',509,1),('IMP_TOPOL_INDEX','DOUBLE','0\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',510,1),('IMP_R_EXP','DOUBLE','2.5\n','md','Umbrella Sampling parameter\n\n<p>\nFor details, ask Seunghwa Ryu.\n',511,1),('VIRIAL_Ewald','DOUBLE','N/A','md','Ewald contribution to the <tt>VIRIAL</tt> tensor.\n',512,6),('VIRIAL_Ewald_Real','DOUBLE','N/A','md','Real space part of the Ewald contribution to the <tt>VIRIAL</tt> tensor.\n',513,6),('VIRIAL_Ewald_Rec','DOUBLE','N/A','md','Reciprocal space part of the Ewald contribution to the <tt>VIRIAL</tt> tensor.\n\n',514,6),('EPOT_Ewald','DOUBLE','N/A','md','Ewald contribution to the potential energy of the entire simulation cell.\n',515,6),('EPOT_Ewald_Real','DOUBLE','N/A','md','The real space part of the Ewald contribution to the potential energy of the entire simulation cell.\n',516,6),('EPOT_Ewald_Rec','DOUBLE','N/A','md','The reciprocal space part of the Ewald contribution to the potential energy of the entire simulation cell.\n',517,6),('EPOT_Ewald_Self','DOUBLE','N/A','md','The self-energy part of the Ewald contribution to the potential energy of the entire simulation cell.\n',518,6),('Ewald_CE_or_PME','INT','0\n','md','0 to choose the classical Ewald (CE) method\n\n<p>\n1 to choose the particle mesh Ewald (PME) method\n',519,7),('Ewald_option_Alpha','INT','0\n','md','Specifies whether or not the value for Alpha in the Ewald method is to be determined\nautomatically or specified manually.\n\n<p>\nIf <tt>Ewald_option_Alpha = 0</tt>, then <tt>Ewald_Alpha</tt> is determined automatically, and\n<tt>Ewald_Rcut = Ewald_precision / Ewald_Alpha</tt>.\n\n<p>\nIf <tt>Ewald_option_Alpha = 1</tt>, then <tt>Ewald_precision</tt> and <tt>Ewald_Rcut</tt>\nare specified manually, and \n<tt>Ewald_Alpha = Ewald_precision / Ewald_Rcut</tt>.\n\n',520,7),('Ewald_Alpha','DOUBLE','0\n','md','A parameter in the Ewald method.\n\n<p>\nAlso see <tt>Ewald_option_Alpha</tt>, <tt>Ewald_precision</tt>.\n',521,7),('Ewald_precision','DOUBLE','N/A','md','A parameter in the Ewald method.\n\n<p>\nFor details, ask Hark Lee.\n\n<p>\nAlso see <tt>Ewald_Alpha</tt>, <tt>Ewald_option_Alpha</tt>.\n',522,7),('Ewald_time_ratio','DOUBLE','N/A','md','A parameter in the Ewald method.\n\n<p>\nFor details, ask Hark Lee.\n\n<p>\nAlso see <tt>Ewald_option_Alpha</tt>, <tt>Ewald_precision</tt>.\n',523,7),('Ewald_Rcut','DOUBLE','9\n','md','Real space cut-off radius in Ewald method.\n\n<p>\nAlso see <tt>Ewald_precision</tt>, <tt>Ewald_option_Alpha</tt>.\n',524,7),('CE_Kc','DOUBLE','0\n','md','Cut off in the reciprocal space for the classical Ewald (CE) method.\n',525,7),('PME_K1','INT','N/A','md','Parameter for Particle Mesh Ewald method\n',526,7),('PME_K2','INT','N/A','md','Parameter for Particle Mesh Ewald method\n',527,7),('PME_K3','INT','N/A','md','Parameter for Particle Mesh Ewald method\n',528,7),('PME_bsp_n','INT','N/A','md','Parameter for Particle Mesh Ewald method\n',529,7),('crystalstructure','STRING','N/A','md','The crystal structure to be created by command <tt>makecrystal</tt>.\n\n<p>\nExample: <tt>MD++/scripts/Example/example00-makecrystal.script</tt>\n',530,2),('latticeconst','DOUBLE','N/A','md','The lattice constant (in &Aring;) of the crystal to be created by command <tt>makecrystal</tt>.\n\n<p>\nExample: <tt>MD++/scripts/Example/example00-makecrystal.script</tt>\n\n',531,2),('latticesize','DOUBLE','N/A','md','<tt>latticesize = [ <br><i>\n     &nbsp; &nbsp; &nbsp; &nbsp; a_1  a_2  a_3  repeat_a <br>\n     &nbsp; &nbsp; &nbsp; &nbsp; b_1 b_2 b_3  repeat_b <br>\n     &nbsp; &nbsp; &nbsp; &nbsp; c_1 c_2 c_3  repeat_c </i> ] </tt>\n\n<p>\nwhere <tt>[<i>a_1 a_2 a_3</i>]</tt> specifies the first repeat vector of\nthe simulation supercell in Miller indices, and <tt><i>repeat_a</i></tt>\nis the number of the repeats in that direction.\n\n<tt>[<i>b_1 b_2 b_3</i>]</tt> specifies the first repeat vector of\nthe simulation supercell in Miller indices, and <tt><i>repeat_b</i></tt>\nis the number of the repeats in that direction.\n\n<tt>[<i>c_1 c_2 c_3</i>]</tt> specifies the first repeat vector of\nthe simulation supercell in Miller indices, and <tt><i>repeat_c</i></tt>\nis the number of the repeats in that direction.\n\n<p>\nAlso see <tt>crystalstructure</tt>, <tt>latticeconst</tt>, <tt>makecrystal</tt>.\n\n<p>\nExample: <tt>MD++/scripts/Example/example00-makecrystal.script</tt>\n',532,2),('torsionsim','INT','0\n','md','If <tt>torsionsim = 1</tt>, it activates the torsional Periodic Boundary Condition (tPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n\n',533,2),('torquespec','DOUBLE','0\n','md','Simulation settings pertaining to torsional Periodic Boundary Condition (tPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n',534,2),('Torque','DOUBLE','0\n','md','Total torque in torsional Periodic Boundary Condition (tPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n',535,2),('bendsim','INT','0\n','md','If <tt>bendsim = 1</tt>, it activates the bending Periodic Boundary Condition (bPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n\n',536,2),('bendspec','DOUBLE','0\n','md','Simulation settings pertaining to bending Periodic Boundary Condition (bPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n',537,2),('BendMoment','DOUBLE','0\n','md','Total bending moment in bending Periodic Boundary Condition (bPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n',538,2),('P_com','DOUBLE','N/A','md','A vector specifying the total linear momentum of the simulation cell (i.e. its center of mass).\nThis quantity is conserved in Molecular Dynamics simulations without an external potential.\n\n<p>\nThe command <tt>initvelocity</tt> is supposed to make sure this quantity is zero.\n',539,2),('F_com','DOUBLE','N/A','md','A (3x1) vector containing total force on all the atoms (i.e. the center-of-mass) of the simulation cell.\n\n<p>\nUsually this vector should be zero during the MD simulation unless an\nexternal potential is applied. \n',540,2),('L_com','DOUBLE','N/A','md','A vector specifying the total angular momentum of the simulation cell (i.e. its center of mass).\nFor a nano-particle or nano-wire simulation, this quantity is conserved along certain direction\nwhen PBC is not applied in the perpendicular directions.\n\n<p>\nThe command <tt>initvelocity</tt> is supposed to make sure this quantity is zero in such cases.\n\n',541,2),('Ptheta_com','DOUBLE','0\n','md','The momentum for the generalized coordinate &Theta; of the center of mass of the simulation cell under\ntorsional periodic boundary condition (tPBC) or bending periodic boundary condition (bPBC).\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#36\">J. Mech. Phys. Solids 56, 3242, (2008)</a>.\n\n<p>\nAlso see <tt>P_com</tt>, <tt>L_com</tt>.\n\n',542,2),('latticestructure','STRING','N/A','md','Same as <tt>crystalstructure</tt>.\n',543,2),('makecnspec','DOUBLE','N/A','md','Same as <tt>latticesize</tt>.\n',544,2),('mkdipole','DOUBLE','N/A','md','Same as <tt>input</tt>.\n',545,2),('mkdislspec','DOUBLE','N/A','md','Same as <tt>input</tt>.\n',546,2),('mkcylinderspec','DOUBLE','N/A','md','Same as <tt>input</tt>.\n',547,2),('savecn','INT','0\n','md','If <tt>savecn = 1</tt> and <tt>savecnfreq != 0</tt>, then during MD simulation\n(invoked by the <tt>run</tt> command), an intermediate .cn file is \nsaved every <tt>savecnfreq</tt> steps.\n',548,3),('saveprop','INT','0\n','md','If <tt>saveprop = 1</tt> and <tt>savepropfreq != 0</tt>, then during MD simulation\n(invoked by the <tt>run</tt> command), a line is written in the property file\n(named by variable <tt>outpropfile</tt>) every <tt>savepropfreq</tt> steps. The\ncontent of the property file is specified by the <tt>outputfmt</tt> variable.\n',549,3),('savecfg','INT','0\n','md','If <tt>savecfg = 1</tt> and <tt>savecfgfreq != 0</tt>, then during MD simulation\n(invoked by the <tt>run</tt> command), an intermediate Atomeye .cfg file is \nsaved every <tt>savecfgfreq</tt> steps.\n',550,3),('savecnfreq','INT','100\n','md','If <tt>savecn = 1</tt> and <tt>savecnfreq != 0</tt>, then during MD simulation\n(invoked by the <tt>run</tt> command), an intermediate .cn file is \nsaved every <tt>savecnfreq</tt> steps.\n',551,3),('savecontinuecnfreq','INT','0\n','md','If <tt>savecontinuecnfreq</tt> > 0, then the atomic configuration will be saved\nin a .cn file specified by <tt>continuecnfile</tt> every <tt>savecontinuecnfreq</tt>\nsteps during MD simulation (<tt>run</tt>).\n\n<p>\nUnlike <tt>intercnfile</tt>, the file name specified by <tt>continuecnfile</tt> does\nnot automatically increase.  This means that a new <tt>continuecnfile</tt> will overwrite\nthe old file (unless the file name <tt>continuecnfile</tt> is changed intentionally).\nThis allows the hard disk to always hold a copy of the latest configuration\nfor restarting purposes, without requiring a huge disk space.  If you want to record\nthe configurations during MD simulations all in different files, use <tt>savecnfreq</tt>\ninstead.\n\n<p>\nAlso see <tt>readcontinuecn</tt>, <tt>continuecnfile</tt>, <tt>intercnfile</tt>.\n',552,3),('savepropfreq','INT','100\n','md','If <tt>saveprop = 1</tt> and <tt>savepropfreq != 0</tt>, then during MD simulation\n(invoked by the <tt>run</tt> command), a line is written in the property file\n(named by variable <tt>outpropfile</tt>) every <tt>savepropfreq</tt> steps. The\ncontent of the property file is specified by the <tt>outputfmt</tt> variable.\n',553,3),('savecfgfreq','INT','100\n','md','If <tt>savecfg = 1</tt> and <tt>savecfgfreq != 0</tt>, then during MD simulation\n(invoked by the <tt>run</tt> command), an intermediate Atomeye .cfg file is \nsaved every <tt>savecfgfreq</tt> steps.\n',554,3),('printfreq','INT','100\n','md','If <tt>printfreq > 0</tt>, then the current time step information <tt>curstep</tt>\nis printed to the terminal (if <tt>setnolog</tt> has been set) or the A.log file (if\n<tt>setnolog</tt> has not bee set) during the MD simulation every <tt>printfreq</tt>\nsteps.  In Monte Carlo simulations other diagnostic information, such as acceptance \nratio, is also printed.\n',555,3),('filecounter','INT','1\n','md','The number added to the base name of intermediate .cn files.  It is automatically\nincremented by one when a previous intermediate .cn file is closed and a new one is\nto be opened.\n\n<p>\nAlso see <tt>setfilecounter</tt>, <tt>intercnfile</tt>, <tt>savecn</tt>.\n',556,3),('FFSfilecounter','INT','N/A','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',557,3),('incnfile','STRING','con.cn\n','md','Name of the file containing atomic positions and other information (optional)\nthat command <tt>readcn</tt> will read from.  Other commands, such as <tt>readMDCASK</tt>\nand <tt>readPOSCAR</tt> also use <tt>incnfile</tt> to specify the input\nconfiguration file name.\n',558,3),('finalcnfile','STRING','final.cn\n','md','Name of the file containing atomic positions and other information (optional)\nthat command <tt>writecn</tt> will write to.  Other commands, such as <tt>writeMDCASK</tt>,\n<tt>writePOSCAR</tt>, and <tt>writeatomeyecfg</tt> also use <tt>finalcnfile</tt> to specify \nthe output configuration file name.\n',559,3),('continuecnfile','STRING','continue.cn\n','md','The name of the file that the latest configuration gets saved to (for restarting purposes)\nduring MD simulation if <tt>savecontinuecnfreq</tt> &gt; 0.\n\n<p>\nIt is also the name of the file that <tt>readcontinuecn</tt> reads from.\n\n<p>\nAlso see <tt>intercnfile</tt>.\n\n~\n',560,3),('outpropfile','STRING','prop.out\n','md','The name of the file in which thermal properties (such as <tt>EPOT</tt>, <tt>Tinst</tt>) are saved\nperiodically during MD simulation.\n\n<p>\nAlso see <tt>saveprop</tt>, <tt>output_fmt</tt>.\n',561,3),('intercnfile','STRING','inter.cn\n','md','The base name of the intermediate .cn files that will be saved periodically\nduring MD simulation.  The actual file names will have numbers added to them,\ne.g. <tt>inter0001.cn</tt>, <tt>inter0002.cn</tt>, &hellip;\n\n<p>\nAlso see <tt>savecn</tt>, <tt>savecnfreq</tt>.\n',562,3),('FFScnfile','STRING','FFS.cn\n','md','Parameter in Forward Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',563,3),('intercfgfile','STRING','auto.cfg\n','md','The base name of the intermediate .cfg files that will be saved periodically\nduring MD simulation.  The actual file names will have numbers added to them,\ne.g. <tt>auto0001.cfg</tt>, <tt>auto0002.cfg</tt>, &hellip;\n\n<p>\nAlso see <tt>savecfg</tt>, <tt>savecfgfreq</tt>.\n',564,3),('potfile','STRING','../Mo.pot\n','md','Name of the file that contains the information on the interatomic potential model.\n\n<p>\nAlso see <tt>readpot</tt>, <tt>readeam</tt>.\n',565,3),('writevelocity','INT','0\n','md','If <tt>writevelocity = 1</tt>, then subsequent saving of <tt>.cn</tt> files \nby <tt>writecn</tt> will contain the following information for each atom: \n\n<p>\n<tt>SR.x SR.y SR.z VSR.x VSR.y VSR.z</tt>\n\n<p>\nSee <a href=\"http://micro.stanford.edu/wiki/Output_File_Formats_in_MD++#Configuration_.cn_File\">wiki\npage</a> for more details.\n',566,3),('writeall','INT','0\n','md','If <tt>writeall = 1</tt>, then subsequent saving of <tt>.cn</tt> files \nby <tt>writecn</tt> will contain much more information than the default, \ni.e. each atomic line will contain:\n\n<p>\n<tt>SR.x SR.y SR.z VSR.x VSR.y VSR.z EPOT_IND fixed TOPOL species group image</tt>\n\n<p>\nSee <a href=\"http://micro.stanford.edu/wiki/Output_File_Formats_in_MD++#Configuration_.cn_File\">wiki\npage</a> for more details.\n',567,3),('zipfiles','INT','0\n','md','If <tt>zipfiles = 1</tt>, then the .cn, .cfg and property files that MD++ creates\nwill be automatically zipped to save space.  MD++ will automatically unzip zipped\n.cn files when reading them, so you don\'t have to unzip them manually.\n\n<p>\nAlso see <tt>writecn</tt>, <tt>writeatomeyecfg</tt>.\n',568,3),('fortranpath','STRING','N/A','md','A string containing the path that holds a Fortran compiled executable.  \nMust be set before calling <tt>fortranrelax</tt>.\n',569,3),('fortranexe','STRING','N/A','md','A string containing the name of a Fortran compiled executable.  \nMust be set before calling <tt>fortranrelax</tt>.\n',570,3),('atomeyepath','STRING','N/A','md','A string containing the path that holds the Atomeye executable.\n\n<p>\nMust be set before calling <tt>atomeye</tt>.\n',571,3),('atomeyerepeat','INT','N/A','md','<tt>atomeyerepeat = [ <i>activate  n_1  n_2  n_3</i> ]</tt>\n\n<p>\nIf <tt><i>activate</i> = 1</tt>, then the atomic configuration exported to the\nAtomeye cfg format will be repeated \nby <tt><i>n_1</i></tt>, <tt><i>n_2</i></tt>, and <tt><i>n_3</i></tt> times\nalong the first, second and third repeat direction of the simulation supercell.\n\n<p>\nAlso see <tt>H</tt>, <tt>writeatomeyecfg</tt>.\n',572,3),('atomeyeexe','STRING','N/A','md','A string containing the name of the Atomeye executable, e.g.\n<tt>A.i686</tt>, <tt>A.exe</tt>.  \n\n<p>\nMust be set before calling <tt>atomeye</tt>.\n',573,3),('MDCASKpot','STRING','SW\n\n','md','Specify the potential model used in MDCASK. Choices are\n<tt>SW</tt>, <tt>TERSOFF</tt>, <tt>ROCKETT</tt>, <tt>ZBL</tt>,\n<tt>EAM</tt>, <tt>EDIP</tt>, <tt>MEAM</tt>.  \nIt needs to be set before calling <tt>readMDCASK</tt>.\n',574,3),('win_width','INT','350\n','md','The initial width of the X-window.  The window size can be adjusted using mouse after it is opened.\n\n<p>\nAlso see <tt>win_height</tt>, <tt>openwin</tt>.\n',575,8),('win_height','INT','350\n','md','The initial height of the X-window.  The window size can be adjusted using mouse after it is opened.\n\n<p>\nAlso see <tt>win_width</tt>, <tt>openwin</tt>.\n',576,8),('plotfreq','INT','1\n','md','If the X-window is opened, then during MD simulation (invoked by the <tt>run</tt> command)\nor conjugate gradient relaxation (invoked by the <tt>relax</tt> command), the atomic \npositions will be refreshed in the X-window every <tt>plotfreq</tt> steps.\n\n<p>\nAlso see <tt>openwin</tt>, <tt>plot</tt>\n',577,8),('atomradius','DOUBLE','0.1\n','md','An array specifying the size of each atomic species in the X-window.\n\n<p>\nAlso see <tt>atomcolor</tt>, <tt>plot</tt>.\n',578,8),('bondradius','DOUBLE','0.1\n','md','The width of the line representing bonds between atoms in the X-window.\n\n<p>\nAlso see <tt>bondcolor</tt>, <tt>bondlength</tt>.\n',579,8),('bondlength','DOUBLE','0\n','md','In the X-window, two atoms whose distance is less than <tt>bondlength</tt> (in &Aring;)\nwill have a bond drawn between them.\n',580,8),('bondcolor','STRING','red\n','md','The color names for drawing bonds between atoms in the X-window.\n\n<p>\nAlso see <tt>bondradius</tt>, <tt>bondlength</tt>.\n',581,8),('highlightcolor','STRING','purple\n','md','The color names for atoms that are highlighted.  These atoms\nare specified by <tt>plot_highlight_atoms</tt>.\n',582,8),('fixatomcolor','STRING','N/A','md','The color names for atoms that are marked as fixed (<tt>fixed[i] = 1</tt>).\nThis variable need to be set before calling <tt>alloccolor</tt>.\n',583,8),('backgroundcolor','STRING','N/A','md','The color name for the background of the X-window to be allocated by <tt>alloccolor</tt>.\n\n<p>\nAlso see <tt>highlightcolor</tt>.\n',584,8),('rotateangles','DOUBLE','N/A','md','Specify the HOME viewing orientation of the X-window. This is the viewing orientation\nwhen the X-window is first opened, and is also the viewing orientation the X-winndow\nreturns to whenever the HOME key is pressed.\n\n<p>\nThe default HOME orientation is such that the <i>x</i> axis points from left to right, \nand the <i>y</i> axis points points from bottom to top, and the <i>z</i> axis points \nout of the screen.  But this can be changed by setting <tt>rotateangle</tt> and then\ncall <tt>rotate</tt> and <tt>saverot</tt>.\n\n<p>\n<tt>rotateangle = [ <i>h_rot v_rot s_rot scale</i> ] </tt>\n<br>\nwhere <tt><i>h_rot</i></tt> is the rotation angle (in degrees) from left to right (i.e.\nequivalent to dragging the mouse in the horizontal direction), \n<tt><i>v_rot</i></tt> is the rotation angle (in degrees) from bottom to up (i.e.\nequivalent to dragging the mouse in the vertical direction), \n<tt><i>s_rot</i></tt> is the rotation angle (in degrees) in the clockwise direction (i.e.\nequivalent to pressing the Page-Down key in the X-window),\n<tt><i>scale</i></tt> is scales the size of all objects plotted in the X-window.\n\n<p>\nAlso see <tt>openwin</tt>, <tt>plot</tt>.\n',585,8),('coloratoms','INT','0\n','md','If <tt>coloratoms = 0</tt> (default), then atoms are colored according to their species.\nIf <tt>coloratoms = 1</tt> (default), then atoms are colored according to their group ID.\n\n\n\n<p>\nAlso see <tt>color00</tt>, <tt>color01</tt>, <tt>color02</tt>, <tt>alloccolors</tt>.\n',586,8),('plot_limits','DOUBLE','0\n','md','Limits which atoms will be plotted in the X-window by their scaled coordinates.\nAlso affects which atoms will be exported to the Atomeye .cfg file.\n\n<p>\nFormat: <tt>plot_limits = [ <i>enable sxmin sxmax symin symax szmin szmax</i> ] </tt>\n\n<p>\nIf <tt><i>enable</i> == 1</tt>, the only atoms whose scaled coordinates falls within\nthe limits defined by the subsequent parameters are plotted (or exported).\n',587,8),('plot_atom_info','INT','1\n','md','A flag indicating what information will be printed to the screen (or A.log file)\nwhen an atom in the X-window is clicked.\n\n<p>\n1: print scaled coordinates of the atom <br>\n2: print real coordinates of the atom <br>\n3: print <tt>color_ind</tt>, which can mean <tt>EPOT_IND</tt> (default) or <tt>TOPOL</tt> depending on\n   <tt>plot_color_axis</tt>. <br>\n4: print force acting on the atom <br>\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap3/sect3.3/al-fr-eng.script</tt>\n<p>\nAlso see <tt>plot_color_windows</tt>, <tt>plot_color_axis</tt>.\n',588,8),('plot_map_pbc','INT','0\n','md','If <tt>plot_map_pbc = 1</tt>, atoms will be mapped to the primary domain, i.e. with scaled\ncoordinates in the domain [-0.5, 0.5), when plotting in the X-window.  Note that this is only\nfor visualization purposes.  The actual (scaled or real) coordinates are not changed.\n\n<p>\nBy default, the actual coordinates of the atoms are used in the plotting, so atoms can appear \noutside the primary domain (i.e. the purple-colored simulation box).\n',589,8),('plot_color_windows','DOUBLE','0\n','md','<tt>plot_color_window = [ <i>n</i>   <br>\n   &nbsp; &nbsp; &nbsp;  <i>fmin_1</i>  <i>fmax_1</i>  <i>cw_1</i> <br>\n   &nbsp; &nbsp; &nbsp;  <i>fmin_2</i>  <i>fmax_2</i>  <i>cw_2</i> <br>\n   &nbsp; &nbsp; &nbsp;  &hellip;  <br>\n   &nbsp; &nbsp; &nbsp;  <i>fmin_n</i>  <i>fmax_n</i>  <i>cw_n</i> ] </tt>\n   \n<p>\nWhen <tt><i>n</i></tt> > 0, this option is activated.  It specifies that there\nwill be <tt><i>n</i></tt> windows.  An atom <tt>i</tt> falls into window <tt>k</tt>\nif <tt>fmin_k</tt> < = <tt>color_ind[i]</tt> <= <tt>fmax_k</tt>.\n<tt><i>cw_k</i></tt> specifies the color to be used for window <tt><i>k</i></tt>.\nFor example, if <tt><i>cw_k</i></tt> = 6, \nthen atoms in window k will be plotted with <tt>color06</tt>.\n\n<p>\nBy default, <tt>color_ind[i]</tt> is the same as <tt>EPOT_IND[i]</tt> (the\npotential energy contribution from atom <tt>i</tt>).  But it can be changed to\n<tt>TOPOL[i]</tt> (the central symmetry parameter) if <tt>plot_color_axis = 2</tt>.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap3/sect3.3/al-fr-eng.script</tt>\n\n<p>\nFor more information, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">\nComputer Simulations of Dislocations</a> Chapter 3, Section 3.3.\n\n',590,8),('plot_color_bar','DOUBLE','N/A','md','<tt>plot_color_bar = [ <i>enable  fmin  fmax</i> ] </tt>\n\n<p>\nIf <tt><i>enable</i> == 1</tt>, then the atoms will be colored using a continuous\ncolor bar according to their <tt>color_ind[i]</tt> values.  When  <tt>color_ind[i]</tt>\nreaches <tt><i>fmin</i></tt> or <tt><i>fmax</i></tt>, the color on the end of the\ncolor bar is used.\n\n<p>\n<tt>color_ind</tt> is either <tt>EPOT_IND</tt> or <tt>TOPOL</tt> depending on the value of\n<tt>plot_color_axis</tt>.\n',591,8),('plot_highlight_atoms','INT','N/A','md','<tt>plot_highlight_atoms = [ <i>n  i<sub>1</sub>  i<sub>2</sub> &hellip; i<sub>n</sub> </i> ] </tt>\n\n<p>\nWhen <tt><i>n</i></tt> > 0, then atoms <tt>i<sub>1</sub>  i<sub>2</sub> &hellip; i<sub>n</sub> </i> ] </tt>\nwill be highlighted.\n\n<p>\nAlso see <tt>highlightcolor</tt>.\n',592,8),('energycolorbar','DOUBLE','N/A','md','Same as <tt>plot_color_bar</tt>.\n',593,8),('plot_color_axis','INT','0\n','md','When <tt>plot_color_axis = 0</tt>, the array <tt>color_ind[i]</tt> is the same as\n<tt>EPOT_IND[i]</tt>.  This means that the potential energy contribution of each atom\nis used to determine the color of atoms (when <tt>plot_color_windows</tt> is activated).\n\n<p>\nWhen <tt>plot_color_axis = 2</tt>, the array <tt>color_ind[i]</tt> is the same as\n<tt>TOPOL[i]</tt>.  This means that the central symmetry parameter\nis used to determine the color of atoms (when <tt>plot_color_windows</tt> is activated).\n\n<p>\nAlso see <tt>plot_color_windows</tt>.\n\n',594,8),('NCS','INT','12\n','md','Number of nearest neighbors for each atom in the perfect crystal in central symmetry deviation (CSD)\nanalysis.  Use <tt>NCS = 12</tt> for FCC crystal, and <tt>NCS = 8</tt> for BCC crystal.\n\n<p>\nAlso see <tt>TOPOL</tt>, <tt>calcentralsymmetry</tt>. \n',595,8),('autowritegiffreq','INT','0\n','md','If <tt>autowritegiffreq != 0</tt> and if an X-window is open during\nan MD simulation (i.e. interactive run), then a screen snapshot (.gif)\nis taken every <tt>autowritegiffreq</tt> steps.\n',596,8),('NNM_plot','INT','4\n','md','Maximum number of neighbors for each atom in the plot-neighbor-list, i.e. the neighbor list\nused for plotting and geometric analysis purposes.  If this neighbor list is constructed for\na reference configuration, and is not updated when a newer configuration is loaded, it allows\nus to compute the change of bond lengths between atoms and their original neighbors.\n\n<p>\nAlso see <tt>construct_plot_nnlist</tt>, <tt>caldisregistry</tt>.\n',597,8),('rc_plot','DOUBLE','N/A','md','Cut-off radius for each atom in the plot-neighbor-list, i.e. the neighbor list\nused for plotting and geometric analysis purposes.  If this neighbor list is constructed for\na reference configuration, and is not updated when a newer configuration is loaded, it allows\nus to compute the change of bond lengths between atoms and their original neighbors.\n\n<p>\nAlso see <tt>construct_plot_nnlist</tt>, <tt>caldisregistry</tt>.\n',598,8),('L_for_QLM','INT','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',599,8),('Rc_for_QLM','DOUBLE','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',600,8),('Rc_for_QLM','STRING','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',601,8),('Rc_for_QLM','STRING','0\n','md','Setting for computing the crystalline order parameter.\n\n<p>\nAlso see <tt>calcrystalorder</tt>, <tt>allocQLM</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',602,8),('atomcolor','STRING','orange\n','md','The color names for atoms of different species to be allocated by <tt>alloccolor</tt>.\n<tt>atomcolor0</tt>, <tt>atomcolor1</tt>, &hellip; are for species <tt>0</tt>, <tt>1</tt>,\n&hellip;.  \n\n<p>\n<tt>atomcolor</tt> is the same as <tt>atomcolor0</tt>.\n',603,8),('atomcolor','STRING','orange\n','md','The color names for atoms of different species to be allocated by <tt>alloccolor</tt>.\n<tt>atomcolor0</tt>, <tt>atomcolor1</tt>, &hellip; are for species <tt>0</tt>, <tt>1</tt>,\n&hellip;.  \n\n<p>\n<tt>atomcolor</tt> is the same as <tt>atomcolor0</tt>.\n',604,8),('opendir','COMMAND','N/A','md','Create the directory specified by <tt>dirname</tt> (if it does not exist) and enter \nthis directory.\n\n<p>\nNote: This command is usually not called directly in the input file.  It is automatically\ncalled when the <tt>dirname</tt> variable is set.\n',605,5),('print_randseed','COMMAND','N/A','md','Print the value of <tt>randseed</tt> to the screen or the <tt>A.log</tt> file.\n',606,5),('runcommand','COMMAND','N/A','md','Execute a shell command specified in <tt>command</tt>.\n\n<p>\nFor example: <tt>command = \"ls\" runcommand</tt>\n\n',607,5),('relax','COMMAND','N/A','md','Conjugate gradient relaxation.\n\n<p>\nVariables <tt>conj_ftol</tt>, <tt>conj_itmax</tt>, <tt>conj_fevalmax</tt>, <tt>conj_fixbox</tt>, \n<tt>conj_fixboxvec</tt> (optional) should be \nset before calling this command.\n',608,7),('relax_by_group','COMMAND','N/A','md','Usage: <tt>input = [ <i>ng  group_1 group_2 &hellip; group_ng</i> ]  relax_by_group<tt>\n\n<p>\nIf <tt><i>ng</i></tt> > 0, then all atoms <tt>i</tt> whose <tt>group[i]</tt> value \nmatches any of the <tt><i>group_1 group_2 &hellip; group_ng</i> </tt> will be relaxed, while\nother atoms remain fixed.\n\n<p>\nRedundant function.  Can be reproduced by <tt>fixatoms_by_group</tt> and <tt>relax</tt>.\n',609,7),('steepest_descent_relax','COMMAND','N/A','md','Usage: <tt>input = [<i>etol ignoreE</i>] totalsteps = <i>N</i> timestep = &Delta; steepest_descent_relax </tt>\n\n<p>\nPerform steepest descent relaxation for a maximum of <tt><i>N</i></tt> steps with step\nsize &Delta;.  The relaxation will exit if the reduction of <tt>EPOT</tt> is\nless than <tt><i>etol</i></tt>.  The <tt>EPOT</tt> will not be monitored if \n<tt><i>ignoreE</i> = 1</tt>.\n\n<p>\nFor debugging/testing purposes.  Much slower than <tt>relax</tt>, which uses the conjugate\ngradient algorithm.\n',610,7),('step','COMMAND','N/A','md','Perform one (integration) step of the Molecular Dynamics simulation.  This function\nis usually not called directly by the user, but is automatically called within the\n<tt>run</tt> command.  For debugging purposes.\n',611,7),('run','COMMAND','N/A','md','Perform molecular dynamics (MD) simulation.\n\n<p>\nVariables <tt>totalsteps</tt>, <tt>timestep</tt>, <tt>ensemble_type</tt>, \n<tt>integrator_type</tt>, <tt>saveprop</tt>, <tt>savecn</tt>,\n&hellip; etc. should be set before calling this command.\n',612,7),('runMDSWITCH','COMMAND','N/A','md','Run Molecular Dynamics simulations in which the Hamiltonian changes\ngraduately from one model to another, in order to compute free energy\ndifference.\n\n<p>\nAlso see <tt>refpotential</tt>, <tt>lambda0</tt>, <tt>lambda1</tt>, <tt>dEdlambda</tt>,\n<tt>dlambdadt</tt>.\n',613,7),('eval','COMMAND','N/A','md','Call the potential function and compute total potential\nenergy, force, kinetic energy, temperature and Virial stress\nfor the current configuration.  The total potential energy\nand stress are printed to the screen or to the A.log file\n(depending on whether or not <tt>setnolog</tt> is set).\n',614,7),('multieval','COMMAND','N/A','md','Usage: <tt>totalsteps = <i>N</i> multeval</tt>\n\n<p>\nCall the potential function <tt><i>N</i></tt> times.  For debugging and\nspeed benchmark purposes.\n',615,7),('eval_insertparticle','COMMAND','N/A','md','Evaluate the potential energy change if a new particle is randomly inserted into the simulation cell.\nRepeated calls to this function generate statistics that can be used to evaluate the chemical\npotential.  Since the number of atoms will need to increase, make sure to\nset <tt>allocmultiple</tt> to be greater than 1 when calling <tt>makecrystal</tt> or \n<tt>readcn</tt> above.\n\n<p>\nReference: Frenkel and Smit, <i>Understanding Molecular Simulation</i>, 2nd ed., Section 7.2, \nChemical Potentials.\n\n<p>\nAlso see <tt>eval_removeparticle</tt>.\n',616,7),('eval_removeparticle','COMMAND','N/A','md','Evaluate the potential energy change if a randomly chosen particle is removed the simulation cell\n(by setting <tt>fixed[i] = -1</tt>).\n\n<p>\nAlso see <tt>eval_insertparticle</tt>.\n',617,7),('refreshnnlist','COMMAND','N/A','md','Reconstruct the Verlet neighborlist (by first constructing the cell list) if necessary.\nIf the maximum displacement among all atoms since the last neighbor list construction\n(i.e. max<sub>i</sub> |R(i) - R0(i)|) is less than <tt>SKIN</tt> / 2, then there is\nno need to reconstruct the neighbor list.\n\n<p>\nAlso see <tt>R0</tt>, <tt>SKIN</tt>.\n',618,7),('construct_plot_nnlist','COMMAND','N/A','md','Construct the plot-neighbor-list, i.e. the neighbor list\nused for plotting and geometric analysis purposes.  If this neighbor list is constructed for\na reference configuration, and is not updated when a newer configuration is loaded, it allows\nus to compute the change of bond lengths between atoms and their original neighbors.\n\n<p>\nAlso see <tt>rc_plot</tt>, <tt>caldisregistry</tt>.\n',619,7),('printnnlist','COMMAND','N/A','md','Print the neighbor list information to the screen (or to the A.log file)\nfor debugging purposes.\n',620,6),('calphonondisp','COMMAND','N/A','md','Function under development.  Do not use.\n\n<p>\nIntended to compute the phonon dispersion relation based on the Hessian matrix.\n\n<p>\nAlso see <tt>calHessian</tt>.\n',621,6),('calHessian','COMMAND','N/A','md','Compute Hessian matrix by numerical differentiation.\n\n<p>\nThe step size in (&Aring;) for numerical differentiation\nis specified by <tt>timestep</tt>.\n\nResult saved in <tt>hessian.out</tt> in the current directory. \nNote that the results are actually the negative of the Hessian matrix,\ni.e. it is the first derivative of the forces that are computed.\n\n<p>\nTo compute the free energy based on Harmonic Approximation, use\n<tt>MD++/Tools/matlab/free_eng_ha.m</tt> as a starting point.\n\n<p>\nIf <tt>input[0]=0</tt>, then the entire Hessian matrix is computed.\n\n<p>\nIf <tt>input[0] &ne; 0</tt>, then <tt>input[0] = n</tt> specifies the number\nof atoms whose corresponding (3) columns in the Hessian matrix will\nbe computed.  The atom indices are specified in <tt>input[1]</tt>,\n&hellip; , <tt>input[n]</tt>.\n\n<p>\nAlso see: Computer Simulations of Dislocations\n<a href=\"http://micro.stanford.edu/~caiwei/CSD-Book\">web site</a>\nChapter 6, Section 6.2.\n',622,6),('readHessian','COMMAND','N/A','md','Read the Hessian matrix (the second derivative of the potential function with respect to real coordinates)\nfrom file whose name is specified by <tt>incnfile</tt>.\n\n<p>\nAlso see <tt>calHessian</tt>.\n',623,6),('calModeHessian','COMMAND','N/A','md','Function under development.  Do not use.\n',624,6),('calmisfit','COMMAND','N/A','md','Compute the misfit potential of a crystal by tilting the simulation box <tt><b>H</b></tt>.\n\n<p>\nUsage: <tt>input = [ <i>surfacenormal x0 dx x1 y0 dy y1 z0 dz z1</i> ] calmisfit </tt>\n\n<p>\nFor more details, see <a href=\"http://micro.stanford.edu/wiki/M09_Computing_Ideal_Strength#Gamma_Surface\">\nwiki page</a> on ideal strength calculation.\n\n<p>\nAlso see <tt>calmisfit2</tt>.\n',625,6),('calmisfit2','COMMAND','N/A','md','Compute the misfit potential of a crystal without tilting the simulation box <tt><b>H</b></tt>.\n\n<p>\nUsage: <tt>input = [ <i>surfacenormal x0 dx x1 y0 dy y1 z0 dz z1 xmin xmax ymin ymax zmin zmax</i> ] calmisfit2</tt>\n\n<p>\nFor more details, see <a href=\"http://micro.stanford.edu/wiki/M09_Computing_Ideal_Strength#Computing_Ideal_Shear_Strength_without_Tilting_Simulation_Cell\">wiki page</a> on ideal strength calculation.\n\n<p>\nAlso see <tt>calmisfit</tt>.\n\n',626,6),('testpotential','COMMAND','N/A','md','For testing a newly implemented potential.  Print out the maximum force experienced by the atoms \nand check the self-consistency between force and potential energy (by taking numerical derivatives\nof the potential energy).\n',627,6),('calcentralsymmetry','COMMAND','N/A','md','Computes central symmetry deviation (CSD) parameter for each\natom and store them in the <tt>TOPOL</tt> array.\n\n<p>\nRequires <tt>NCS</tt>  to be set\n(number of nearest neighbors in CSD calculation).\n\nFor FCC crystal, use <tt>NCS = 12</tt>.  For BCC crystal, use <tt>NCS = 8</tt>.\n\n<p>\nAlso see <tt>GnuPlotHistogram</tt>.\n',628,6),('caldisregistry','COMMAND','N/A','md','Calculate the distance between atoms and their original neighbors (in the reference\nconfiguration in which the plot-neighbor-list was constructed).\nThis allows us to identify slip events.\n\n<p>\nAlso see <tt>construct_plot_nnlist</tt>.\n',629,6),('findcore','COMMAND','N/A','md','Usage: <tt>input = [ <i>tmin tmax cal_shape</i> ]  findcore</tt>\n\n<p>\nDetermine the average position of defect atoms whose central symmetry deviation (CSD)\nparameter <tt>TOPOL</tt> is within the range of <tt>[<i>tmin</i>, <i>tmax</i>)</tt>.\nThe atoms included in the analysis can be further limited by setting <tt>plot_limits</tt>.\nIf <tt><i>cal_shape</i> = 1</tt> then the <tt>Principal_Inertia</tt> of the defect cluster\nis also computed.\n\n<p>\nAssumes that all defect atoms for a single cluster.\n',630,6),('initvelocity','COMMAND','N/A','md','Initialize the atomic velocities according to desired temperature <tt>TOBJ</tt>.\n\n<p>\nAlso see <tt>initvelocity_type</tt>.\n',631,2),('perturbevelocity','COMMAND','N/A','md','Implementation not complete.  Do not use.\n\n<p>\nAlso see <tt>MCperturbvelocity</tt>, <tt>initvelocity</tt>.\n',632,2),('MCperturbevelocity','COMMAND','N/A','md','Implementation not complete.  Do not use.\n\n<p>\nAlso see <tt>perturbvelocity</tt>, <tt>initvelocity</tt>.\n\n',633,2),('multiplyvelocity','COMMAND','N/A','md','Usage: <tt> input = <i>vratio</i>  multiplyvelocity</tt>\n\n<p>\nThe velocity <tt>VSR</tt> of all atoms is multiplied by <tt><i>vratio</i></tt>.\nIf a thermostat is used, the velocity of the thermostat variable (<tt>zetav</tt>)\n is multiplied by <tt>vratio</tt> as well.  If a barostat is used, the velocity \nof the box matrix <tt>VH</tt> is also multiplied by <tt>vratio</tt>.\n\n<p>\nAlso see <tt>scaleVel</tt>.\n',634,2),('randomposition','COMMAND','N/A','md','Set the scaled coordinates of all atoms to be random numbers uniformly distributed\nin [-0.5, 0.5).  This can be used to initialize the configuration for gas or liquid\nsimulation.  Because some atoms may accidentally get too close to each other (leading\nto very high energy and repulsive forces), <tt>relax</tt> usually is necessary before\nMD simulation (<tt>run</tt>).\n\n<p>\nAlso see <tt>initvelocity</tt>.\n',635,2),('zerorotation','COMMAND','N/A','md','Add rigid body rotation velocity field to the simulation cell so that\nits total angular momentum around a given axis is zero.  The axis is\nspecified by <tt>zerorot</tt> which can be <tt>\"x\"</tt>, or <tt>\"y\"</tt>, \nor <tt>\"z\"</tt>.\n\n<p>\nThere is usually no need to call this command manually.\n<tt>initvelocity</tt> is supposed to accomplish that after randomizing the velocities.\n\n<p>\nAlso see <tt>L_com</tt>.\n',636,2),('zerototmom','COMMAND','N/A','md','Add a constant velocity to all atoms so that the center of mass velocity of the entire\nsimulation cell is zero.\n\n<p>\nThere is usually no need to call this command manually.\n<tt>initvelocity</tt> is supposed to accomplish that after randomizing the velocities.\n\n<p>\nAlso see <tt>P_com</tt>.\n',637,2),('applyconstraint','COMMAND','N/A','md','Move the current configuration to the hyperplane perpendicular to <tt>SR2 - SR1</tt>\nspecified by the parameter <tt>constrainS</tt>.\n\n<p>\nAlso see <tt>constrainedMD</tt>, <tt>constrainedrelax</tt>.\n',638,7),('runMC','COMMAND','N/A','md','Perform Monte Carlo (MC) simulation.\n\n<p>\nVariables <tt>totalsteps</tt>, <tt>timestep</tt>, <tt>ensemble_type</tt>, \n<tt>saveprop</tt>, <tt>savecn</tt>,\n&hellip; etc. should be set before calling this command.\n\n',639,7),('runMCSWITCH','COMMAND','N/A','md','Run Monte Carlo simulations in which the Hamiltonian changes\ngraduately from one model to another, in order to compute free energy\ndifference.\n\n<p>\nAlso see <tt>refpotential</tt>, <tt>lambda0</tt>, <tt>lambda1</tt>, <tt>dEdlambda</tt>,\n<tt>dlambdadt</tt>.\n\n',640,7),('runTAMC','COMMAND','N/A','md','Temperature accelerated Monte Carlo simulation to find transition pathways.\nSimulation only performed for atoms specified by <tt>constrainatoms</tt>.\nDuring the simulation (at high temperature), the configuration is periodically\nchecked (by <tt>relax</tt>) to see whether a transition has occured.\nIf a transition has occurred, the command will exit.  The transition path thus\nidentified can be saved by calling <tt>writeRchain</tt>.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap7/sect7.5/si-kink-tas.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 7, Section 7.5.\n\n<p>\nAlso see <tt>constrainatoms</tt>.\n\n\n\n',641,7),('srand','COMMAND','N/A','md','Do not use.  Use <tt>srand48</tt> instead</tt>.\n\n<p>\nRandomize random number generator using <tt>randseed</tt>,\nwhich must be set before calling this command.  This affects\nfuture calls to <tt>drand()</tt>.\n\nNotice that by default MD++ uses <tt>drand48()</tt> (which should be\ninitialized by <tt>srand48</tt>) as random number generators (e.g.\nin <tt>initvelocity</tt>).\n\n<p>\nOnly use this command if <tt>drand48</tt> is not available from the\ncompiler, in which case you need to use <tt>rand()</tt> instead.  In this case\nyou need to modify the MD++ source code.\n\n<p>\nAlso see <tt>srandbytime</tt>.\n',642,7),('srand48','COMMAND','N/A','md','Randomize random number generator using <tt>randseed</tt>,\nwhich must be set before calling this command.  This affects\nfuture calls to <tt>drand48()</tt>.\n',643,7),('srandbytime','COMMAND','N/A','md','Do not use.  Use <tt>srand48bytime</tt> instead</tt>.\n\n<p>\nRandomize random number generator using current CPU time\nas the seed.  This affects future calls to <tt>rand()</tt>.  \n\nNotice that by default MD++ uses <tt>drand48()</tt> (which should be\ninitialized by <tt>srand48</tt>) as random number generators (e.g.\nin <tt>initvelocity</tt>).\n\n<p>\nOnly use this command if <tt>drand48</tt> is not available from the\ncompiler, in which case you need to use <tt>rand()</tt> instead.  In this case\nyou need to modify the MD++ source code.\n\n<p>\nAlso see <tt>srand</tt>.\n',644,7),('srand48bytime','COMMAND','N/A','md','Randomize random number generator using current CPU time\nas the seed.  This affects future calls to <tt>drand48()</tt>.\n',645,7),('stringrelax','COMMAND','N/A','md','Finding the minimum energy path and the energy barrier using the\nstring method.\n\n<p>\n<tt>stringrelax</tt> is more stable than <tt>nebrelax</tt> (in which we\nneed to choose the spring constant carefully).\nHowever, the parallel version of <tt>nebrelax</tt> is faster than\nthe parallel version of <tt>stringrelax</tt> (because reparametrization\nrequires communication between all CPUs).\n\n<p>\nAlso see <tt>nebrelax</tt>, <tt>nebspec</tt>.\n',646,7),('runstringmethod','COMMAND','N/A','md','Alternative implementation. Do not use.  Use <tt>stringrelax</tt> instead.\n\n<p>\nReference: J. Chem. Phys. vol.126, 164103 (2007).\n\n<p>\nFor details, ask Keonwook Kang.\n',647,7),('nebrelax','COMMAND','N/A','md','Finding the minimum energy path and the energy barrier using the\nNudged Elastic Band (NEB) method.\n\n<p>\nFor details, ask Keonwook Kang.\n\n<p>\nReference: Journal of Chemical Physics Vol.113 9978-9985, 2000\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap7/sect7.3/si-kink-nebmep.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 7, Section 7.3.\n\n<p>\nAlso see <tt>stringrelax</tt>, <tt>nebspec</tt>.\n',648,7),('constrainedrelax','COMMAND','N/A','md','Conjugate gradient relaxation with a selected set of atoms constrained in the \nhyperplane perpendicular to <tt>SR2 - SR1</tt>.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap7/sect7.3/si-kink-cstmep.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 7, Section 7.3.\n\n\n<p>\nAlso see <tt>relax</tt>, <tt>constrainatoms</tt>.\n',649,7),('annealpath','COMMAND','N/A','md','Simulated annealing of transition path between two states by Monte Carlo.\n\n<p>\nUsage: <tt>annealspec = [ <i>rmax T0 &lambda; alg</i> ] annealpath </tt>\n\n<p>\n<tt><i>rmax</i></tt> is the maximum allowed distance between neighboring states during the\nMonte Carlo (annealing) simulation.\n<br>\n<tt><i>T0</i></tt> is the initial temperature of the simulation.\n<br>\n<tt><i>&lambda;</i></tt> is the annealing rate.  The actual temperature during the simulation\nis computed by <tt>T = <i>T0</i> * exp(-<i>&lambda;</i> * curstep / totalsteps)</tt>.\n<br>\n<tt><i>alg</i></tt> specifies which energy function is used to compute the acceptance\nprobability of the Monte Carlo simulation.  <tt><i>alg</i> = 0</tt> means using the maximum \npotential energy along the path; <tt><i>alg</i> = 1</tt> means using the sum of \n<tt>max(Ec[j]-Ec[j-1],0)</tt>, where <tt>j</tt> is the index along the path; \n<tt><i>alg</i> = 2</tt> means using the sum of all potential energies along the path.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap7/sect7.4/si-kink-pathmc.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 7, Section 7.4.\n\n<p>\nAlso see <tt>runTAMC</tt>.\n\n\n',650,7),('statedistance','COMMAND','N/A','md','Compute the distance (sqrt of two-norm) between <tt>SR1</tt> and <tt>SR2</tt>.\nIf <tt>constrainedatoms[0] = 0</tt>, then all atoms are included in computing this\ndistance.  \nIf <tt>constrainedatoms[0] &gt; 0</tt>, then only constrained atoms are included in \ncomputing this distance.  \n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>setconfig2</tt>.\n',651,6),('cutpath','COMMAND','N/A','md','Usage: <tt>annealspec = [ <i>step n0 n1</i> ]  cutpath</tt>\n\n<p>\nSelect a subset of configurations along the chain <tt>Rc</tt>, with id\n<tt><i>n0</i>, <i>n0</i>+<i>step</i>, <i>n0</i>+2*<i>step</i>, &hellip;, \n<i>n1</i></tt>, and make that the new chain.\n\n<p>\nAlso see <tt>chainlength</tt>.\n\n',652,2),('initRchain','COMMAND','N/A','md','Initialize the array <tt>Rc</tt> as a linear chain connecting \n<tt>SR1</tt> and <tt>SR2</tt>.\n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>setconfig2</tt>, <tt>nebrelax</tt>, <tt>stringrelax</tt>.\n\n\n',653,2),('allocchain','COMMAND','N/A','md','Allocate replicas for the chain-of-state relaxation methods (<tt>nebrelax</tt> \nand <tt>stringrelax</tt>) to find the minimum energy path between two states.\n\n<p>\nAlso see <tt>chainlength</tt>, <tt>nebrelax</tt>, <tt>stringrelax</tt>.\n',654,2),('interpCN','COMMAND','N/A','md','Usage: <tt>input = <i>s</i>  interpCN</tt>\n\n<p>\nMake the current configuration <tt>SR</tt> a linear interpolation between\n<tt>SR1</tt> and <tt>SR2</tt>.  <tt>SR[i] = (1-<i>s</i>)*SR1[i] + s*SR2[i]</tt>.\nThe center of mass difference between <tt>SR1</tt> and <tt>SR2</tt> is removed\nfrom <tt>SR</tt>.\n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>setconfig2</tt>, <tt>constrainedrelax</tt>.\n\n',655,2),('copyRchaintoCN','COMMAND','N/A','md','Usage: <tt>input = <i>j</i>  copyRchaintoCN</tt>\n\n<p>\nCopy the scaled coordinates of its constrained atoms (specified by <tt>constrainedatoms</tt>) \nfrom replica <tt><i>j</i></tt> (<tt>Rc0[<i>j</i>]</tt>) to <tt>SR</tt>.\n\n',656,2),('copyCNtoRchain','COMMAND','N/A','md','Usage: <tt>input = <i>j</i>  copyCNtoRchain</tt>\n\n<p>\nCopy the scaled coordinates of its constrained atoms (specified by <tt>constrainedatoms</tt>) \nfrom <tt>SR</tt> to replica <tt><i>j</i></tt> (<tt>Rc0[<i>j</i>]</tt>).\n\n',657,2),('moveRchain','COMMAND','N/A','md','Usage: <tt>input = [ <i>j_des j_src</i> ]  moveRchain</tt>\n\n<p>\nCopy atomic positions in replica <tt><i>j_src</i></tt> to replica <tt><i>j_des</i></tt>\nin array <tt>Rc</tt>.\n\n<p>\nAlso see <tt>initRchain</tt>, <tt>copyCNtoRchain</tt>.\n',658,2),('Fold_into_Unitcell','COMMAND','N/A','md','Same as <tt>maptoprimarycell</tt>.\n',659,2),('allocUMBorder','COMMAND','N/A','md','Umbrella Sampling utility\n\n<p>\nFor details, ask Seunghwa Ryu.\n',660,6),('assignUMBslipvec','COMMAND','N/A','md','Umbrella Sampling utility\n\n<p>\nFor details, ask Seunghwa Ryu.\n',661,6),('calcrystalorder','COMMAND','N/A','md','Compute the crystalline order parameter.\n\n<p>\nFor details, ask Seunghw Ryu.\n\n<p>\nAlso see <tt>calqlml</tt>.\n\n',662,6),('calqlwl','COMMAND','N/A','md','Compute the crystalline order parameter using GSL functions.\n\n<p>\nFor details, ask Seunghw Ryu.\n\n<p>\nAlso see <tt>calcrystalorder</tt>.\n',663,6),('allocqlm','COMMAND','N/A','md','Allocate the qlm array and other arrays needed for <tt>calqlwl</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n\n<p>\nAlso see <tt>allocQLM</tt>.\n\n',664,6),('caldislocationorder','COMMAND','N/A','md','Calculate the order parameter for Umbrella Sampling of dislocation nucleation.\nNot a general purpose utility.\n\n<p>\nReference: Proc. Natl. Acad. Sci. <a href=\"http://www.stanford.edu/~caiwei/papers.html#59\">\n108, 5174 (2011)</a>, J. Mater. Res. <a href=\"http://www.stanford.edu/~caiwei/papers.html#63\">\n26, 2335 (2011)</a>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n\n',665,6),('allocQLM','COMMAND','N/A','md','Allocate the QLM array and other arrays needed for <tt>calcrystalorder</tt>.\n\n<p>\nFor details, ask Seunghwa Ryu.\n\n<p>\nAlso see <tt>allocqlm</tt>.\n',666,6),('assign_Lam','COMMAND','N/A','md','Allocate and assign the Lam_array for Forward-Flux Sampling (FFS) simulations.\n\n<p>\nFor details, ask Seunghwa Ryu.\n',667,6),('Ewald_init','COMMAND','N/A','md','Initialize parameters in the Ewald method.\n\n<p>\nFor details, ask Hark Lee.\n\n<p>\nAlso see <tt>Ewald_Alpha</tt>, <tt>Ewald_option_Alpha</tt>, <tt>Ewald_precision</tt>.\n\n',668,7),('CE','COMMAND','N/A','md','Calculates the electrostatic potential energy and forces using the classical Ewald (CE) method.\n\n<p>\nAlso see <tt>Ewald_CE_or_PME</tt>.\n',669,7),('CE_clear','COMMAND','N/A','md','Free variables used in the classical Ewald (CE) calculation.\n\n<p>\nAlso see <tt>CE</tt>.\n',670,7),('PME','COMMAND','N/A','md','Calculates the electrostatic potential energy and forces using the particle-mesh Ewald (PME) method.\n\n<p>\nAlso see <tt>Ewald_CE_or_PME</tt>.\n\n',671,7),('PME_clear','COMMAND','N/A','md','Free variables used in the particle mesh Ewald (PME) calculation.\n\n<p>\nAlso see <tt>PME</tt>.\n\n',672,7),('makecrystal','COMMAND','N/A','md','Create a perfect crystal structure specified by <tt>crystalstructure</tt>,\n<tt>latticeconst</tt> and <tt>latticesize</tt>.\n\n<p>\nAlso see <tt>allocmultiple</tt>.\n',673,2),('makecn','COMMAND','N/A','md','Same as <tt>makecrystal</tt>.\n',674,2),('makecut','COMMAND','N/A','md','Fix all atoms that are on one side of a plane specified in crystal coordinate system,\ni.e. by Miller indices.\nThis command allows one to expose crystallograhic planes for visualization.\n\n<p>\nUsage: <tt>input = [ <i>ind nx ny nz x0 y0 z0</i> ] makecut</tt>\n\n<p>\n<tt><i>ind</i> = 1</tt> or <tt>-1</tt> allows one to easily flip the positive direction\nof the plane.\n<br>\n<tt><i>nx, ny, nz,</i></tt> specify the normal vector of the plane in crystal coordinate\nsystem (i.e. by Miller indices, such as 1 1 -1).  This means that before calling <tt>makecut</tt>\nthe array <tt>latticesize</tt> must be assigned to the values that were used to create the perfect \ncrystal in the first place.  The program needs that information to figure out the relationship\nbetween the crystal coordinate system and the lab coordinate system.\n<br>\n<tt><i>x0, y0, z0</i></tt> is a point on the plane.\n\n<p>\nAlso see <tt>removefixedatoms</tt>.\n\n\n',675,2),('makedipole','COMMAND','N/A','md','Create a dislocation dipole in a crystal.  The dislocation line and dipole\ndirection must be parallel to one of the repeat vectors of the simulation box.\n\n<p>\nUsage: <tt>input = [ <i>zind yind sbx sby sbz sx0 sy0 sy1 nu nimg_xmin nimg_xmax \n       nimg_ymin nimg_ymax tilt_box  limit_sz  sz_min sz_max store</i> ] \n       makedipole</tt>\n\n<p>\n<tt><i>zind</i></tt> = 1, 2 or 3 specifies the direction of the dislocation line\n(to be parallel to <tt><b>c</b><sub>1</sub></tt>, <tt><b>c</b><sub>2</sub></tt>, \nor <tt><b>c</b><sub>3</sub></tt>).\n<br>\n<tt><i>yind</i></tt> = 1, 2 or 3 specifies the direction of the dislocation\ndipole (also the direction that contains the cut plane of the dislocation).\n<br>\n<tt><i>sbx, sby, sbz</i></tt> specify the Burgers vector in <b>scaled</b> coordinates.\n<br>\n<tt><i>sx0, sy0</i></tt> specify the location of one dislocation in scaled coordinates,\n<tt><i>sy1</i></tt> specifies the location of the other dislocation.\n<br>\n<tt><i>nu</i></tt> is the Poisson\'s ratio of the crystal, needed in the expression \n for the displacement field of non-screw dislocations.  \n<tt>nu</tt> is usually set to be 0.3.  \n<br>\n<tt><i>nimg_xmin, nimg_xmax, nimg_ymin, nimg_ymax</i></tt> specify the number of \nperiodic images to be summed to obtain a periodic solution.  They are commonly set to be\n<tt>-10 10 -10 10</tt>.\n<br>\nIf <tt><i>tilt_box</i> = 1</tt>, then the box <b>H</b> is allowed to tilt to accommodate\nthe plastic strain produced by the dislocation dipole.  If <tt><i>tilt_box</i> = 0</tt>,\nthen the box <b>H</b> is fixed, and there will be an (usually huge) internal stress\ninside the simulation box.\n<br>\nIf <tt><i>limit_sz</i> = 1</tt>, then this operation is only performed for atoms \nwhose <tt><i>zind</i></tt>-th scaled coordinate lies between <tt>szmin</tt> and \n<tt>szmax</tt>.\n<br>\nIf <tt><i>store</i> = 1</tt>, the displacement field is not committed to the atoms\npositions, but is stored/accumulated in array <tt>storedr</tt>, until this command is\n(or other commands such as <tt>makedislocation</tt>) is called again with option \n<tt><i>store</i> = 0</tt>.\n\n<p>\nNote: atoms may need to be removed or inserted when executing this command.\nIf atoms need to be inserted, you will need to set <tt>allocmultiple</tt> to be\ngreater than 1 when calling <tt>makecrystal</tt> or <tt>readcn</tt> above.\n\n\n<p>\nAlso see <tt>makedislocation</tt>.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap5/sect5.1/mo-screw-dipole.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 5, Section 5.1.\n\n',676,2),('makedislcylinder','COMMAND','N/A','md','Outdated function.  Use <tt>makecylinder</tt> and <tt>makedislocation</tt> instead.\n',677,2),('makecylinder','COMMAND','N/A','md','Cut a cylinder out of the current configuration.\n\n<p>Usage: <tt> input = [ <i>zind yind sx0 sy0 rrem flag szmin szmax</i> ]  makecylinder</tt>\n\n<p>\n<tt><i>zind</i></tt> = 1, 2 or 3 specifies the direction of the cylinder axis (to be\nparallel to <tt><b>c</b><sub>1</sub></tt>, <tt><b>c</b><sub>2</sub></tt>, \nor <tt><b>c</b><sub>3</sub></tt>).\n<br>\n<tt><i>yind</i></tt> = 1, 2 or 3 specifies a direction perpendicular to the cylinder axis.\nThis input simplies the implementation of this function --- the code does not have to guess\nthe coordinate system.\n<br>\n<tt><i>sx0, sy0</i></tt> specifies the location of the cylinder axis in scaled coordinates.\n<br>\n<tt><i>rrem</i></tt> specifies the radius (in &Aring;) of the cylinder.\n<br>\nIf <tt><i>flag</i> = 0</tt>, then all atoms outside the cylinder is removed.\nIf <tt><i>flag</i> = 1</tt>, then all atoms outside the cylinder is fixed.\n<br>\nThe operation is only applied for atoms whose <tt><i>zind</i></tt>-th scaled coordinate \nlies between <tt>szmin</tt> and <tt>szmax</tt>.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap3/sect3.1/ta-screw.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 3, Section 3.1.\n',678,2),('makedislocation','COMMAND','N/A','md','Create an arbitrarily oriented straight dislocation line.\n\n<p>\nUsage: <tt>input = [ <i>enable a bx by bz lx ly lz nx ny nz x0 y0 z0 nu store</i> ] \n       makedislocation</tt>\n\n<p>\n<p>\n<tt><i>enable = 1</i></tt> activates this command.  <br>\n<tt><i>a</i></tt> is a length scale (in &Aring;) for the Burgers vector.<br>\n<tt><i>bx, by, bz</i></tt> is the Burgers vector (in real coordinates) in unit of \n  <tt><i>a</i></tt>.<br>\n<tt><i>lx, ly, lz</i></tt> is the dislocation line orientation (in real coordinates).<br>\n<tt><i>nx, ny, nz</i></tt> is the normal vector (in real coordinates) of the cut plane.<br>\n<tt><i>x0, y0, z0</i></tt> is a point on the cut-plane.<br>\n<tt><i>nu</i></tt> is the Poisson\'s ratio of the crystal, needed in the expression \n for the displacement field of non-screw dislocations. <tt><i>nu</i></tt> is usually set to be 0.3.\n<br>\nIf <tt><i>store</i> = 1</tt>, the displacement field is not committed to the atoms\npositions, but is stored/accumulated in array <tt>storedr</tt>, until this command is\n(or other commands such as <tt>makedipole</tt>) is called again with option \n<tt><i>store</i> = 0</tt>.\n\n<p>\nNote: vectors <b>b</b>, <b>l</b>, <b>n</b> are all expressed in the lab coordinate system,\nnot the crystal coordinate system.\n\n<p>\nNote: This cannot work if the simulation cell is subjected to periodic boundary\ncondition (PBC) in all three directions.  Use <tt>makedipole</tt> instead\nin such conditions.\n\n<p>\nAlso see <tt>makecylinder</tt>.\n\n<p>\nExample: <tt>MD++/scripts/CSD-book/chap3/sect3.1/ta-screw.script</tt>\n\n<p>\nFor details, see <a href=\"http://micro.stanford.edu/~caiwei/CSD-Book/\">Computer Simulations\nof Dislocations</a>, Chapter 3, Section 3.1.\n\n',679,2),('makedislpolygon','COMMAND','N/A','md','Introduce an arbitrarily shaped dislocation polygon (loop) into the crystal.\n\n<p>\nUsage: <tt>input = [ <i>enable  store nu  a bx by bz  n x_1 y_1 z_1 x_2 y_2 z_2 &hellip; x_n y_n z_n</i> ] \n       makedislellipse </tt>\n\n<p>\n<tt><i>enable = 1</i></tt> activates this command.  \n<br>\nIf <tt><i>store</i> = 1</tt>, the displacement field is not committed to the atoms\npositions, but is stored/accumulated in array <tt>storedr</tt>, until this command is\n(or other commands such as <tt>makedipole</tt>) is called again with option \n<tt><i>store</i> = 0</tt>.\n<br>\n<tt><i>nu</i></tt> is the Poisson\'s ratio of the crystal.\n<br>\n<tt><i>a</i></tt> is a length scale (in &Aring;) for the Burgers vector.\n<br>\n<tt><i>bx, by, bz</i></tt> is the Burgers vector (in real coordinates) in unit of \n  <tt><i>a</i></tt>.\n<br>\n<tt><i>n</i></tt> is the number of nodes of the polygon.\n<br>\n<tt><i>x1, y1, z1, x_2 y_2 z_2 &hellip; x_n y_n z_n</i></tt> are the polygon nodes in \n real coordinates (in &Aring;).\n\n\n<p>\nNote: all cut planes go through the first node <tt><i>x_1 y_1 z_1</i></tt>.\n\n<p>\nReferences: D. M. Barnett, <i>The displacement field of a triangular dislocation loop</i>,\n  Phil. Mag. A. (1985) vol.51 383--387;\n  D. M. Barnett and R. W. Balluffi, <i>The displacement field of a triangular\n  dislocation loop -- a correction with commentary</i>, Phil. Mag. Lett. (2007) vol.87 943--944;\n  A. Van Oosterom and J. Strackee, <i>The Solid angle of a plane trangle</i>,\n  IEEE transactions on biomedical engr. (1983) vol.bme-30 125--126.\n\n<p>\nFor more information, ask Keonwook Kang.\n\n<p>\nAlso see <tt>makedislellipse</tt>.\n\n',680,2),('makedislellipse','COMMAND','N/A','md','Introduce an elliptical shaped dislocation loop into the crystal.\n\n<p>\nUsage: <tt>input = [ <i>enable  Ra Rb a bx by bz lx ly lz nx ny nz x0 y0 z0 store</i> ] \n       makedislellipse </tt>\n\n<p>\n<tt><i>enable = 1</i></tt> activates this command.  <br>\n<tt><i>Ra, Rb</i></tt> defines the major and minor axes of the ellipse (in &Aring;). <br>\n<tt><i>a</i></tt> is a length scale (in &Aring;) for the Burgers vector.<br>\n<tt><i>bx, by, bz</i></tt> is the Burgers vector (in real coordinates) in unit of \n  <tt><i>a</i></tt>.<br>\n<tt><i>lx, ly, lz</i></tt> is the line orientation (in real coordinates)\n  of the major axis of the ellipse.<br>\n<tt><i>nx, ny, nz</i></tt> is the plane normal vector (in real coordinates)\n  of the ellipse.<br>\n<tt><i>x0, y0, z0</i></tt> is the center point (in real coordinates) of the ellipse.<br>\nIf <tt><i>store</i> = 1</tt>, the displacement field is not committed to the atoms\npositions, but is stored/accumulated in array <tt>storedr</tt>, until this command is\n(or other commands such as <tt>makedipole</tt>) is called again with option \n<tt><i>storedr</i> = 0</tt>.\n\n<p>\nNote: the displacement field used in this function is only an approximation.  It is simply\nproportional to the solid angle of the ellipse viewed from the field point.  The actual\ndisplacement field must contain a term that depends on the Poisson\'s ratio.\n\n<p>\nAlso see <tt>makedislpolygon</tt>.\n',681,2),('makegrainboundary','COMMAND','N/A','md','Make a grain boundary by rotating the current crystal in two different \norientations and put the two copies of the crystal together.  Can be\nused to create certain types of grain boundaries.  Not a general utility.\n\nUsage: <tt>input = [ <i>gb_type sx0 sy0 p q shift_x shift_y shift_z</i> ] makegrainboundary </tt>\n\n<p>\n<tt><i>gb_type</i></tt> has to be non-zero.  The two crystals are rotated from the\nparent crystal around the z-axis by angle &alpha; and -&alpha;, respectively, \nwhere arctan(&alpha;) = <tt><i>p</i></tt>/<tt><i>q</i></tt>.  <tt><i>sx0, sy0</i></tt>\nspecify the center of the rotation.  The plane sx = <tt><i>sx0</i></tt> is also\nthe boundary between the two crystals.  So the grain boundary thus created is\na pure tilt boundary.\n\n<p>\nWARNING: the values of <tt><i>shift_x, shift_y, shift_z</i></tt> are currently ignored?\n\n<p>\nFor details, ask Hark Lee.\n',682,2),('makegb','COMMAND','N/A','md','Same as <tt>makegrainboundary</tt>.\n',683,2),('makewave','COMMAND','N/A','md','Usage: <tt>input = [ <i>enable A dx dy dz skx sky skz </i> ] makewave </tt>\n\n<p>\nAssign a displacement field to the atoms in the form of a plane wave.\n<tt><i>A</i></tt> is the amplitude of the wave.\n<b>dr</b> = (<tt><i>dx,dy,dz</i></tt>) is a unit vector (it is automatically normalized\nat the beginning of this command).  <b>sk</b> = (<tt><i>skx,sky,skz</i></tt>) is the\nwave vector for scaled coordinates.  The displacement field in real coordinates is\n\n<p>\n <tt><b>du</b>[i] = A * <b>dr</b> * exp( <b>sk</b> &middot; <b>SR</b>[i] * 2&pi; ) </tt>\n\n<p>\nBe ware of the use of real and scaled coordinates in this expression.\nNote that the velocity is not assigned, so that the configuration corresponds to\na superposition of two plane waves travelling in opposite directions.\n\n<p>\nNote that this only works for a simple crystal structure (with one atom basis).\nThe displacement field of a complex lattice (with more than one atom basis)\nis not known a priori.\n',684,2),('cutbonds','COMMAND','N/A','md','Create a slit-like atomically sharp crack by removing the interaction between two\nsides of a cut-plane.  All atomic pairs that reside on two sides of the cut plane\nare registered in the <tt>nl_skip_pairs</tt> array, so that they will not appear \non each other\'s neighbor list, effectively removing their interactions.\n\n<p>\nUsage: <tt>input = [ <i> enable zind  yind  sx0 sy0 sy1 sz0 sz1 </i> ]</tt>\n\n<p>\nThe input parameters are similar to those of <tt>makedipole</tt>.\n\n<p>\nAlso see <tt>cutbonds_by_ellipse</tt>.\n',685,2),('cutbonds_by_ellipse','COMMAND','N/A','md','Create an elliptic atomically sharp crack by removing the interaction between two\nsides of a cut-plane.  All atomic pairs that reside on two sides of the cut plane\nare registered in the <tt>nl_skip_pairs</tt> array, so that they will not appear \non each other\'s neighbor list, effectively removing their interactions.\n\n<p>\nUsage: <tt>input = [ <i> enable zind  yind  sx0 sy0 sy1 sz0 sz1 </i> ]</tt>\n\n<p>\nAlso see <tt>cutbonds</tt>.\n',686,2),('scaleH','COMMAND','N/A','md','Usage: <tt>input = <i>s</i>  scaleH</tt>\n\n<p>\nMultiply the <tt><b>H</b></tt> matrix by scalar <tt>s</tt>.\n',687,2),('setH','COMMAND','N/A','md','Obsolete command.  Do no use.  Instead, assign a value to a given\ncomponent of <b>H</b> by, for example,\n\n<p>\n<tt> H_23 = <i>value</i> </tt>\n',688,2),('saveH','COMMAND','N/A','md','Copy <tt><b>H</b></tt> to <tt><b>H0</b></tt>.\n\n<p>\nAlso see <tt>restoreH</tt>.\n\n',689,2),('restoreH','COMMAND','N/A','md','Copy <tt><b>H0</b></tt> to <tt><b>H</b></tt>.\n\n<p>\nAlso see <tt>saveH</tt>.\n',690,2),('reorientH','COMMAND','N/A','md','Rotate the simulation box <tt><b>H</b> = [<b>c</b><sub>1</sub> |\n <b>c</b><sub>2</sub> | <b>c</b><sub>3</sub> ] </tt> so that\n <tt><b>H</b></tt> is an upper triangle matrix.  This means that\n <b>c</b><sub>1</sub> is parallel to the x-axis, and <b>c</b><sub>2</sub>\n is on the x-y plane.\n\n<p>\nThe scaled coordinates are not changed so that the real coordinates\nare rotated by this operation.\n\n  \n',691,2),('changeH_keepR','COMMAND','N/A','md','When <tt>input = [ i j &alpha; ]</tt> is set before calling this command, then\n\n<p>\nchange the supercell <b>H</b> while keeping the real\ncoordinates of the atoms <b>r</b><sub>k</sub> constant.  The scaled\ncoordinates <b>s</b><sub>k</sub> change because\n<b>r</b><sub>k</sub> = <b>H</b> &sdot; <b>s</b><sub>k</sub>.\n\nThe matrix <b>H</b> consists of three column vectors\n[<b>c</b><sub>1</sub> | <b>c</b><sub>2</sub> | <b>c</b><sub>3</sub> ], and will be changed by\n<b>c</b><sub>i</sub> = <b>c</b><sub>i</sub> + &alpha; <b>c</b><sub>j</sub>.\n\n<p>\nSame as <tt>redefinepbc</tt>.   Also see <tt>changeH_keepS</tt>.\n',692,2),('changeH_keepS','COMMAND','N/A','md','When <tt>input = [ i j &alpha; ]</tt> is set before calling this command, then\n\n<p>\nchange the supercell <b>H</b> while keeping the scaled\ncoordinates of the atoms <b>s</b><sub>k</sub> constant.  The real\ncoordinates <b>r</b><sub>k</sub> change because\n<b>r</b><sub>k</sub> = <b>H</b> &sdot; <b>s</b><sub>k</sub>.\n\nThe matrix <b>H</b> consists of three column vectors\n[<b>c</b><sub>1</sub> | <b>c</b><sub>2</sub> | <b>c</b><sub>3</sub> ], and will be changed by\n<b>c</b><sub>i</sub> = <b>c</b><sub>i</sub> + &alpha; <b>c</b><sub>j</sub>.\n\n<p>\nSame as <tt>shiftbox</tt>.   Also see <tt>changeH_keepR</tt>.\n',693,2),('shiftbox','COMMAND','N/A','md','Same as <tt>changeH_keepS</tt>.\n',694,2),('redefinepbc','COMMAND','N/A','md','Same as <tt>changeH_keepR</tt>.\n',695,2),('switchindex','COMMAND','N/A','md','Usage: <tt>input = [ <i>i_dir  j_dir</i> ] switchindex</tt> \n\n<p>\nSwitch the two indices for every atom\'s scaled coordinates. <tt><i>i_dir, j_dir</i></tt>\n= 1, 2, 3 for x, y, z.\n\nVector arrays <tt>SR, R, R0, VSR, VR</tt> and box matrix <tt>H</tt>\nare changed.\n\n<p>\nWARNING: There seems to be a bug.  The real coordinate should not change\nif both scaled coordinate and H matrix have changed.\n\n',696,2),('maptoprimarycell','COMMAND','N/A','md','Map every component of the scaled coordinate of all atoms <tt>SR</tt> to the \ndomain of [-0.5, 0.5) by subtracting the closest integer.\n\n<p>\nAlso see <tt>pbcshiftatom</tt>.\n',697,2),('RHtoS','COMMAND','N/A','md','For every atom <tt>k</tt>, update its scaled coordinates from its real coordinates.\n\n<p>\n <b>s</b><sub>k</sub> = inv(<b>H</b>) &sdot; <b>r</b><sub>k</sub>.\n\n<p>\nThis command must be called if you have changed the real coordinates <tt>R</tt> manually, \nbecause MD++ always computes the real coordinates from the scaled coordinate \ninside the potential function.\n\n<p>\nAlso see <tt>SHtoR</tt>.\n\n\n',698,2),('SHtoR','COMMAND','N/A','md','For every atom <tt>k</tt>, update its real coordinates from its scaled coordinates.\n\n<p>\n <b>r</b><sub>k</sub> = <b>H</b> &sdot; <b>s</b><sub>k</sub>.\n\n<p>\nUsually we don\'t need to call this command, because always computes the real coordinates \nfrom the scaled coordinate inside the potential function.\n\n<p>\nAlso see <tt>RHtoS</tt>.\n\n\n',699,2),('RtoR0','COMMAND','N/A','md','Make a copy of the <tt>R</tt> array to <tt>R0</tt>, i.e. for all <tt>i</tt>, do\n\n<p>\n<tt>R0[i] = R[i]</tt>\n\n<p>\nAlso see <tt>R0toR</tt>.\n',700,2),('R0toR','COMMAND','N/A','md','Copy the <tt>R0</tt> array back to <tt>R</tt>, i.e. for all <tt>i</tt>, do\n\n<p>\n<tt>R[i] = R0[i]</tt>\n\n<p>\nand then call <tt>RHtoS</tt>.\n\n<p>\nAlso see <tt>RtoR0</tt>.\n\n',701,2),('clearR0','COMMAND','N/A','md','Set vector <tt>R0[i]</tt> = (0, 0, 0) for all atoms <tt>i</tt>.  This has the\nconsequence that the neighbor list will certainly be constructed again the next\ntime command <tt>refreshnnlist</tt> is called.\n',702,2),('applystrain','COMMAND','N/A','md','Usage: <tt>input = [ <i> M11 M12 M13 M21 M22 M23 M31 M32 M33 <br>\n  &nbsp;  &nbsp;  &nbsp;  &nbsp; s11 s12 s13 s21 s22 s23 s31 s32 s33 <br>\n  &nbsp;  &nbsp;  &nbsp;  &nbsp; eps </i> ] </tt>\n\n<p>\nApply a strain to box matrix <tt>H</tt> while keeping the scaled coordinates\nof the atoms fixed.  The first nine components of the <tt>input</tt> array\nspecify the transformation matrix <tt><b>M</b></tt>, the next nine components specify\nthe strain matrix <tt><b>EPSILON</b></tt> in a rotated coordinate system.  The\nrow vectors of matrix <tt><b>M</b></tt> are normalized by MD++ if they were not\nalready normalized in the input.\n\n<p>\n<tt><b>H</b> += <b>M</b> * <b>EPSILON</b> * <b>M</b><sup>T</sup> * eps </tt>\n\n<p>\nThe box matrix prior to applying the strain is saved into <tt>H0</tt>.\n\n',703,2),('extendbox','COMMAND','N/A','md','Usage: <tt>input = [ <i>dir n</i> ] extendbox</tt>\n\n<p>\nExtend the current configuration along the <tt><i>dir</i></tt>-th \ndirection (1, 2, 3 for x, y, z) by replicating it <tt><i>n</i></tt> times.\n\n<p>\n<tt>allocmultiple = <i>n</i></tt> must be set when calling <tt>readcn</tt> or <tt>makecrystal</tt>\nif command <tt>extendbox</tt> will be called later.\n\n<p>\nAlso see <tt>cutslice</tt>.\n',704,2),('scaleVel','COMMAND','N/A','md','Usage: <tt> input = <i>vratio</i>  scaleVel</tt>\n\n<p>\nThe velocity <tt>VSR</tt> of all atoms whose <tt>fixed[i] != 0</tt>\nis multiplied by <tt><i>vratio</i></tt>.\n\n<p>\nA more complete implementation is <tt>multiplyvelocity</tt>.\n',705,2),('cutslice','COMMAND','N/A','md','Usage: <tt>input = [ <i>dir n</i> ] cutslice</tt>\n\n<p>\nCut an 1/<tt><i>n</i></tt> slice of the configuration along the <tt><i>dir</i></tt>-th\ndirection (1, 2, 3 for x, y, z).  This operation is the inverse of <tt>extendbox</tt>.\n\n<p>\nFor this to work well, the current configuration better be created by a previous call\nto command <tt>extendbox</tt>.\n\n\n',706,2),('splicecn','COMMAND','N/A','md','Usage: <tt>input = [ <i>dir</i> ] splicecn</tt>\n\n<p>\nPut the configuration stored in <tt>incnfile</tt> next to the configuration in memory\n(in array <tt>SR</tt>) along the direction <tt><i>dir</i></tt> (1, 2, 3 for x, y, z).\nThe <tt><i>dir</i></tt>-th column of the <tt>H</tt> matrix is incremented by the \namount specified in <tt>incnfile</tt>.\n\n<p>\nAlso see <tt>cutslice</tt>.\n',707,2),('cutpastecn','COMMAND','N/A','md','Usage: <tt>input = [ <i>dir  s0 s1 ds </i>] cutpastecn</tt>\n\n<p>\nReplace all atoms whose <tt><i>dir</i></tt>-th scaled coordinates falls within <tt>[<i>s0,s1</i>]</tt>\nto those given in the <tt>incnfile</tt>, and then displace these atoms by <tt><i>ds</i></tt>\nin the <tt><i>dir</i></tt>-th direction.  (<tt><i>dir</i> = 1, 2, 3</tt> for x, y, z.)\n\n',708,2),('setconfig1','COMMAND','N/A','md','Copy the current configuration <tt>SR</tt> (scaled coordinate) to <tt>SR1</tt> for all atoms.\n\n<p>\nAlso see <tt>setconfig2</tt>, <tt>constrainatoms</tt>.\n',709,2),('setconfig2','COMMAND','N/A','md','Copy the current configuration <tt>SR</tt> (scaled coordinate) to <tt>SR2</tt> for all atoms.\n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>constrainatoms</tt>.\n',710,2),('copytoconfig1','COMMAND','N/A','md','Usage: <tt>input = <i>i</i> copytoconfig1</tt>\n\nCopy the current configuration <tt>SR</tt> (scaled coordinate) to <tt>SR1</tt> only for atom \n<tt><i>i</i></tt>.\n\n<p>\nAlso see <tt>setconfig1</tt>.\n\n',711,2),('copytoconfig2','COMMAND','N/A','md','Usage: <tt>input = <i>i</i> copytoconfig2</tt>\n\nCopy the current configuration <tt>SR</tt> (scaled coordinate) to <tt>SR2</tt> only for atom \n<tt><i>i</i></tt>.\n\n<p>\nAlso see <tt>setconfig2</tt>.\n\n',712,2),('switchconfig','COMMAND','N/A','md','Change the scaled coordinates <tt>SR[i]</tt> of all atoms <tt>i</tt> to\n\n<p>\nSR[i] - SR1[i] + SR2[i]\n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>setconfig2</tt>, <tt>runMDSWITCH</tt>, <tt>nebrelax</tt>.\n',713,2),('replacefreeatom','COMMAND','N/A','md','Replace the scaled coordinates of atoms whose <tt>fixed[i] == 0</tt> by those\ngiven in the .cn file <tt>incnfile</tt>.  The scaled coordinates of other atoms\nas well as the <tt>H</tt> matrix are not changed.  At the end of <tt>replacefreeatom</tt>\nthe real coordinates are updated by a call to <tt>SHtoR</tt>.\n\n<p>\nAlso see <tt>readcn</tt>.\n',714,2),('relabelatom','COMMAND','N/A','md','Usage: <tt>input = [ <i>n0 n1</i> ]  relabelatom </tt>\n\n<p>\nSwitch the scaled coordinates (<tt>SR</tt>) between atom <tt><i>n0</i></tt> and <tt><i>n1</i></tt>.\n\n<p>\nNote that other properties, such as velocity, force, etc. are not switched by this command.\n',715,2),('moveatom','COMMAND','N/A','md','Usage: <tt>input = [ <i>n dx dy dz  i_1  i_2  &hellip; i_n</i> ] moveatom</tt>\n\n<p>\nMove real coordinates of all atoms whose indices are given in\n<tt><i>i_1, i_2, &hellip; i_n</i></tt> by <tt><i>dx, dy, dz</i></tt> (in &Aring;).\n\n<p>\nAlso see <tt>movegroup</tt>.\n\n',716,2),('movegroup','COMMAND','N/A','md','Usage: <tt>input = [ <i>ng dx dy dz  gID_1  gID_2  &hellip; gID_ng</i> ] movegroup</tt>\n\n<p>\nMove real coordinates of all atoms belonging to groups with ID <tt><i>gID_1, gID_2, &hellip; gID_ng</i></tt>\nby <tt><i>dx, dy, dz</i></tt> (in &Aring;).\n\n<p>\nAlso see <tt>setfixedatomsgroup</tt>, <tt>moveatom</tt>.\n\n',717,2),('setgroupcomvel','COMMAND','N/A','md','Usage: <tt>input = [ <i>ng vx vy vz  gID_1  gID_2  &hellip; gID_ng</i> ] setgroupcomvel</tt>\n\n<p>\nSet the center of mass velocity (times <tt>timestep</tt>)\nof all groups with ID <tt><i>gID_1, gID_2, &hellip; gID_ng</i></tt>\nto <tt><i>vx, vy, vz</i></tt> (in &Aring;).\n\n<p>\nAlso see <tt>P_com</tt>.\n\n',718,2),('printatoms_in_sphere','COMMAND','N/A','md','Usage: <tt>input = [ <i>x0 y0 z0 r</i> ] printatoms_in_sphere</tt>\n\n<p>\nPrint the indices of all atoms whose real coordinates fall within a sphere\ncentered at <tt><i>x0 y0 z0</i></tt> with radius <tt><i>r</i></tt>.  These\natoms can then be fixed by <tt>fixatoms_by_ID</tt>.\n\n',719,2),('pbcshiftatom','COMMAND','N/A','md','Usage: <tt>input = [ <i>dsx dsy dsz</i> ] pbcshiftatom</tt>\n\n<p>\nAdd <tt>dsx, dsy, dsz</tt> to the scaled coordinates of all atoms and then\nmap the scaled coordinates to the domain [-0.5, 0.5).\n',720,2),('maketorquehandle','COMMAND','N/A','md','Utility function pertaining to torsional Periodic Boundary Condition (tPBC).\n\n<p>\nAlso see <tt>torsionsim</tt>, <tt>torquespec</tt>.\n',721,2),('addtorque','COMMAND','N/A','md','Utility function pertaining to torsional Periodic Boundary Condition (tPBC).\n\n<p>\nAlso see <tt>torsionsim</tt>, <tt>torquespec</tt>.\n',722,2),('copytorqueatoms','COMMAND','N/A','md','Utility function pertaining to torsional Periodic Boundary Condition (tPBC).\n\n<p>\nAlso see <tt>torsionsim</tt>, <tt>torquespec</tt>.\n',723,2),('makebendhandle','COMMAND','N/A','md','Utility function pertaining to bending Periodic Boundary Condition (bPBC).\n\n<p>\nAlso see <tt>bendsim</tt>, <tt>bendspec</tt>.\n',724,2),('addbend','COMMAND','N/A','md','Utility function pertaining to bending Periodic Boundary Condition (bPBC).\n\n<p>\nAlso see <tt>bendsim</tt>, <tt>bendspec</tt>.\n',725,2),('copybendatoms','COMMAND','N/A','md','Utility function pertaining to bending Periodic Boundary Condition (bPBC).\n\n<p>\nAlso see <tt>bendsim</tt>, <tt>bendspec</tt>.\n',726,2),('writeimagefile','COMMAND','N/A','md','Empty function.  Do not use.\n',727,2),('readimagefile','COMMAND','N/A','md','Empty function.  Do not use.\n',728,2),('fixatoms_by_ID','COMMAND','N/A','md','When <tt>input = [ n i<sub>1</sub> &hellip; i<sub>n</sub> ]</tt> is set before\ncalling this command, then\n\n<p>\nmark all atoms <i>i</i> = <tt>i<sub>1</sub>, &hellip; , i<sub>n</sub>$ \nwith <tt>fixed[i] = 1</tt>.\n\n',729,2),('fixatoms_by_position','COMMAND','N/A','md','Fix all atoms whose position falls within a specified domain.\n\n<p>\nUsage: <tt>input = [ <i>enable  sx_min sx_max sy_min sy_max sz_min sz_max</i> ]</tt>\n<br>\nIf <tt><i>enable</i></tt> = 1, then all atoms <tt>i</tt> whose scaled coordinates fall\nwithin a rectangular region, i.e. \n<tt>sx_min <= SR[i].x < sx_max</tt>, \n<tt>sy_min <= SR[i].y < sy_max</tt>, \n<tt>sz_min <= SR[i].z < sz_max</tt>, will be fixed (i.e. <tt>fixed[i] = 1</tt>).\n\n<p>\nIf, however, <tt><i>enable</i></tt> = 2, then all atoms whose real coordiantes fall \nwithin a cylindrical (tube) region will be fixed.  In this case, the <tt>input</tt> array \nwill be interpreted differently.<br>\nUsage: <tt>input = [ <i>enable  ind  x0 y0 z0 r_min r_max h_min h_max </i> ]</tt>\n<br>\n<tt><i>ind</i></tt> = 1, 2, or 3 specifies whether the cylinder is aligned along the x, y, or z\naxis.  <tt><i>x0, y0, z0</i></tt> is a point (in real coordinates) on the center axis of the cylinder.  \n<tt><i>r_min, r_max</i></tt> is the inner and outer radii of the cylindrical tube,\n<tt><i>h_min, h_max</i></tt> specifies the length of the cylinder.\n\n<p>\nAlso see <tt>fixatoms_by_pos_topol</tt>.\n\n',730,2),('fixatoms_by_group','COMMAND','N/A','md','Usage: <tt>input = [ <i>ng  group_1 group_2 &hellip; group_ng</i> ]  fixatoms_by_group<tt>\n\n<p>\nIf <tt><i>ng</i></tt> > 0, then all atoms <tt>i</tt> whose <tt>group[i]</tt> value matches any of \nthe <tt><i>group_1 group_2 &hellip; group_ng</i> </tt> will have <tt>fixed[i] = 1</tt> set.\n\n<p>\nAlso see <tt>setfixedatomsgroup</tt>.\n',731,2),('RtoR0_by_group','COMMAND','N/A','md','Usage: <tt>input = [ <i>ng  gID_1  gID_2  &hellip; gID_ng</i> ] RtoR0_by_group</tt>\n\n<p>\nMake a copy of the <tt>R</tt> array to <tt>R0</tt> for all atoms whose\ngroup id (<tt>group[i]</tt>) matches one of those specified by <tt>input</tt>.\n\n<p>\nAlso see <tt>RtoR0</tt>.\n\n',732,2),('R0toR_by_group','COMMAND','N/A','md','Usage: <tt>input = [ <i>ng  gID_1  gID_2  &hellip; gID_ng</i> ] R0toR_by_group</tt>\n\n<p>\nCopy <tt>R0</tt> array back to <tt>R</tt> for all atoms whose\ngroup id (<tt>group[i]</tt>) matches one of those specified by <tt>input</tt>.\n\n<p>\nAlso see <tt>R0toR</tt>.\n\n\n',733,2),('fixatoms_by_species','COMMAND','N/A','md','Usage: <tt>input = [ <i>ns  species_1 species_2 &hellip; species_ns</i> ]  fixatoms_by_species<tt>\n\n<p>\nIf <tt><i>ns</i></tt> > 0, then all atoms <tt>i</tt> whose <tt>species[i]</tt> value matches any of \nthe <tt><i>species_1 species_2 &hellip; species_ns</i> </tt> will have <tt>fixed[i] = 1</tt> set.\n\n<p>\nAlso see <tt>setfixedatomsspecies</tt>.\n',734,2),('fixatoms_by_pos_topol','COMMAND','N/A','md','Fix all atoms whose position falls within a specified domain and whose <tt>TOPOL[i]</tt> value\nfalls within a range.\n\n<p>\nUsage: <tt>input = [ <i>enable  sx_min sx_max sy_min sy_max sz_min sz_max t_min t_max</i> ]</tt>\n<br>\nIf <tt><i>enable</i></tt> = 1, then all atoms <tt>i</tt> whose scaled coordinates fall\nwithin a rectangular region, i.e. \n<tt>sx_min <= SR[i].x < sx_max</tt>, \n<tt>sy_min <= SR[i].y < sy_max</tt>, \n<tt>sz_min <= SR[i].z < sz_max</tt>, and whose central symmetry parameter falls within a range\n<tt>t_min  <= TOPOL[i] < t_max</tt>, will be fixed (i.e. <tt>fixed[i] = 1</tt>).\n\n<p>\nAlso see <tt>fixatoms_by_position</tt>.\n',735,2),('fixallatoms','COMMAND','N/A','md','Mark all atoms with <tt>fixed[i] = 1</tt>, for <i>i</i> = 0, &hellip; <tt>NP-1</tt>.\n',736,2),('freeallatoms','COMMAND','N/A','md','Mark all atoms with <tt>fixed[i] = 0</tt>, for <i>i</i> = 0, &hellip; <tt>NP-1</tt>.\n',737,2),('reversefixedatoms','COMMAND','N/A','md','For all atoms <tt>i = 0, &hellip;, NP</tt>, set <tt>species[i]</tt> to 1 if it was 0, \nset <tt>species[i]</tt> to 0 if it was 1.\n\n<p>\nAlso see <tt>setfixedatomsspecies</tt>.\n',738,2),('constrain_fixedatoms','COMMAND','N/A','md','Set <tt>constrainedatoms</tt> array to include all fixed atoms.  This is usually used as\n<br>\n<tt>&nbsp; fixatoms_by_position  constrain_fixedatoms  freeallatoms</tt>\n\n<p>\nAlso see <tt>fixatoms_by_pos_topol</tt>, <tt>fixatoms_by_ID</tt>.\n',739,2),('fix_constrainedatoms','COMMAND','N/A','md','Set all atoms specified in the <tt>constrainatoms<tt> array to have be fixed\n(i.e. <tt>fixed[i] = 1</tt>).\n\n<p>\nThis is the inverse of the command <tt>constrain_fixedatoms</tt>.  This command\nis useful to visualize which atoms are included in the <tt>constrainatoms</tt>\nbecause fixed atoms are usually plotted in yellow.\n\n<p>\nAlso see <tt>fixatomcolor</tt>.\n',740,2),('fix_imageatoms','COMMAND','N/A','md','All atoms <tt>i</tt> whose <tt>image[i]</tt> value is >= 0 will have <tt>fixed[i]</tt> set to 1.\n\n<p>\nAlso see <tt>fixatoms_by_group</tt>.\n',741,2),('setfixedatomsspecies','COMMAND','N/A','md','Usage: <tt>input = <i>id</i> setfixedatomsspecies</tt>\n\n<p>\nSet <tt>species[i] = <i>id</i></tt> for all atoms <tt>i</tt> whose <tt>fixed[i] == 1</tt>.\n\n<p>\nAlso see <tt>fixatoms_by_pos_topol</tt>, <tt>fixatoms_by_ID</tt>, <tt>fixatoms_by_species</tt>.\n',742,2),('setfixedatomsgroup','COMMAND','N/A','md','Usage: <tt>input = <i>id</i> setfixedatomsgroup</tt>\n\n<p>\nSet <tt>group[i] = <i>id</i></tt> for all atoms <tt>i</tt> whose <tt>fixed[i] == 1</tt>.\n\n<p>\nAlso see <tt>fixatoms_by_pos_topol</tt>, <tt>fixatoms_by_ID</tt>, <tt>fixatoms_by_group</tt>.\n',743,2),('reversespecies','COMMAND','N/A','md','For all atoms <tt>i = 0, &hellip;, NP</tt>, set <tt>fixed[i]</tt> to 1 if it was 0, \nset <tt>fixed[i]</tt> to 0 if it was 1.\n',744,2),('movefixedatoms','COMMAND','N/A','md','Usage: <tt>input = [ <i>dsx dsy dsz</i> ] movefixedatoms </tt>\n\n<p>\nAdd <tt><i>dsx, dsy, dsz</i></tt> to the scaled coordinates <tt>SR[i]</tt> of\nall atoms <tt>i</tt> whose <tt>fixed[i] == 1</tt>.\n\n<p>\nAlso see <tt>fixatoms_by_pos_topol</tt>, <tt>fixatoms_by_ID</tt>, <tt>removefixedatoms</tt>.\n\n',745,2),('removefixedatoms','COMMAND','N/A','md','Remove all atoms <tt>i</tt> whose <tt>fixed[i] == 1</tt>.\n\n<p>\nAlso see <tt>markremovefixedatoms</tt>.\n',746,2),('markremovefixedatoms','COMMAND','N/A','md','Mark all atoms <tt>i</tt> whose <tt>fixed[i] == 1</tt> as removed, i.e. set <tt>fixed[i] = -1</tt>.\nAn atom <tt>i</tt> with <tt>fixed[i] == -1</tt> will be ignored in potential function / force evaluations.\nSo they are effectively removed, but can be quickly restored without changing the indices of other\natoms.\n\n<p>\nAlso see <tt>removefixedatoms</tt>.\n',747,2),('removeellipsoid','COMMAND','N/A','md','Usage: <tt>input = [ <i>enable x0 y0 z0 a b c</i> ] removeellipsoid</tt>\n\n<p>\nIf <tt><i>enable</i> = 1</tt> then this command is activated.\n<tt><i>x0 y0 z0</i></tt> specify the center of the ellipsoid (in real coordinates)\nand <tt><i>a b c</i></tt> specify the semi-axes of the ellipsoid (in real coordinates).\nAll atoms falling within the ellipsoid are removed.\n\n',748,2),('removerectbox','COMMAND','N/A','md','Usage: <tt>input = [ <i>ax ay az La bx by bz Lb cx cy cz Lc x0 y0 z0 plotonly outside</i> ] \n       removerectbox </tt>\n\n<p>\nThe regions to be removed are specified in the crystal coordinate system (so coordinate\ntransformation is involved).  Sorry this one is too complicated to explain.  Please read\nthe source code (<tt>md.cpp</tt>) or find an example that uses this command.\n\n<p>\nThis function is useful for creating a prismatic dislocation loop by removing atoms.\n',749,2),('removeoverlapatoms','COMMAND','N/A','md','Usage: <tt>input = [ <i>rc</i> ] removeoverlapatoms</tt>\n\n<p>\nFor every pair of atoms that are closer to each other than <tt><i>rc</i></tt>\nremove one of them, until no two atoms are closer to each other than <tt><i>rc</i></tt>.\n',750,2),('find_com','COMMAND','N/A','md','Apply rigid-body rotation around the center of mass (COM) so that the current configuration\nbest matches that stored in <tt>SR1</tt>.\n\n<p>\nRequires <tt>input = 1</tt> or <tt>2</tt> or <tt>3</tt> to be set before calling this command,\nto specify whether rotation is around x or y or z axis.  Currently only rotation around z axis \nhas been implemented.\n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>translate_com</tt>.\n',751,2),('translate_com','COMMAND','N/A','md','Compute the the center of mass (COM) of the current configuration (stored in <tt>SR</tt>).\nThe result (although not accessible from the user) will be used in subsequent calls of functions\n<tt>translate_com</tt>, <tt>rotate_com</tt>.\n\n',752,2),('rotate_com','COMMAND','N/A','md','Apply rigid-body translation so that the center of mass (COM) of the current configuration\nmatches that stored in <tt>SR1</tt>.\n\n<p>\nAlso see <tt>setconfig1</tt>, <tt>rotate_com</tt>.\n',753,2),('clearFext','COMMAND','N/A','md','Reset the <tt>Fext</tt> vector array, <tt>Fext[i] = 0</tt> for all <tt>i</tt> from 0 to <tt>NP</tt>.\n\n<p>\nAlso see <tt>Fext</tt>, <tt>addFext_to_group</tt>.\n',754,2),('addFext_to_group','COMMAND','N/A','md','When <tt>input = [ <i>g_id</i> <i>fx</i> <i>fy</i> <i>fz</i> ]</tt> is set before \ncalling this command, then atoms with <tt>group[i] == <i>g_id</i></tt> will have\ntheir <tt>Fext[i]</tt> vector set to <tt>(<i>fx</i>, <i>fy</i>, <i>fz</i>).  \n\n<p>\nIf <tt>enable_Fext</tt> is set to 1, then <tt>Fext[i]</tt> will be added to the\nforce experienced by atom <tt>i</tt> for all atoms.\n',755,2),('writecn','COMMAND','N/A','md','Requires <tt>finalcnfile = </tt><i>file</i> to be set before calling\nthis command.  Write atomic positions of the current configuration to <i>file</i>.\n\n<p>\nIf <tt> write_all = 1</tt> is also set,\nthe atomic velocities and other information are written in <i>file</i> as well.\n\n<p>\nSee <a href=\"http://micro.stanford.edu/wiki/Output_File_Formats_in_MD++#Configuration_.cn_File\">wiki page</a> for more details.\n\n<p>\nAlso see <tt>zipfiles</tt>.\n',756,3),('writeavgcn','COMMAND','N/A','md','Write array <tt>SRA</tt> into file whose name is specified by <tt>finalcnfile</tt>.\n\n<p>\n<tt>SRA</tt> contains a running average of atomic configurations during MD simulation.\n\n<p>\nFor details, ask Keonwook Kang.\n',757,3),('readcn','COMMAND','N/A','md','When <tt>incnfile = <i>file</i></tt> is set before calling this command, then\n\n<p>\nread atomic positions, velocities (optional) and other information from \n<tt><i>file</i></tt> to the current configuration.\n\n<p>\nSee <a href=\"http://micro.stanford.edu/wiki/Output_File_Formats_in_MD++#Configuration_.cn_File\">wiki page</a> for more details.\n\n\n',758,3),('readcontinuecn','COMMAND','N/A','md','Read atomic configuration from the file speficied by <tt>continuecnfile</tt>.\n\n<p>\nAlso see <tt>savecontinuecnfreq</tt>, <tt>readcn</tt>.\n',759,3),('readPOSCAR','COMMAND','N/A','md','Read atomic position from <tt>incnfile</tt> written in POSCAR (VASP) format.\n',760,3),('readOUTCAR','COMMAND','N/A','md','Read atomic force from \n<a href=\"http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html\">VASP</a> OUTCAR file.\nThe file name has to be <tt>OUTCAR</tt> and must be in the current directory\n(specified by <tt>dirname</tt>).\n\n<p>\nAlso see <tt>readPOSCAR</tt>.\n\n',761,3),('readMDCASK','COMMAND','N/A','md','Read atomic position and <tt>EPOT_IND</tt> array\nfrom <tt>incnfile</tt> written in MDCASK format.\n\n<p>\nAlso see <tt>writeMDCASK</tt>.\n',762,3),('readMDCASKJAIME','COMMAND','N/A','md','Read atomic position from <tt>incnfile</tt> written in MDCASK format.\n',763,3),('readXYZ','COMMAND','N/A','md','Read atomic position from <tt>incnfile</tt> written in XYZ format.\n',764,3),('writeMDCASKXYZ','COMMAND','N/A','md','Write atomic position (in real coordinates) \ninto MDCASK format with file name specified\nby  <tt>finalcnfile</tt>.  \n\n<p>\nAlso see <tt>readMDCASK</tt>.\n\n',765,3),('readLAMMPS','COMMAND','N/A','md','Read atomic position and velocity from a file in LAMMPS format with file name specified\nby  <tt>incnfile</tt>.  \n\n<p>\nAlso see <tt>writeLAMMPS</tt>.\n\n',766,3),('readRchain','COMMAND','N/A','md','Read a chain of configurations <tt>Rc</tt> from file <tt>incnfile</tt>.\n\n<p>\nAlso see <tt>readrchainspec</tt>, <tt>initRchain</tt>, <tt>writeRchain</tt>.\n',767,3),('convertXDATCAR','COMMAND','N/A','md','Convert a series of atomic configurations stored in a single file\n(in XDATCAR format of <a href=\"http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html\">VASP</a>) \ninto a series of .cn files using <tt>writeintercn</tt>.\n',768,3),('openintercnfile','COMMAND','N/A','md','Open the first intermediate .cn file so that they can be written subsequently\neither by calling <tt>writeintercn</tt> or during MD simulation <tt>run</tt> \nif <tt>savecn = 1</tt>.\n\n<p>\nAlso see <tt>intercnfile</tt>\n\n',769,3),('openFFScnfile','COMMAND','N/A','md','Open the first intermediate cn file so that they can be written to during FFS simulations.\nSimilar to <tt>openintercnfile</tt>.\n\n<p>\nAlso see <tt>FFScnfile</tt>.\n',770,3),('writeintercn','COMMAND','N/A','md','Write the current atomic configuration in the intermediate .cn file whose\nname is specified by <tt>intercnfile</tt> and <tt>filecounter</tt>.  Usually\nthis is command is not called directly by the user.  Instead, it is called periodically\nin MD simulation <tt>run</tt> if <tt>savecn = 1</tt>.\n\n<p>\nAlso see <tt>openintercnfile</tt>.\n\n\n',771,3),('writeFFScn','COMMAND','N/A','md','Write the current configuration in FFS simulation into a file whose base name is specified by <tt>FFScnfile</tt>\nand increment the counter by 1.\n\nSimilar to <tt>writeintercn</tt>.\n\n<p>\nAlso see <tt>FFSfilecounter</tt>.\n\n',772,3),('setfilecounter','COMMAND','N/A','md','Usage: <tt>filecounter = <i>n</i>  setfilecounter</tt>\n\n<p>\nSet the counter in the file name of <tt>intercnfile</tt> to <tt><i>n</i></tt>.\n',773,3),('setFFSfilecounter','COMMAND','N/A','md','Usage: <tt>FFSfilecounter = <i>n</i>  setFFSfilecounter</tt>\n\n<p>\nSet the counter in the file name of <tt>FFScnfile</tt> to <tt><i>n</i></tt>.\n\n<p>\nAlso see <tt>openFFScnfile</tt>.\n\n',774,3),('openpropfile','COMMAND','N/A','md','Open the property file whose name is specified by <tt>outpropfile</tt> and\nin which thermal properties (such as EPOT, Tinst) are saved periodically during MD simulation. \n\n<p>\nAlso see <tt>savepropfreq</tt>, </tt>output_fmt</tt>.\n\n',775,3),('closepropfile','COMMAND','N/A','md','Close the property file in which thermal properties (such as EPOT, Tinst) have been\n saved periodically during MD simulation, to ensure the file on disk is up to date\n before exiting the program.\n\n<p>\nAlso see <tt>openpropfile</tt>.\n\n',776,3),('writePOSCAR','COMMAND','N/A','md','Write atomic position and velocity\ninto <a href=\"http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html\">VASP</a> POSCAR format \nwith file name specified by <tt>finalcnfile</tt>.  \n\n<p>\nAlso see <tt>readPOSCAR</tt>.\n\n',777,3),('writeMDCASK','COMMAND','N/A','md','Write atomic position (in scaled coordinates) \ninto MDCASK format with file name specified\nby  <tt>finalcnfile</tt>.  \n\n<p>\nAlso see <tt>readMDCASK</tt>.\n\n',778,3),('writePINYMD','COMMAND','N/A','md','Write atomic position (in real coordinates) and velocity \ninto PINYMD format with file name specified\nby  <tt>finalcnfile</tt>.  \n\n',779,3),('writeLAMMPS','COMMAND','N/A','md','Write atomic position (in real coordinates) and velocity \ninto LAMMPS format with file name specified\nby  <tt>finalcnfile</tt>.  \n\n<p>\nAlso see <tt>readLAMMPS</tt>.\n',780,3),('writeRchain','COMMAND','N/A','md','Save the vector array <tt>Rc[j][i]</tt> into file specified by <tt>finalcnfile</tt>.\n<tt>Rc</tt> contains the real coordinates of the atoms specified by <tt>constrainatoms</tt>.\n\n<p>\nNote that the file format created by <tt>writeRchain is different from that of the <tt>.cn</tt> file.\n\n<p>\nAlso see <tt>readRchain</tt>, <tt>chainlength</tt>.\n',781,3),('fortranrelax','COMMAND','N/A','md','Call an external program (compiled by Fortran) to relax the atomistic configuration.\n\n<p>\nAlso see <tt>fortranpath</tt>, <tt>fortranexe</tt>.\n',782,7),('atomeye','COMMAND','N/A','md','Call Atomeye to visualize atomic structure.\n\n<p>\n<a href=\"http://li.mit.edu/Archive/Graphics/A\">Atomeye</a>\n is an external visualization tool developed by Dr. Ju Li.\n\n<p>\nRequires variables <tt>atomeyepath</tt> and <tt>atomeyeexe</tt> to be set\nbefore calling this command.  \nMD++ saves the atomic configuration into file <tt>atomeye.cfg</tt>\nin the current directory before calling Atomeye.\n\n',783,8),('writeatomeyecfg','COMMAND','N/A','md','Write Atomeye .cfg file from the current atomic configuration. \nBefore calling this function, the filename must be specified in variable <tt>finalcnfile</tt>.\n\n\n<p>\nAlso see <tt>zipfiles</tt>.\n\n',784,3),('convertCNtoCFG','COMMAND','N/A','md','Usage: <tt>input = [ <i> istart iend</i> ] convertCNtoCFG </tt>\n\n<p>\nRead several files named <tt>inter####.cn</tt> from the current folder\n(specified by <tt>dirname</tt>) and write them into Atomeye cfg files\n<tt>inter####.cfg</tt>, where the index number goes from <tt><i>istart</i></tt>\nto <tt><i>iend</i></tt>.\n\n\n<p>\nThis functionality can be reproduced in Tcl by calling <tt>readcn</tt>\nand <tt>writeatomeyecfg</tt> in a <tt>for</tt> loop.\n',785,3),('writepovray','COMMAND','N/A','md','Write atomic position into <a href=\"http://www.povray.org/\">POVRAY</a>\nformat with file name specified by  <tt>finalcnfile</tt>.\n\n<p>\nBy default all atoms are exported, but a subset of atoms can be selected\nby the <tt>plot_color_windows</tt> and <tt>plot_limits</tt> variables.\n',786,3),('writeRASMOLXYZ','COMMAND','N/A','md','Write atomic position into RASMOL-XYZ format with file name specified\nby  <tt>finalcnfile</tt>.  Each ine of the file contains\n\n<p>\n<tt>element[0] R[i].x R[i].y R[i].z EPOT_IND[i] TOPOL[i]</tt>\n',787,3),('readRASMOLXYZ','COMMAND','N/A','md','Read atomic position from <tt>incnfile</tt> written in RASMOL-XYZ format.\n',788,3),('writeatomtv','COMMAND','N/A','md','Write atomic position into atomtv format with file name specified\nby  <tt>finalcnfile</tt>.  Each ine of the file contains\n\n<p>\n<tt>R[i].x R[i].y R[i].z EPOT_IND[i] TOPOL[i]</tt>\n\n<p>\nBy default all atoms are exported, but a subset of atoms can be selected\nby the <tt>plot_color_windows</tt> and <tt>plot_limits</tt> variables.\n',789,3),('writeENERGY','COMMAND','N/A','md','Write a single columned file containing the <tt>color_ind</tt> array\nfor all atoms.  The file name is specified by <tt>finalcnfile</tt>.\n\n<p>\nThe content of the <tt>color_ind</tt> array depends on the value of <tt>plot_color_axis</tt>.\nWhen <tt>plot_color_axis = 0</tt> or 1, <tt>color_ind</tt> is the same as the potential energy\ncontribution from each atom (<tt>EPOT_IND</tt>).  When <tt>plot_color_axis = 2</tt>, \n<tt>color_ind</tt> is the same as the central symmetry deviation parameter (<tt>TOPOL</tt>).\n\n\n\n',790,3),('writeFORCE','COMMAND','N/A','md','Write force <tt>F</tt> on all atoms into a text file with filename specified by <tt>finalcnfile</tt>.\n\n<p>\nEach line of the file contains <tt>i _F[i].x _F[i].y _F[i].z fixed[i]</tt>.\n\n<p>\nIf <tt>input = 1</tt> is set before calling this command, then only atoms with <tt>fixed[i] == 1</tt>\nhave their information written into the file.  In this case, \neach line of the file contains <tt>i _F0[i].x _F0[i].y _F0[i].z fixed[i]</tt>.\n\n',791,3),('writePOSITION','COMMAND','N/A','md','Write the real coordinates of atoms into a file whose name is specified by <tt>finalcnfile</tt>.\nEach line of the file has the format of:\n<p>\n<tt><i>i</i> R[<i>i</i>].x R[<i>i</i>].y R[<i>i</i>].z fixed[<i>i</i>]</tt>\n\n<p>\nIf <tt>input = 1</tt> is set before calling this command, only atoms whose <tt>fixed[<i>i</i>]</tt>\nvalue is nonzero are written.\n',792,3),('GnuPlotHistogram','COMMAND','N/A','md','Call <a href=\"http://www.gnuplot.info/\">gnuplot</a>\n to plot the histogram of atom energy\ni.e. <tt>EPOT_IND</tt> (by default).\n\n<p>\nIf <tt>plot_color_axis = 2</tt> then the histogram of\n<tt>TOPOL</tt> is plotted instead.  \n\nThe array <tt>TOPOL</tt> stores the computes the central symmetry \ndeviation (CSD) parameters for each atom\ncomputed by <tt>calcentralsymmetry</tt>.\n',793,3),('openwin','COMMAND','N/A','md','Open X-window to display current atom position in 3D.\n\n<p>\nClick and drag in the X-window to rotate.  Press F1 for help.\n\n<p>\nUsually used as \n<tt>openwin alloccolors rotate saverot eval plot</tt>\n',794,8),('plot','COMMAND','N/A','md','Plot atoms in the X-window in an interactive run.  This command can be called manually\nin the input file to visualize the current configuration.  It is also called periodically\nwithin <tt>run</tt> and <tt>relax</tt> according to <tt>plotfreq</tt>.\n\n<p>\nAlso see <tt>openwin</tt>, <tt>alloccolors</tt>.\n',795,8),('alloccolors','COMMAND','N/A','md','Allocate colors for the X-window display.\n\n<p>\nUse after <tt>openwin</tt> and before <tt>plot</tt>.\n\n<p>\nVariables <tt>atomcolor</tt>, <tt>backgroundcolor</tt>, <tt>bondcolor</tt>,\n<tt>color00</tt>, &hellip;, <tt>color10</tt> may be set before calling\nthis command.\n',796,8),('alloccolorsX','COMMAND','N/A','md','Allocate colors for the X-window display.  Use this only on computers where\n command <tt>alloccolors</tt> does not work.\n',797,8),('testcolor','COMMAND','N/A','md','(For debugging purposes.  Not for general use.)\n',798,8),('reversergb','COMMAND','N/A','md','On some computers, you may find that an atom that is supposed to be red appears blue, while an\natom that is supposed to be blue appears red.  These computers uses the opposite RGB convention\nto indicate colors than most others.  Use <tt>reversergb</tt> to fix this problem.\n\n<p>\nAlso see <tt>alloccolors</tt>.\n',799,8),('writeps','COMMAND','N/A','md','Export the current view in the X-window as a post script file named <tt>Yshot####.ps</tt>, \nwhere the number automatically increases by 1 when the function is called again.  Pressing\nthe F10 key in the X-window has the same effect.\n\n<p>\nAlso see <tt>openwin</tt>, <tt>plot</tt>.\n',800,8),('rotate','COMMAND','N/A','md','Rotate the viewing orientation and scale the size of the plot for the X-window as \nspecified in <tt>rotateangles</tt>.\n\n<p>\nAlso see <tt>saverot</tt>.\n',801,8),('saverot','COMMAND','N/A','md','Save the current viewing orientation and scaling parameter for the X-window as \nthe HOME value, which will be returned to when the HOME key is pressed in the X-window.\n\n<p>\nAlso see <tt>rotate</tt>.\n\n',802,8),('wintogglepause','COMMAND','N/A','md','When the X-window is open, toggle between the pause and continue state for the MD simulation \n(<tt>run</tt>).  The same effect is produced whe pressing \"p\" in the X-window.\n\n<p>\nAlso see <tt>openwin</tt>.\n',803,8),('SR','DOUBLE','N/A','md','A vector array containing the scaled coordinates of atoms (dimensionless).\n\n<p>\nThe real coordinates  <b>r</b><sub>k</sub> and scaled coordinats <b>s</b><sub>k</sub>\nof atom k is related to each other by\n <b>r</b><sub>k</sub> = <b>H</b> &sdot; <b>s</b><sub>k</sub>.\n\n<p>\nAlso see <tt>R</tt>, <tt>H</tt>, <tt>SHtoR</tt>, <tt>RHtoS</tt>, \n<tt>changeH_keepS</tt>, <tt>changeH_keepR</tt>.\n\n\n',804,6),('fixed','INT','N/A','md','An integer array specifying whether atom <tt>i</tt> is fixed (<tt>fixed[i] = 1</tt>)\nor is free (<tt>fixed[i] = 0</tt>).  The atom is considered to be removed (i.e. not\nincluded in the calculation of potential energy and forces) if <tt>fixed[i] = -1</tt>.\n\n<p>\nAlso see <tt>species</tt>, <tt>group</tt>, <tt>fixatoms_by_ID</tt>, <tt>fixatoms_by_position</tt>.\n',805,6),('R','DOUBLE','N/A','md','A vector array containing the real coordinates of atoms (in &Aring;).\n\n<p>\nThe real coordinates  <b>r</b><sub>k</sub> and scaled coordinats <b>s</b><sub>k</sub>\nof atom k is related to each other by\n <b>r</b><sub>k</sub> = <b>H</b> &sdot; <b>s</b><sub>k</sub>.\n\n<p>\nAlso see <tt>SR</tt>, <tt>H</tt>, <tt>SHtoR</tt>, <tt>RHtoS</tt>, \n<tt>changeH_keepS</tt>, <tt>changeH_keepR</tt>.\n\n\n',806,6),('R0','DOUBLE','N/A','md','A vector array to hold a copy of the <tt>R</tt> vector array \n(containing real coordinates of atoms) to assist configuration manipulations.\n',807,6),('F','DOUBLE','N/A','md','A vector array containing the forces on each atom (in eV/&Aring;).\n\n<p>\nAlso see <tt>EPOT_IND</tt>.\n\n\n',808,6),('EPOT_IND','DOUBLE','N/A','md','An array containing the contributions to the potential energy <tt>EPOT</tt>\nfrom each atom (in eV).\n\n<p>\nAlso see <tt>F</tt>.\n\n',809,6),('species','INT','0\n','md','An integer array specifying the chemical species of each atom.\n\n<p>\nAlso see <tt>group</tt>.\n',810,6),('VR','DOUBLE','N/A','md','A vector array containing the velocity multiplied by <tt>timestep</tt>\nof atoms in real coordinates (in &Aring;).\n\n<p>\nAlso see <tt>VSR</tt>, <tt>H</tt>.\n',811,6),('VSR','DOUBLE','N/A','md','A vector array containing the velocity multiplied by <tt>timestep</tt>\nof atoms in scaled coordinates (dimensionless).\n\n<p>\nAlso see <tt>VR</tt>, <tt>H</tt>.\n',812,6),('image','INT','N/A','md','Empty variable.  Do not use.\n',813,6),('TOPOL','DOUBLE','N/A','md','An array storing the geometric information of each atom, such as the central symmetry deviation (CSD)\nparameter.\n\n<p>\nAlso see <tt>plot_color_axis</tt>.\n',814,6),('group','INT','0\n','md','An integer array specifying the group ID of each atom.\n\n<p>\nAlso see <tt>species</tt>.\n',815,6),('F0','DOUBLE','N/A','md','A vector array to store the forces on atoms.  It is an intermediate variable when the potential\nis a linear combination of two existing potentials, as in adiabatic switching.\n\n<p>\nAlso see <tt>runMDSWITCH</tt>, <tt>runMCSWITCH</tt>, <tt>refpotential</tt>.\n',816,6),('Fext','DOUBLE','0\n','md','A vector array containing the external forces on each atom (in eV/&Aring;).\nThey will be added to the vector array <tt>F</tt> if <tt>enable_Fext = 1</tt>.\nThe <tt>Fext</tt> array can be set manually, but is more convenient to use\ncommand <tt>addFext_to_group</tt>.\n\n',817,6),('EPOT_RMV','DOUBLE','0\n','md','An array.  <tt>EPOT_RMV[i]</tt> is the change of the potential energy of the entire simulation cell\nif atom <tt>i</tt> were removed. For a pair potential, it is twice of <tt>EPOT_IND</tt>.\n\n<p>\nAlso see <tt>EPOT_IND</tt>.\n\n',818,6),('VIRIAL_IND','DOUBLE','0\n','md','A (3x3) matrix array containing the contributions to the <tt>VIRIAL</tt>\nmatrix from each atom (in eV).\n\n<p>\nAlso see <tt>EPOT_IND</tt>.\n\n\n',819,6),('TORQUE_IND','DOUBLE','0\n','md','An array storing the contribution from each atom to the Virial Torque of the simulation\ncell subjected to torsional Periodic Boundary Condition.\n\n<p>\nAlso see <tt>torquespec</tt>, <tt>EPOT_IND</tt>.\n',820,6),('BENDMOMENT_IND','DOUBLE','0\n','md','An array storing the contribution from each atom to the Virial Bending Moment of the simulation\ncell subjected to bending Periodic Boundary Condition.\n\n<p>\nAlso see <tt>bendspec</tt>, <tt>EPOT_IND</tt>.\n',821,6),('storedr','DOUBLE','N/A','md','For debugging purposes.\n\n<p>\nIn many configuration manipulation tools, such as <tt>makedipole</tt>, the\ndisplacement field of one dislocation is not immediately applied to the atomic positions.\nInstead, there is an option to accumulate the displacement fields\nin the vector array <tt>storedr</tt> when multipole dislocations are to be introduced.\nThe displacement field is applied to the atomic positions after the displacement field\nof the last dislocation has been included in the sum.\n\n',822,2),('myIX','INT','0\n','mdparallel','ID of this CPU in x direction.  Values range from <tt>0, &hellip;, nXdoms</tt>.\n',823,4),('myIY','INT','0\n','mdparallel','ID of this CPU in y direction.  Values range from <tt>0, &hellip;, nYdoms</tt>.\n\n',824,4),('myIZ','INT','0\n','mdparallel','ID of this CPU in z direction.  Values range from <tt>0, &hellip;, nZdoms</tt>.\n\n',825,4),('nXdoms','INT','1\n','mdparallel','Numer of divisions in x direction in spatial domain decomposition for parallel MD simulation\nor relaxation.\n\n<p>\nNote: parallel simulation not implemented except <tt>nebrelax_parallel</tt>\nand <tt>stringrelax_parallel</tt>, which do not require spatial domain decomposition.\n\n<p>\nAlso see <tt>nYdoms</tt>, <tt>nZdoms</tt>.\n',826,4),('nYdoms','INT','1\n','mdparallel','Numer of divisions in y direction in spatial domain decomposition for parallel MD simulation\nor relaxation.\n\n<p>\nNote: parallel simulation not implemented except <tt>nebrelax_parallel</tt>\nand <tt>stringrelax_parallel</tt>, which do not require spatial domain decomposition.\n\n<p>\nAlso see <tt>nXdoms</tt>, <tt>nZdoms</tt>.\n',827,4),('nZdoms','INT','1\n','mdparallel','Numer of divisions in z direction in spatial domain decomposition for parallel MD simulation\nor relaxation.\n\n<p>\nNote: parallel simulation not implemented except <tt>nebrelax_parallel</tt>\nand <tt>stringrelax_parallel</tt>, which do not require spatial domain decomposition.\n\n<p>\nAlso see <tt>nXdoms</tt>, <tt>nYdoms</tt>.\n',828,4),('myDomain','INT','0\n','mdparallel','The ID of current domain (i.e. CPU) in a parallel run.\n\n<p>\n<tt>myDomain == 0</tt> for the master domain.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with \n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n\n',829,4),('numDomains','INT','1\n','mdparallel','Total number of domains (i.e. CPUs) in a parallel run.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',830,4),('myXmin','DOUBLE','-10\n','mdparallel','Boundary in x axis (in scaled coordinates) for spatial domain decomposition.  Not fully implemented.\n',831,4),('myYmin','DOUBLE','-10\n','mdparallel','Boundary in y axis (in scaled coordinates) for spatial domain decomposition.  Not fully implemented.\n',832,4),('myZmin','DOUBLE','-10\n','mdparallel','Boundary in z axis (in scaled coordinates) for spatial domain decomposition.  Not fully implemented.\n',833,4),('myXmax','DOUBLE','10\n','mdparallel','Boundary in x axis (in scaled coordinates) for spatial domain decomposition.  Not fully implemented.\n',834,4),('myYmax','DOUBLE','10\n','mdparallel','Boundary in y axis (in scaled coordinates) for spatial domain decomposition.  Not fully implemented.\n',835,4),('myZmax','DOUBLE','10\n','mdparallel','Boundary in z axis (in scaled coordinates) for spatial domain decomposition.  Not fully implemented.\n',836,4),('Master_to_Slave','COMMAND','N/A','mdparallel','When <tt>command = <i>cmd</i></tt> is set before calling this command, then\n\n<p>\nCPU 0 (master) request other CPUs (slaves) to execute <tt><i>cmd</i></tt>,\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\nwhich can be any MD++ command or variable assignment.\n',837,4),('Broadcast_Atoms','COMMAND','N/A','mdparallel','CPU 0 (master) broadcast all atom positions to other CPUs (slaves).\n\n<p>\nNeeded before <tt>eval_parallel</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',838,4),('Slave_to_Master_Atoms','COMMAND','N/A','mdparallel','Slave CPUs send its atom position <tt>SR</tt> and velocity <tt>VSR</tt> (in scaled coordinates)\nto Master CPU (whose <tt>myDomain == 0</tt>).\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',839,4),('Slave_chdir','COMMAND','N/A','mdparallel','Slave CPUs change the directory to that specified by <tt>dirname</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',840,4),('Partition_Domains','COMMAND','N/A','mdparallel','Decide the boundary of spatial domain decomposition.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n\n',841,4),('Mark_Local_Atoms','COMMAND','N/A','mdparallel','Each CPU marks atoms <tt><i>i</i></tt> outside the domain boundary (by more than a skin distance)\nas <tt>fixed[<i>i</i>] = -1</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',842,4),('eval_parallel','COMMAND','N/A','mdparallel','CPU 0 (Master) calls <tt>eval</tt> with the help of all other CPUs (slaves).\n\n<p>\n<tt>Broadcast_Atoms</tt> must be called before calling this command.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',843,7),('run_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>run</tt> (MD simulation). (Not fully tested)\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',844,7),('alloc_all','COMMAND','N/A','mdparallel','Every processor (master and slave) allocate memory\nfor arrays such as <tt>SR</tt>, <tt>F</tt>, &hellip; according to the number\nof atoms <tt>NP</tt>.\n\n<p>\nNeeded before calling <tt>eval_parallel</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',845,7),('quit_all','COMMAND','N/A','mdparallel','All processes (master and slavev) call <tt>quit</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',846,7),('nebrelax_parallel','COMMAND','N/A','mdparallel','Running <tt>nebrelax</tt> in parallel mode.  Each replica occupies one CPU.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with \n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',847,7),('stringrelax_parallel','COMMAND','N/A','mdparallel','Running <tt>stringrelax</tt> in parallel mode.  Each replica occupies one CPU.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with \n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',848,7),('allocchain_parallel','COMMAND','N/A','mdparallel','Running <tt>allocchain</tt> in parallel mode. Each replica occupies one CPU. \nEffective only when MD++ is compiled for parallel runs, e.g. with <tt>SYS = mpicc</tt>\nor <tt>SYS = mpigpp</tt>. \n\n<p>\nAlso see <tt>nebrelax_parallel</tt>, <tt>stringrelax_parallel</tt>.\n\n',849,2),('initRchain_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>initRchain</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n<p>\nAlso see <tt>nebrelax_parallel</tt>, <tt>stringrelax_parallel</tt>.\n',850,2),('readRchain_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>readRchain</tt>.  If <tt>incnfile = <i>fname</i></tt>,\neach CPU writes the file named <tt><i>fname</i>.cpu00</tt>, <tt><i>fname</i>.cpu01</tt>,\n&hellip;, where the integer is the value of  <tt>myDomain</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',851,3),('writeRchain_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>writeRchain</tt>.  If <tt>finalcnfile = <i>fname</i></tt>,\neach CPU writes the file named <tt><i>fname</i>.cpu00</tt>, <tt><i>fname</i>.cpu01</tt>,\n&hellip;, where the integer is the value of  <tt>myDomain</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',852,3),('copyRchaintoCN_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>copyCNtoRchain</tt>, with the difference that the <tt>input</tt>\nvariable is no longer needed. Each CPU copy the scaled coordinates of its constrained atoms \n(specified by <tt>constrainedatoms</tt>) from <tt>Rc0</tt> to <tt>SR</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',853,2),('copyCNtoRchain_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>copyRchaintoCN</tt>, with the difference that the <tt>input</tt>\nvariable is no longer needed. Each CPU copy the scaled coordinates of its constrained atoms \n(specified by <tt>constrainedatoms</tt>) from <tt>SR</tt> to <tt>Rc0</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with\n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',854,2),('readcnfile_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>readcn</tt>.  If <tt>incnfile = <i>fname</i></tt>,\neach CPU reads the file named <tt><i>fname</i>.cpu00</tt>, <tt><i>fname</i>.cpu01</tt>,\n&hellip;, where the integer is the value of  <tt>myDomain</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with \n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',855,3),('writefinalcnfile_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>writecn</tt>.  If <tt>finalcnfile = <i>fname</i></tt>,\neach CPU writes the file named <tt><i>fname</i>.cpu00</tt>, <tt><i>fname</i>.cpu01</tt>,\n&hellip;, where the integer is the value of  <tt>myDomain</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with \n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n\n',856,3),('writeatomeyecfg_parallel','COMMAND','N/A','mdparallel','Parallel version of <tt>writeatomeyecfg</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs, e.g. with \n<tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',857,3),('domainID','INT','N/A','mdparallel','An array containing the information of which domain (i.e. CPU) does each atom belong to.\n\n<p>\nAlso see <tt>myDomain</tt>.\n',858,4),('rho','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',859,6),('rho0','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',860,6),('rho1','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',861,6),('rho2','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',862,6),('rho3','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',863,6),('frhop','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',864,6),('gamma','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',865,6),('dgamma1','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',866,6),('dgamma2','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',867,6),('dgamma3','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',868,6),('arho2b','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',869,6),('arho1','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',870,6),('arho2','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',871,6),('arho3','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',872,6),('arho3b','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',873,6),('t_ave','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',874,6),('tsq_ave','DOUBLE','N/A','meam-lammps','Internal array when computing the MEAM-LAMMPS potential.\n\n<p>For diagnostic purposes.\n',875,6),('meamfile','STRING','N/A','meam-lammps','Name of the file containing parameters for the MEAM-LAMMPS potential.\n\n<p>\nAlso see <tt>meafile</tt>.\n',876,3),('meafile','STRING','N/A','meam-lammps','Name of the file containing parameters for the MEAM-LAMMPS potential.\n\n<p>\nAlso see <tt>meamfile</tt>.\n',877,3),('rcut','DOUBLE','N/A','meam-lammps','Cut off radius of the MEAM-LAMMPS potential.\n',878,7),('readMEAM','COMMAND','N/A','meam-lammps','Read parameters for the MEAM-LAMMPS potential contained in the <tt>meamfile</tt> and <tt>meafile</tt>.\n',879,3),('printpairpot','COMMAND','N/A','meam-lammps','(For debugging purposes.  Not for general use.)\n',880,3),('Broadcast_MEAM_Param','COMMAND','N/A','meam-lammps','CPU 0 (master) broadcast MEAM-LAMMPS potential parameters to other CPUs (slaves).\n\n<p>\nNeeded before <tt>eval_parallel</tt>.\n\n<p>\nEffective only when MD++ is compiled for parallel runs,\ne.g. with <tt>SYS = mpicc</tt> or <tt>SYS = mpigpp</tt>.\n',881,4),('setoverwrite','COMMAND','N/A','organizer','By default, MD++ will abort if the directory specified by\n<tt>dirname</tt> already exists, to avoid overwriting previous\nsimulation data.  Use this command before assigning <tt>dirname</tt> if\nyou want to remove this protection and allow overwriting the data in\nthe existing directory.\n',882,5),('setnolog','COMMAND','N/A','organizer','This command tells MD++ not to open the A.log file in the directory\nspecified by <tt>dirname</tt>.  Instead, the output is directed to the screen.\n\n<p>\nUse this command before assigning variable <tt>dirname</tt>.\n',883,5),('quit','COMMAND','N/A','organizer','Quit MD++.  Print total CPU time.\n',884,5),('sleep','COMMAND','N/A','organizer','Put MD++ to sleep for the number of seconds specified in <tt>sleepseconds</tt>.\nThe X-window (if opened) remain responsive to mouse and keyboard.\nThis allows you to visually examine the final structure of your simulation \nbefore it exits.\n',885,5),('dirname','STRING','N/A','organizer','MD++ immediately opens a directory specified by this variable and\nenters (i.e. <tt>cd</tt> into) this directory.  This becomes the working\ndirectory for all future operations and the place for all output\nfiles.\nOutput to screen is redirected to the A.log file in this directory\nif <tt>setnolog</tt> is not set beforehand.\n',886,5),('sleepseconds','INT','600\n','organizer','Number of seconds used by command <tt>sleep</tt>.  \n',887,5),('intval','INT','N/A','organizer','(For debugging purposes.  Not for general use.)\n',888,5),('x','DOUBLE','N/A','organizer','(For debugging purposes.  Not for general use.)\n',889,5),('y','DOUBLE','N/A','organizer','(For debugging purposes.  Not for general use.)\n',890,5),('z','DOUBLE','N/A','organizer','(For debugging purposes.  Not for general use.)\n',891,5),('str','STRING','N/A','organizer','(For debugging purposes.  Not for general use.)\n',892,5),('printall','COMMAND','N/A','organizer','(For debugging purposes.  Not for general use.)\n',893,5),('openfile','COMMAND','N/A','organizer','(For debugging purposes.  Not for general use.)\n',894,5),('closefile','COMMAND','N/A','organizer','(For debugging purposes.  Not for general use.)\n',895,5),('rebofile','STRING','N/A','rebo','Name of the file containing parameters for the REBO potential.\n',896,3),('rcut','DOUBLE','N/A','rebo','Cut-off radius for the REBO potential.\n',897,6),('readREBO','COMMAND','N/A','rebo','Read parameters for the REBO potential contained in the <tt>rebofile</tt>.\n',898,3),('C12_ij','DOUBLE','0\n','rebolj','Parameter in the LJ potential between species i and j.\n\nThe actual parameters to set in MD++ are: <tt>C12_00</tt>, <tt>C12_01</tt>, &hellip;\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',899,6),('C6_ij','DOUBLE','0\n','rebolj','Parameter in the LJ potential between species i and j.\n\nThe actual parameters to set in MD++ are: <tt>C6_00</tt>, <tt>C6_01</tt>, &hellip;\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',900,6),('LJ_Rcut','DOUBLE','N/A','rebolj','Cut-off radius of the LJ potential.\n',901,6),('NUM_REBO_GROUPS','INT','N/A','rebolj','Number of groups of atoms that are treated separately in the REBOLJ potential.\n\n<p>\nAtoms within the same <tt>group</tt> interact with the REBO potential.  Atoms\nin different <tt>group</tt> interact with the LJ potential.  The atomic configuration\nneed to have the <tt>group</tt> array (in addition to the <tt>species</tt> array, if\nboth Carbon and Hydrogen are present) set up accordingly for this to work properly.\n\n',902,7),('substrate_Z','DOUBLE','N/A','rebolj','Parameter for an external potential mimicing the substrate.\n\n',903,7),('substrate_REP','DOUBLE','N/A','rebolj','Parameter for an external potential mimicing the substrate.\n\n',904,7),('substrate_ATR','DOUBLE','N/A','rebolj','Parameter for an external potential mimicing the substrate.\n\n',905,7),('initLJ','COMMAND','N/A','rebolj','Initialize the parameters in the LJ potential.\n\n',906,7),('ncpu','INT','N/A','scparser','(For debugging purposes.  Not for general use.)\n',907,5),('shmsize','INT','N/A','scparser','(For debugging purposes.  Not for general use.)\n',908,5),('abort','COMMAND','N/A','scparser','Abort the parser program, i.e. stop reading the input file.\n',909,5),('a','DOUBLE','N/A','scparser','(For debugging purposes.  Not for general use.)\n',910,5),('I','INT','N/A','scparser','(For debugging purposes.  Not for general use.)\n',911,5),('L','LONG','N/A','scparser','(For debugging purposes.  Not for general use.)\n',912,5),('s','STRING','N/A','scparser','(For debugging purposes.  Not for general use.)\n',913,5),('help','COMMAND','N/A','scparser','Print out a short message on the available commands and variables for this parser.\n',914,5),('printall','COMMAND','N/A','scparser','Print the values of all variables (<tt>a, I, L, s</tt>) \ndefined in this test parser program.\n',915,5),('quit','COMMAND','N/A','scparser','Exit the entire program.\n\n<p>\nIn the source code: <tt>exit(2);</tt>\n',916,5),('ALPHA_BKS','DOUBLE','N/A','silica-bksmod','Parameters in the SILICA-BKSMOD potential.\n\n<p>\nThe potential parameters are set by the <tt>initBKS</tt> command.\n',917,6),('initBKS','COMMAND','N/A','silica-bksmod','Initialize the parameters in the the SILICA-BKSMOD potential.\n',918,7),('sw3b_multiply','DOUBLE','1\n','sw','Ad hoc multiplication factor to the three-body term of the original Stillinger-Weber potential.\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#33\">Philosophical Magazine, 87, 2169, (2007)</a>.\n',919,6),('sw2b_multiply','DOUBLE','1\n','sw','Ad hoc multiplication factor to the two-body term of the original Stillinger-Weber potential.\n\n<p>\nFor details, see <a href=\"http://www.stanford.edu/~caiwei/papers.html#33\">Philosophical Magazine, 87, 2169, (2007)</a>.\n',920,6),('tote2','DOUBLE','0\n','sw','Two-body term contribution to the potential energy.\n\n<p>\n<tt>EPOT = tote2 + tote3</tt>.\n',921,6),('tote3','DOUBLE','0\n','sw','Three-body term contribution to the potential energy.\n\n<p>\n<tt>EPOT = tote2 + tote3</tt>.\n',922,6),('C12','DOUBLE','N/A','swlj','Parameter in the LJ potential.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',923,6),('C6','DOUBLE','N/A','swlj','Parameter in the LJ potential.\n\n<p>\n&Phi;(r) = <tt>C12</tt> / r<sup>12</sup> - <tt>C6</tt> / r<sup>6</sup>\n',924,6),('tipforce','DOUBLE','N/A','swlj','This is an output array of length 3.  It contains the total force felt by atoms \nin <tt>group = 0</tt> and <tt>group = 4</tt>.\n\n<p>\nWhen the simulation is set up such that an indentor consisting of\nthese two groups of atoms is pressing against a substrate (consisting\nof other groups of atoms), then <tt>tipforce</tt> measures the total\nforce on the indentor tip from the substrate.\n\n',925,6),('initLJ','COMMAND','N/A','swlj','Initialize the parameters in the LJ potential.\n\n',926,7);

--
-- Table structure for table `schema_info`
--

CREATE TABLE `schema_info` (
  `version` int(11) DEFAULT NULL
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

--
-- Dumping data for table `schema_info`
--

INSERT INTO `schema_info` VALUES (7);

--
-- Table structure for table `sessions`
--

CREATE TABLE `sessions` (
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  `session_id` varchar(255) NOT NULL,
  `data` text,
  `created_at` datetime DEFAULT NULL,
  `updated_at` datetime DEFAULT NULL,
  PRIMARY KEY (`id`),
  KEY `index_sessions_on_session_id` (`session_id`),
  KEY `index_sessions_on_updated_at` (`updated_at`)
) ENGINE=InnoDB AUTO_INCREMENT=545 DEFAULT CHARSET=latin1;

--
-- Dumping data for table `sessions`
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--
-- Table structure for table `users`
--

CREATE TABLE `users` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `login` varchar(255) DEFAULT NULL,
  `email` varchar(255) DEFAULT NULL,
  `name` varchar(255) DEFAULT NULL,
  `organization` varchar(255) DEFAULT NULL,
  `terms_and_conditions` tinyint(1) DEFAULT NULL,
  `research` text,
  `role` varchar(20) DEFAULT NULL,
  `activation_code` varchar(40) DEFAULT NULL,
  `activated_at` datetime DEFAULT NULL,
  `crypted_password` varchar(40) DEFAULT NULL,
  `salt` varchar(40) DEFAULT NULL,
  `created_at` datetime DEFAULT NULL,
  `updated_at` datetime DEFAULT NULL,
  `remember_token` varchar(255) DEFAULT NULL,
  `remember_token_expires_at` datetime DEFAULT NULL,
  `mailing_address` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`id`),
  KEY `index_users_on_role` (`role`)
) ENGINE=InnoDB AUTO_INCREMENT=480 DEFAULT CHARSET=latin1;

--
-- Dumping data for table `users`
--

INSERT INTO `users` VALUES (1,'caiwei@stanford.edu','caiwei@stanford.edu','Wei Cai','Stanford University',1,'Things','admin','ae3018ff7dafd6d19cba7c509da222c488c3116b','2007-11-09 03:58:17','3118b693382effc9792686e65b5e47cbd50045c1','7fdd0054ec88b9f58ace458081098feadf1f1f36','2007-11-08 19:58:17','2012-04-25 22:07:41',NULL,NULL,NULL),(2,'wcash@stanford.edu','wcash@stanford.edu','William Cash','Stanford Univeristy',1,'Dislocation Dynamics','admin',NULL,'2007-12-19 23:56:44','a601bb1382575f55c79d10345d2ee2b4b29276a0','760f191e65d06e25ebadd3ea624f78658ae1e8d5','2007-12-19 14:44:17','2012-04-30 16:05:03',NULL,NULL,NULL),(479,'wdcash@att.net','wdcash@att.net','Testing MD++ sign up','Test MD++',1,'testing testing testing MD++',NULL,'9910453a1a50e765c35932deaddf8984283072cc',NULL,'e97b9406abb75c01678ce5aefc482dd3e43c3a84','2c552b846516b7fde2b51147b54f715a96eb6181','2012-04-30 00:12:55','2012-04-30 00:12:55',NULL,NULL,'test 123 ');


