MD++ An Example Script File - Revision history

Caiwei at 20:52, 4 May 2012

2012-05-04T20:52:34Z

← Older revision		Revision as of 20:52, 4 May 2012
Line 88:		Line 88:
	The [[Output_File_Formats_in_MD%2B%2B#Configuration_.cn_File \| .cn file]] starts with the number of atoms, then followed by that number of lines, each line giving the scaled coordinates of one atom. If other options are set (e.g. <tt>writevelocity = 1</tt> or <tt>writeall = 1</tt>), it may also save other things, such as velocities, in each line.		The [[Output_File_Formats_in_MD%2B%2B#Configuration_.cn_File \| .cn file]] starts with the number of atoms, then followed by that number of lines, each line giving the scaled coordinates of one atom. If other options are set (e.g. <tt>writevelocity = 1</tt> or <tt>writeall = 1</tt>), it may also save other things, such as velocities, in each line.

	== Plotting ~~setup~~ ==		== Plotting set up ==

	This section if pretty standard, so we will be brief. The usual lines of code you can have in your .script file are:		This section if pretty standard, so we will be brief. The usual lines of code you can have in your .script file are:
Line 119:		Line 119:
	After the various variables for the CGR algorithm have been set in the first two lines, the <tt>relax</tt> calls the CG algorithm to relax the structure. The relaxed structure is saved into a configuration file (specified as <tt>relaxed.cn</tt> here).		After the various variables for the CGR algorithm have been set in the first two lines, the <tt>relax</tt> calls the CG algorithm to relax the structure. The relaxed structure is saved into a configuration file (specified as <tt>relaxed.cn</tt> here).

	== MD simulation ~~setup~~ ==		== MD simulation set up ==

	In this part of the code you define parameters such as ensemble type or integrator to be used in your subsequent MD simulation. Generic lines of code that might be useful are:		In this part of the code you define parameters such as ensemble type or integrator to be used in your subsequent MD simulation. Generic lines of code that might be useful are:

Wpkuykendall: /* Initialize atoms positions */

2012-04-24T00:26:47Z

Initialize atoms positions

← Older revision		Revision as of 00:26, 24 April 2012
Line 74:		Line 74:
	makecrystal writecn		makecrystal writecn

	<tt>crystalstructure = diamond-cubic</tt> specifies the crystal structure. In this example, it specifies diamond-cubic, which is the crystal structure for Silicon. <tt>latticeconst = 5.4309529817532409</tt> specifies the lattice constant (<math>a_0</math>) in Angstrom. The lines <tt>latticesize = ...</tt> specifies the size of the lattice you wish to create. The first three values <tt>1 0 0</tt> specify the orientation of the first simulation cell vector (in Miller indices notation), followed by the number of repeats (4) in that direction. The next three values <tt>0 1 0</tt> specify the orientation of the second simulation cell vector, followed by the number of repeats (4) in that ~~direction.in each line are an axis~~ direction. The next three values <tt>0 0 1</tt> specify the orientation of the third simulation cell vector, followed by the number of repeats (4) in that ~~direction.in each line are an axis~~ direction.		<tt>crystalstructure = diamond-cubic</tt> specifies the crystal structure. In this example, it specifies diamond-cubic, which is the crystal structure for Silicon. <tt>latticeconst = 5.4309529817532409</tt> specifies the lattice constant (<math>a_0</math>) in Angstrom. The lines <tt>latticesize = ...</tt> specifies the size of the lattice you wish to create. The first three values <tt>1 0 0</tt> specify the orientation of the first simulation cell vector (in Miller indices notation), followed by the number of repeats (4) in that direction. The next three values <tt>0 1 0</tt> specify the orientation of the second simulation cell vector, followed by the number of repeats (4) in that direction. The next three values <tt>0 0 1</tt> specify the orientation of the third simulation cell vector, followed by the number of repeats (4) in that direction.

	For example, <tt>1 0 0 4</tt> will produce the crystal structure as <tt>2 0 0 2</tt>. The atoms will be labeled differently, but the structure will be the same.		For example, <tt>1 0 0 4</tt> will produce the crystal structure as <tt>2 0 0 2</tt>. The atoms will be labeled differently, but the structure will be the same.
Line 86:		Line 86:
	Finally, <tt>makecrystal</tt> is the command that actually creates the crystal structure. It first computes the number of atoms to be allocated and then specifies their coordinates. The command <tt>writecn</tt> writes the configuration to a file in the [[Output_File_Formats_in_MD%2B%2B#Configuration_.cn_File \| .cn format]]. By default, the file name is <tt>final.cn</tt>, but you can change it by specifying variable, e.g. <tt>finalcnfile = perf.cn</tt> '''before''' calling <tt>writecn</tt>.		Finally, <tt>makecrystal</tt> is the command that actually creates the crystal structure. It first computes the number of atoms to be allocated and then specifies their coordinates. The command <tt>writecn</tt> writes the configuration to a file in the [[Output_File_Formats_in_MD%2B%2B#Configuration_.cn_File \| .cn format]]. By default, the file name is <tt>final.cn</tt>, but you can change it by specifying variable, e.g. <tt>finalcnfile = perf.cn</tt> '''before''' calling <tt>writecn</tt>.

	The [[Output_File_Formats_in_MD%2B%2B#Configuration_.cn_File \| .cn file]] starts with the number of atoms, then followed by that number of lines, each line giving the scaled coordinates of one atom. If other options are set (e.g. <tt>writevelocity = 1</tt> or <tt>writeall = 1</tt>), it may also save other things, such as velocities, in each line.		The [[Output_File_Formats_in_MD%2B%2B#Configuration_.cn_File \| .cn file]] starts with the number of atoms, then followed by that number of lines, each line giving the scaled coordinates of one atom. If other options are set (e.g. <tt>writevelocity = 1</tt> or <tt>writeall = 1</tt>), it may also save other things, such as velocities, in each line.


	== Plotting setup ==		== Plotting setup ==

Caiwei: /* MD simulation */

2012-04-23T21:56:52Z

MD simulation

← Older revision		Revision as of 21:56, 23 April 2012
Line 160:		Line 160:
	run		run

	The parameters of this MD simulation has been defined in the previous section.		The parameters of this MD simulation has been defined in the previous section. It is a good idea to put the command

			closepropfile

			before exiting the simulation. This makes sure that the output file on your hard disk gets updated before the simulation terminates.

	The <tt>quit</tt> command instructs MD++ to exit without reading the rest of the script file. MD++ will also exit when it reaches the end of the script file. Sometimes, you want to view the atomic structure at the end of your simulation before MD++ exits. You can do so by putting the main program to sleep (the X-window is still awake) before exiting,		The <tt>quit</tt> command instructs MD++ to exit without reading the rest of the script file. MD++ will also exit when it reaches the end of the script file. Sometimes, you want to view the atomic structure at the end of your simulation before MD++ exits. You can do so by putting the main program to sleep (the X-window is still awake) before exiting,

Caiwei: /* MD simulation setup */

2012-04-23T21:53:54Z

MD simulation setup

← Older revision		Revision as of 21:53, 23 April 2012
Line 145:		Line 145:

	Lastly, <tt>ensemble_type = NVE</tt> defines the simulation ensemble. Typical ensembles are <tt>NVE</tt> and <tt>NVT</tt>. <tt>integrator_type = VVerlet</tt> sets the integrator type to be ''Velocity Verlet''. You can also try <tt>Gear6</tt> to see the difference.		Lastly, <tt>ensemble_type = NVE</tt> defines the simulation ensemble. Typical ensembles are <tt>NVE</tt> and <tt>NVT</tt>. <tt>integrator_type = VVerlet</tt> sets the integrator type to be ''Velocity Verlet''. You can also try <tt>Gear6</tt> to see the difference.


	Suppose you do want to output simulation properties into a file, then you can do so by setting, e.g.		Suppose you do want to output simulation properties into a file, then you can do so by setting, e.g.
Line 153:		Line 152:
	outpropfile = thermo.out		outpropfile = thermo.out

	These lines instruct MD++ to print out a line into the <tt>thermo.out</tt> file every 10 simulation steps. Each line will contain four entries: current simulation step, potential energy, kinetic energy, and instantaneous temperature.		These lines instruct MD++ to print out a line into the <tt>thermo.out</tt> file every 10 simulation steps. Each line will contain four entries: current simulation step, potential energy (in eV), kinetic energy (in eV), and instantaneous temperature (in K).

	== MD simulation ==		== MD simulation ==

Caiwei: /* MD simulation setup */

2012-04-23T21:53:03Z

MD simulation setup

← Older revision		Revision as of 21:53, 23 April 2012
Line 147:		Line 147:


			Suppose you do want to output simulation properties into a file, then you can do so by setting, e.g.

			saveprop = 1 savepropfreq = 10 openpropfile
			output_fmt = "curstep EPOT KATOM Tinst"
			outpropfile = thermo.out

			These lines instruct MD++ to print out a line into the <tt>thermo.out</tt> file every 10 simulation steps. Each line will contain four entries: current simulation step, potential energy, kinetic energy, and instantaneous temperature.

	== MD simulation ==		== MD simulation ==

Wcash: fixed mathbf{H}

2012-04-23T21:27:00Z

fixed mathbf{H}

← Older revision		Revision as of 21:27, 23 April 2012
Line 116:		Line 116:
	relax finalcnfile = relaxed.cn writecn		relax finalcnfile = relaxed.cn writecn

	The first line sets up the function tolerance, maximum iterations and maximum number of times the code is allowed to call the potential function. In the second line <tt>conj_fixbox = 1</tt>, indicates that the simulation box (i.e. the <mathbf>H</~~mathbf~~>) is not allowed to change. If this parameter is set to 0, the box size will go to the equilibrium size. Thus, for however many repeat cells you have, the box will go to the equilibrium size for that number of repeat cells. This is a convenient way to determine the equilibrium lattice constant of your crystal structure.		The first line sets up the function tolerance, maximum iterations and maximum number of times the code is allowed to call the potential function. In the second line <tt>conj_fixbox = 1</tt>, indicates that the simulation box (i.e. the <math>\mathbf{H}</math>) is not allowed to change. If this parameter is set to 0, the box size will go to the equilibrium size. Thus, for however many repeat cells you have, the box will go to the equilibrium size for that number of repeat cells. This is a convenient way to determine the equilibrium lattice constant of your crystal structure.

	After the various variables for the CGR algorithm have been set in the first two lines, the <tt>relax</tt> calls the CG algorithm to relax the structure. The relaxed structure is saved into a configuration file (specified as <tt>relaxed.cn</tt> here).		After the various variables for the CGR algorithm have been set in the first two lines, the <tt>relax</tt> calls the CG algorithm to relax the structure. The relaxed structure is saved into a configuration file (specified as <tt>relaxed.cn</tt> here).


	== MD simulation setup ==		== MD simulation setup ==

Caiwei at 17:53, 23 April 2012

2012-04-23T17:53:05Z

← Older revision		Revision as of 17:53, 23 April 2012
Line 1:		Line 1:
	<H1 ALIGN="CENTER"> An ~~Example Script File~~ </H1>		<P ALIGN="CENTER"> MD++ Tutorial </P>
			<P ALIGN="CENTER"> <FONT SIZE="+2" color="darkred"><STRONG>
			An Example Script File</STRONG></font></P>
	<DIV>		<DIV>

	<P ALIGN="CENTER"><STRONG>Adrian Buganza, William Kuykendall and Wei Cai</STRONG></P>		<P ALIGN="CENTER"><STRONG>Adrian Buganza, William Kuykendall and Wei Cai</STRONG></P>
	</DIV>		</DIV>

	<P ALIGN="CENTER">[[ Apr 23 ]], [[2012]]</P>
			This tutorial walks you through a complete .script file that performs an MD simulation.
⚫	<P>

	<BR><HR>
		⚫	<HR>

	To run a simulation using MD++ the basic approach consists on writing a ''script'' file. The ''script'' file consists of a series of variable assignments (e.g. <tt>latticeconst = 5.430</tt>) and commands (e.g. <tt>openwin</tt>) that MD++ uses to setup and run the simulation. The disadvantage of ''script'' files is that they do not allow for more complex programming such as <tt>for</tt> loops or similar programming tools. To incorporate this type of features the user can write a ''.tcl'' file. More information on ''.tcl'' files can be found in a different manual.		To run a simulation using MD++ the basic approach consists on writing a ''script'' file. The ''script'' file consists of a series of variable assignments (e.g. <tt>latticeconst = 5.430</tt>) and commands (e.g. <tt>openwin</tt>) that MD++ uses to setup and run the simulation. The disadvantage of ''script'' files is that they do not allow for more complex programming such as <tt>for</tt> loops or similar programming tools. To incorporate this type of features the user can write a ''.tcl'' file. More information on ''.tcl'' files can be found in a different manual.

Caiwei at 17:48, 23 April 2012

2012-04-23T17:48:08Z

← Older revision		Revision as of 17:48, 23 April 2012
Line 1:		Line 1:
	<H1 ALIGN="CENTER">~~<FONT~~ ~~SIZE="-1">Manual~~ 04 ~~for~~ ~~MD++~~ </~~FONT~~>		<H1 ALIGN="CENTER"> An Example Script File </H1>
	<BR>
	An Example Script File</H1>
	<DIV>		<DIV>

Line 116:		Line 114:
	relax finalcnfile = relaxed.cn writecn		relax finalcnfile = relaxed.cn writecn

	The first line sets up the function tolerance, maximum iterations and maximum number of times the code is allowed to call the potential function. In the second line <tt>conj_fixbox = 1<tt>, indicates that the simulation box (i.e. the <mathbf>H</mathbf>) is not allowed to change. If this parameter is set to 0, the box size will go to the equilibrium size. Thus, for however many repeat cells you have, the box will go to the equilibrium size for that number of repeat cells. This is a convenient way to determine the equilibrium lattice constant of your crystal structure.		The first line sets up the function tolerance, maximum iterations and maximum number of times the code is allowed to call the potential function. In the second line <tt>conj_fixbox = 1</tt>, indicates that the simulation box (i.e. the <mathbf>H</mathbf>) is not allowed to change. If this parameter is set to 0, the box size will go to the equilibrium size. Thus, for however many repeat cells you have, the box will go to the equilibrium size for that number of repeat cells. This is a convenient way to determine the equilibrium lattice constant of your crystal structure.

	After the various variables for the CGR algorithm have been set in the first two lines, the <tt>relax</tt> calls the CG algorithm to relax the structure. The relaxed structure is saved into a configuration file (specified as <tt>relaxed.cn</tt> here).		After the various variables for the CGR algorithm have been set in the first two lines, the <tt>relax</tt> calls the CG algorithm to relax the structure. The relaxed structure is saved into a configuration file (specified as <tt>relaxed.cn</tt> here).
Line 134:		Line 132:
	ensemble_type = NVE		ensemble_type = NVE

	~~T\_OBJ~~ = 300~~\rm \,~~ sets the target temperature to 300 Kelvin; ~~that~~ will be used to initialize velocities. The second line sets total number of steps and the time step ~~as a fraction of~~ ~~pico-seconds~~. ~~Command~~		<tt>T_OBJ = 300</tt> sets the target temperature to 300 Kelvin, which will be used to initialize velocities. (It will also be used by the thermostat if the <tt>NVT</tt> ensemble were used, though not in this example.) The second line sets total number of steps and the time step (in picosecond).
	\tt atommass = 28.0855 ~~\rm~~ specifies atomic mass in grams/mole. \\		<tt> atommass = 28.0855 </tt> specifies atomic mass in grams/mole. <tt> atomTcpl = 200.0 boxTcpl = 20.0</tt> are variables pertaining to the thermostat and bariostat for certain ensembles (not needed for <tt>NVE</tt>).

	Commands \tt atomTcpl = 200.0 boxTcpl = 20.0 \rm are variables to help control the thermostat and bariostat for certain ensembles. \\
	In the ~~nest~~ line, If the variable \tt ~~DOUBLE\_T \rm~~ is set to 0 then MD++ will not double ~~T\_OBJ~~ ~~and~~ ~~thus~~ at equilibrium, T will be about ~~T\_OBJ~~/2; if it is set to 1 MD++ will double ~~T\_OBJ~~ at ~~the start of~~ the ~~simulation~~ ~~such~~ that at equilibrium the temperature gets to the desired value ~~T\_OBJ~~. \\		In the next line, if the variable <tt>DOUBLE_T</tt> is set to 0 then MD++ will not double <tt>T_OBJ</tt> when initializing the velocity. When equilibrium is reached for an NVE simulation for solids, the temperature will usually be about half of your initial <tt>T_OBJ</tt>. If <tt>T_OBJ</tt> is set to 1, MD++ will double <tt>T_OBJ</tt> when initializing the velocity, so that at equilibrium the temperature gets close to the desired value <tt>T_OBJ</tt>.

	In the sixth line, \tt srand48bytime \rm seeds the random number generator by the computer's clock time and the next line initializes velocities of all the atoms. \\
			<tt>srand48bytime</tt> seeds the random number generator by the computer's clock time, so that everytime you run the simulation, your atomic trajectories will be different (because <tt>initvelocity</tt> uses pseudo-random numbers when assigning velocities). For debugging purposes, you may want your simulations to be exactly repeatable. You can do so by always assigning the same random seed, e.g.
	Then, if \tt saveprop = 0 \rm, the property file will not be saved, if it is equal to 1, it will be saved; \tt savepropfreq \rm is how many time steps before you save the property and \tt openpropfile \rm opens the property file.\\

⚫	Lastly, \tt ~~ensemble\_type~~ = NVE ~~\rm~~ defines the ensemble. Typical ensembles are NVE and NVT. \tt ~~integrator\_type~~ = VVerlet ~~\rm~~ sets the integrator type~~. In this case, the integrator is chosen~~ to be ~~the \emph{~~Velocity Verlet} ~~algorithm,~~ ~~but \emph{Gear6}~~ can also be ~~used~~.
			randseed = 12345 srand48

			If <tt>saveprop = 0</tt>, the property file will not be saved during your MD simulation. If it were set to 1, a property file will be saved. <tt>savepropfreq = 10</tt> specifies a line will be added to the property file every 10 MD time steps (if <tt>saveprop = 1</tt>). Command <tt>openpropfile</tt> opens the property file to prepare for subsequent MD simulation.

		⚫	Lastly, <tt>ensemble_type = NVE</tt> defines the simulation ensemble. Typical ensembles are <tt>NVE</tt> and <tt>NVT</tt>. <tt>integrator_type = VVerlet</tt> sets the integrator type to be ''Velocity Verlet''. You can also try <tt>Gear6</tt> to see the difference.

Caiwei at 17:30, 23 April 2012

2012-04-23T17:30:57Z

Show changes

Caiwei: Created page with '

Manual 04 for MD++
An Example Script File

Adrian Buganza, William Kuykendall and Wei Cai

2012-04-23T16:45:11Z

Created page with '<H1 ALIGN="CENTER"><FONT SIZE="-1">Manual 04 for MD++ </FONT> <BR> An Example Script File</H1> <DIV> <P ALIGN="CENTER"><STRONG>Adrian Buganza, William Kuykendall and Wei Cai</S…'

New page
<H1 ALIGN="CENTER"><FONT SIZE="-1">Manual 04 for MD++ </FONT>
<BR>
An Example Script File</H1>
<DIV>

<P ALIGN="CENTER"><STRONG>Adrian Buganza, William Kuykendall and Wei Cai</STRONG></P>
</DIV>
<P ALIGN="CENTER">[[ Apr 23 ]], [[2012]]</P>
<P>
<BR><HR>

To run a simulation using MD++ the basic approach consists on writing a ''script'' file. The ''script'' file consists of a series of variable assignments (e.g. ''latticeconst = 5.430'') and commands (e.g. ''openwin'') that MD++ uses to setup and run the simulation. The disadvantage of ''script'' files is that they do not allow for more complex programming such as ''for'' loops or similar programming tools. To incorporate this type of features the user can write a ''*.tcl'' file. More information on ''*.tcl'' files can be found in a different manual.

== Overall Structure of *.script files ==

In general, a ''script'' file will have the following parts:

* MD setup
* Initialize atoms positions
* Plotting setup
* Relaxation
* MD simulation settings
* MD Simulation

The last three items do not always appear because they actually depend on the specific problem to be solved. For example, it is a common practice to relax the structure (find a configuration with minimum potential energy) before running a simulation, but the initial configuration (e.g. read in from a file) might already satisfy such condition. Furthermore, there are some cases in which simulations at zero temperature are done in order to determine characteristic properties of a material like the ideal strength, in such a case, time integration is not needed and the last item on the list won't appear in the code. In summary, what operations are performed by MD++ depend on the commands listed in the ''script'' file. Nonetheless, in the following, we will briefly explain all the items listed above.

Suppose you have installed MD++ in your $HOME/Codes/MD++ folder.

export MDPP=$HOME/Codes/MD++
cd $MDPP

In this example, we will use the follwing ''script'' file:

$MDPP/scripts/Examples/example02a-si-md.script

All characters following the '''#''' (pound) sign are comments. They will be ignored by the MD++ program and we will not discuss them here either.

== Output set up ==

Nearly every script file starts with the following three lines.

setnolog
setoverwrite
dirname = runs/si-example

The first two commands (<tt>setnolog</tt> and <tt>setoverwrite</tt>) are optional, but the line that specifies <tt>dirname</tt> must precede all other commands. Otherwise MD++ will exit with error.

The first line, <tt>setnolog</tt> indicates that everything will be printed to screen and the log file (A.log) created will be empty. If this line is commented out (by adding # in front), MD++ will redirect all screen outputs to the A.log file in the directory specified by <tt>dirname</tt>.

Command <tt>setoverwrite</tt> allows the new output files (including A.log file) to overwrite the old files in the directory (specified by <tt>dirname</tt>). If this line is commented out, MD++ will exit with error if the directory specified by <tt>dirname</tt> already exists.

Finally, <tt>dirname = runs/si-example</tt> specifies the output directory. If it does not exist, it will be created.

== Initialize atoms positions ==

This can be done in two ways, by importing position data from a \emph{*.cn} file or by using the command \tt{makecrystal} \rm. For the former use the following:\\ \\
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{incnfile = relaxed.cn readcn}
}}\\ \\
This is an easy way to get a setup you've already used. This reads in a file ("relaxed.cn") to set up your crystal.
\\There is also \tt{saveintercn} \rm. This will save an intermediate configuration file. It also has a frequency variable \tt{plotfreq} \rm . \\
To create a perfect lattice configuration the following commands can be used\\ \\
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{crystalstructure = diamond-cubic \\ latticeconst = 5.4309529817532409 \begin{tabbing} latticesize = [\= 1 0 0 4\\ \> 0 1 0 4\\ \> 0 0 1 4 ] \end{tabbing} makecrystal\\ writecn }
}}\\ \\
Starting from the first line, \tt{crystalstructure = diamond-cubic} \rm sets up the crystal structure to make a new crystal. \tt{latticeconst = 5.4309529817532409} \rm sets up the lattice constant for the crystal you want to make. Then \tt{latticesize =...} \rm Creates a lattice. The first three values in each line are an axis direction, while the fourth number is the number of repeats of this vector that exists. For example, [1 0 0 4] will produce the same thing as [2 0 0 2]. The atoms will be labeled differently, but the structure will be the same.\\
Again, to emphasize, the crystal structure and lattice constant determine the structure. The lattice size will change the size and orientation of the structure. \\
It is also worth commenting that Periodic Boundary Conditions (PBC) are implied in MD++. Everything is PBC. However, you can create gaps such that the next atoms are outside the cutoff radius. This will effectively create a free surface, for example.\\
Moreover, this code does not create half-atoms or fractional atoms. A simple cubic will have a single full atom at one corner. Then, using PBC, the other 7 corners will also have a single atom because of the repetition.\\
Finally, \tt{makecrystal} \rm is the command that actually creates the crystal structure and the command \tt{writecn} \rm writes the configuration to a file. Every line in the file is an atom. If other options are set, it may also save other things, such as velocities.\\

== Plotting setup ==

This section if pretty standard, so we will be brief. The usual lines of code you can have in your code are:\\
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{atomradius = 0.67 bondradius = 0.3 bondlength = 2.8285\\
atomcolor = orange highlightcolor = purple bondcolor = red backgroundcolor = gray70\\
plotfreq = 10 rotateangles = [ 0 0 0 1.25 ]\\
openwin \\
alloccolors rotate saverot\\ eval \\ plot}
}}\\ \\
The first two lines are parameters for plotting. The \tt bondlegth \rm parameter depends on the atom being modeled. The third line, \tt openwin \rm Opens the x window to display the configuration. The following line allocates the colors according to your specifications (atom colors, highlighting colors, bond colors, etc., then rotates the cell and saves the rotation as the default rotation. \\
The \tt eval \rm command is not a plotting command, but it is usually used before plotting the results. This command evaluates the total potential energy.\\
The final line, \tt plot \rm is the actual plotting command.

== Relaxation ==

Relaxation consists of finding a minimum of the potential energy. This is done with the Conjugate Gradient iteration. To find the relaxed configuration use the following lines of code:
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{ conj\_ftol = 1e-7 conj\_itmax = 1000 conj\_fevalmax = 10000 \\ conj\_fixbox = 1 conj\_summary = 1\\ relax finalcnfile = relaxed.cn writecn }
}}\\ \\
The first line sets up the function tolerance, maximum iterations and maximum number of times the code is allowed to call the potential function. In the second line \tt conj\_fixbox = 1\rm , indicates that the box is not changing. If this parameter is set to 0, the box size will go to the equilibrium size. Thus, for however many repeat cells you have, the box will go to the equilibrium size for that number of repeat cells. \\
After the various variables for the CGR algorithm have been set in the first two lines, the third line relaxes the crystal, then it saves the relaxed configuration file.

== MD simulation setup ==

In this part of the code you define parameters such as ensemble type or integrator to be used. Generic lines of code that might be useful are:\\
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{T\_OBJ = 300\\ equilsteps = 0 totalsteps = 100 timestep = 0.0001\\ atommass = 28.0855\\ atomTcpl = 200.0 boxTcpl = 20.0\\ DOUBLE\_T = 0\\ srand48bytime initvelocity \\saveprop = 0 savepropfreq = 10 openpropfil \\ integrator\_type = 1\, ensemble\_type = NVE}
}}\\ \\
\tt T\_OBJ = 300\rm \, sets the target temperature to 300 Kelvin; that will be used to initialize velocities. The second line sets total number of steps and the time step as a fraction of pico-seconds. Command
\tt atommass = 28.0855 \rm specifies atomic mass in grams/mole. \\
Commands \tt atomTcpl = 200.0 boxTcpl = 20.0 \rm are variables to help control the thermostat and bariostat for certain ensembles. \\
In the nest line, If the variable \tt DOUBLE\_T \rm is set to 0 then MD++ will not double T\_OBJ and thus at equilibrium, T will be about T\_OBJ/2; if it is set to 1 MD++ will double T\_OBJ at the start of the simulation such that at equilibrium the temperature gets to the desired value T\_OBJ. \\
In the sixth line, \tt srand48bytime \rm seeds the random number generator by the computer's clock time and the next line initializes velocities of all the atoms. \\
Then, if \tt saveprop = 0 \rm, the property file will not be saved, if it is equal to 1, it will be saved; \tt savepropfreq \rm is how many time steps before you save the property and \tt openpropfile \rm opens the property file.\\
Lastly, \tt ensemble\_type = NVE \rm defines the ensemble. Typical ensembles are NVE and NVT. \tt integrator\_type = VVerlet \rm sets the integrator type. In this case, the integrator is chosen to be the \emph{Velocity Verlet} algorithm, but \emph{Gear6} can also be used.

== MD simulation ==

To run a simulation there is only one command needed:\\
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{ run }
}}\\ \\
To put MD++ to sleep and then quit the simulation use:\\
\fcolorbox{black}{gray!20}{\parbox{\linewidth}{
\tt{ sleep quit }
}}

MD++ An Example Script File - Revision history

Caiwei at 20:52, 4 May 2012

Wpkuykendall: /* Initialize atoms positions */

Caiwei: /* MD simulation */

Caiwei: /* MD simulation setup */

Caiwei: /* MD simulation setup */

Wcash: fixed mathbf{H}

Caiwei at 17:53, 23 April 2012

Caiwei at 17:48, 23 April 2012

Caiwei at 17:30, 23 April 2012

Caiwei: Created page with '

Manual 04 for MD++ An Example Script File

Manual 04 for MD++
An Example Script File