MDFrame Class Reference
#include <md.h>
Detailed Description
Definition at line 258 of file md.h.
Constructor & Destructor Documentation
| MDFrame::MDFrame | ( | ) | [inline] |
Definition at line 584 of file md.h.
References _ATOMMASS, crystalstructure, input, latticeconst, MC_switchoffatoms, output_fmt, output_str, plot_color_bar, plot_color_windows, plot_highlight_atoms, and plot_limits.
| virtual MDFrame::~MDFrame | ( | ) | [inline, virtual] |
Member Function Documentation
| void MDFrame::addbend | ( | ) |
Referenced by exec().
| void MDFrame::addFext_to_group | ( | ) |
Referenced by exec().
| void MDFrame::addtorque | ( | ) |
Referenced by exec().
| virtual void MDFrame::Alloc | ( | ) | [virtual] |
| void MDFrame::AllocChain | ( | ) |
Referenced by exec().
| void MDFrame::alloccolors | ( | ) |
Referenced by exec().
| void MDFrame::alloccolorsX | ( | ) |
Referenced by exec().
| void MDFrame::allocQLM | ( | ) |
| void MDFrame::annealpath | ( | ) |
Referenced by exec().
| int MDFrame::applyconstraint | ( | ) |
Referenced by exec().
| void MDFrame::applystrain | ( | ) |
Referenced by exec().
| void MDFrame::assign_Lam | ( | ) |
Definition at line 308 of file ffs.cpp.
References _Lam_array, _Lam_check, FFS0_check, input, int(), and Realloc.
Referenced by exec().
| void MDFrame::atomeye | ( | ) |
Referenced by exec().
| bool MDFrame::Bond | ( | int | I, | |
| int | J | |||
| ) | const |
Referenced by SWFrame::stillinger_weber(), and SWFrame::stillinger_weber_energyonly().
| void MDFrame::calcentralsymmetry | ( | ) |
Referenced by exec().
| virtual void MDFrame::calcoutput | ( | ) | [virtual] |
| virtual void MDFrame::calcprop | ( | ) | [virtual] |
Reimplemented in BMBFrame, LJ2Frame, LJBONDFrame, LJDIMERFrame, RODSFrame, BKSFrame, and SWFrame.
Referenced by NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), NVTC_Gear6(), VVerlet_Get_h2(), and VVerlet_Get_s2().
| void MDFrame::calcrystalorder | ( | ) |
Definition at line 18 of file ffs.cpp.
References _NP, _QL, _QLM, _SR, _TOPOL, DFS(), DFS1(), L_for_QLM, N_cluster_temp, N_lgst_cluster, N_lgst_index, N_lgst_skin, N_lgst_skin_index, N_skin_P, N_solid_P, nindex, nn, Vector3::norm(), QLM_cutoff, QLM_mark, QLM_solid, Rc_for_QLM, Vector3::subint(), wSKIN, Vector3::x, Vector3::y, and Vector3::z.
Referenced by exec().
| void MDFrame::caldisregistry | ( | ) |
Referenced by exec().
| void MDFrame::caldscom12 | ( | ) |
| void MDFrame::calDVIRIALDexx | ( | ) |
| void MDFrame::calHessian | ( | ) |
Referenced by exec().
| virtual void MDFrame::call_potential | ( | ) | [virtual] |
Referenced by NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), NVTC_Gear6(), and VVerlet_Get_s2().
| void MDFrame::calmisfit | ( | ) |
Referenced by exec().
| void MDFrame::calmisfit2 | ( | ) |
Referenced by exec().
| void MDFrame::calModeHessian | ( | ) |
Referenced by exec().
| void MDFrame::calphonondisp | ( | ) |
Referenced by exec().
| void MDFrame::CE | ( | ) |
Definition at line 34 of file ewald.cpp.
References _EPOT_Ewald, _EPOT_Ewald_Real, _EPOT_Ewald_Rec, _EPOT_Ewald_Self, _EPOT_IND_Ewald, _EPOT_IND_Ewald_Real, _EPOT_IND_Ewald_Rec, _F_Ewald, _F_Ewald_Real, _F_Ewald_Rec, _NP, _VIRIAL_Ewald, _VIRIAL_Ewald_Real, _VIRIAL_Ewald_Rec, CE_Real(), and CE_Rec().
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), exec(), and BKSFrame::potential().
| void MDFrame::CE_clear | ( | ) |
| void MDFrame::CE_enumKV | ( | ) |
Definition at line 501 of file ewald.cpp.
References _NP, MDFrame::K_rec::a, MDFrame::K_rec::b, MDFrame::K_rec::c, CE_Kc, CE_KV, CE_Mka, CE_Mkb, CE_Mkc, CE_MKV, CE_nKV, CE_scx, CE_scy, CE_scz, Ewald_cell_V, Ewald_H_L1, Ewald_H_L2, Ewald_H_L3, int(), MDFrame::K_rec::k2, MDFrame::K_rec::kx, MDFrame::K_rec::ky, MDFrame::K_rec::kz, M_PI, NULL, and Realloc.
Referenced by CE_init().
| void MDFrame::CE_fillSinCosTables | ( | ) |
Definition at line 455 of file ewald.cpp.
References _NP, _SR, CE_Mka, CE_Mkb, CE_Mkc, CE_scx, CE_scy, CE_scz, EComplex::Im, M_PI, EComplex::Mul(), and EComplex::Re.
Referenced by CE_Rec().
| void MDFrame::CE_init | ( | ) |
Definition at line 411 of file ewald.cpp.
References _NP, CE_enumKV(), CE_Kc, CE_Mka, CE_Mkb, CE_Mkc, CE_MKV, CE_nKV, CE_sc_axby, CE_sckk, Ewald_Alpha, Ewald_precision, and Realloc.
Referenced by Ewald_init().
| void MDFrame::CE_Real | ( | ) |
Definition at line 53 of file ewald.cpp.
References _ATOMCHARGE, _EPOT_Ewald_Real, _EPOT_IND_Ewald_Real, _F_Ewald_Real, _NP, _SR, _VIRIAL_Ewald_Real, Matrix33::addnvv(), CE_eREAL, CE_sREAL, Vector3::clear(), Matrix33::clear(), DUMP, Ewald_Alpha, Ewald_Rcut, fixed, HIG, M_SQRT_PI, nindex, nn, NOR, Vector3::norm2(), P_CLMB, refreshneighborlist, species, SQR, and Vector3::subint().
| void MDFrame::CE_Rec | ( | ) |
Definition at line 130 of file ewald.cpp.
References _ATOMCHARGE, _EPOT_Ewald_Rec, _EPOT_IND_Ewald_Rec, _F_Ewald_Rec, _NP, _VIRIAL_Ewald_Rec, MDFrame::K_rec::a, MDFrame::K_rec::b, MDFrame::K_rec::c, CE_eREC, CE_fillSinCosTables(), CE_KV, CE_nKV, CE_sc_axby, CE_sckk, CE_scx, CE_scy, CE_scz, CE_sREC, Vector3::clear(), Matrix33::clear(), conj_fixbox, Ewald_Alpha, Ewald_cell_V, Ewald_H_L1, Ewald_H_L2, Ewald_H_L3, fixed, EComplex::Im, MDFrame::K_rec::k2, MDFrame::K_rec::kx, MDFrame::K_rec::ky, MDFrame::K_rec::kz, M_PI, EComplex::Mul(), EComplex::MulConjugate(), EComplex::Norm2(), P_SQRT_CLMB, EComplex::Re, species, SQR, Vector3::x, Vector3::y, and Vector3::z.
Referenced by CE().
| void MDFrame::clearFext | ( | ) |
Referenced by exec().
| void MDFrame::clearR0 | ( | ) |
Referenced by exec().
| int MDFrame::closepropfile | ( | ) |
Referenced by exec().
| void MDFrame::closewindow | ( | ) |
| void MDFrame::constrain_fixedatoms | ( | ) |
Referenced by exec().
| int MDFrame::constrainedrelax | ( | ) |
Referenced by exec().
| void MDFrame::convertCNtoCFG | ( | ) |
Referenced by exec().
| int MDFrame::convertXDATCAR | ( | ) |
Referenced by exec().
| void MDFrame::copybendatoms | ( | ) |
Referenced by exec().
| void MDFrame::copyCNtoRchain | ( | int | j | ) |
Referenced by exec().
| void MDFrame::copyRchaintoCN | ( | int | j | ) |
Referenced by exec().
| void MDFrame::copytoconfig1 | ( | int | ) |
Referenced by exec().
| void MDFrame::copytoconfig2 | ( | int | ) |
Referenced by exec().
| void MDFrame::copytorqueatoms | ( | ) |
Referenced by exec().
| static void MDFrame::cstr_potential_wrapper | ( | int * | n, | |
| double | x[], | |||
| double * | f, | |||
| double | df[] | |||
| ) | [static] |
| static void MDFrame::cstr_potential_wrapper_c | ( | int | n, | |
| double | x[], | |||
| double * | f, | |||
| double | df[] | |||
| ) | [static] |
| void MDFrame::cutpastecn | ( | ) |
Referenced by exec().
| void MDFrame::cutpath | ( | ) |
Referenced by exec().
| void MDFrame::cutslice | ( | ) |
Referenced by exec().
| void MDFrame::DFS | ( | int | i, | |
| int | On_Off, | |||
| double | index | |||
| ) |
Definition at line 203 of file ffs.cpp.
References _QL, _SR, _TOPOL, N_cluster_temp, nindex, nn, Vector3::norm(), QLM_mark, QLM_solid, Rc_for_QLM, and Vector3::subint().
Referenced by calcrystalorder().
| void MDFrame::DFS1 | ( | int | i, | |
| int | On_Off, | |||
| double | index, | |||
| double | index1 | |||
| ) |
Definition at line 235 of file ffs.cpp.
References _QL, _SR, _TOPOL, N_cluster_temp, N_lgst_skin, N_skin_P, nindex, nn, Vector3::norm(), QLM_mark, QLM_solid, Rc_for_QLM, and Vector3::subint().
Referenced by calcrystalorder().
| void MDFrame::ECpotential | ( | ) |
| double MDFrame::ECpotential_energyonly | ( | int | iatom | ) |
| void MDFrame::ECpotential_energyonly | ( | ) |
| void MDFrame::eval | ( | ) |
Referenced by exec().
| void MDFrame::eval_insertparticle | ( | ) |
Referenced by exec().
| void MDFrame::eval_removeparticle | ( | ) |
Referenced by exec().
| void MDFrame::Ewald_init | ( | ) |
Definition at line 285 of file ewald.cpp.
References _ATOMCHARGE, _EPOT_Ewald_Self, _EPOT_IND_Ewald, _EPOT_IND_Ewald_Real, _EPOT_IND_Ewald_Rec, _F_Ewald, _F_Ewald_Real, _F_Ewald_Rec, _NP, _RLIST, _SKIN, Organizer::bindvar(), CE_init(), DOUBLE, Ewald_Alpha, Ewald_CE_or_PME, Ewald_cell_V, Ewald_H_L1, Ewald_H_L2, Ewald_H_L3, Ewald_option_Alpha, Ewald_precision, Ewald_qSQRsum, Ewald_Rcut, Ewald_time_ratio, fixed, Matrix33::inv(), M_SQRT_PI, P_SQRT_CLMB, PME_init(), Realloc, species, and SQR.
Referenced by exec().
| int MDFrame::exec | ( | char * | name | ) | [virtual] |
Reimplemented from Organizer.
Reimplemented in ALGLUEFrame, BMBFrame, EAMFrame, FSFrame, LJ2Frame, LJBONDFrame, LJDIMERFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, RODSFrame, BKSFrame, SWFrame, and VaspBox.
Definition at line 432 of file md.cpp.
References _RANDSEED, _SR, addbend(), addFext_to_group(), addtorque(), AllocChain(), alloccolors(), alloccolorsX(), allocQLM(), annealpath(), applyconstraint(), applystrain(), assign_Lam(), atomeye(), bindcommand, bindcommand_sync, calcentralsymmetry(), calcrystalorder(), caldisregistry(), calHessian(), calmisfit(), calmisfit2(), calModeHessian(), calphonondisp(), CE(), CE_clear(), clearFext(), clearR0(), closepropfile(), constrain_fixedatoms(), constrainedrelax(), convertCNtoCFG(), convertXDATCAR(), copybendatoms(), copyCNtoRchain(), copyRchaintoCN(), copytoconfig1(), copytoconfig2(), copytorqueatoms(), cutpastecn(), cutpath(), cutslice(), eval(), eval_insertparticle(), eval_removeparticle(), Ewald_init(), Organizer::exec(), extendbox(), finalcnfile, findcenterofmass(), findcore(), fix_constrainedatoms(), fixallatoms(), fixatoms_by_group(), fixatoms_by_ID(), fixatoms_by_pos_topol(), fixatoms_by_position(), fixatoms_by_species(), fortranrelax(), freeallatoms(), GnuPlotHistogram(), incnfile, initRchain(), initvelocity(), input, interpCN(), makebendhandle(), makecrystal(), makecut(), makecylinder(), makedipole(), makedislcylinder(), makedislocation(), makedisloop(), makegrainboundary(), maketorquehandle(), makewave(), markremovefixedatoms(), MCperturbevelocity(), moveatom(), movefixedatoms(), movegroup(), moveRchain(), multieval(), multiplyvelocity(), NbrList_print(), NbrListPlot_reconstruct(), nebrelax(), NULL, openFFScnfile(), openintercnfile(), openpropfile(), openwin(), pbcshiftatom(), perturbevelocity(), plot(), PME(), PME_clear(), printatoms_in_sphere(), randomposition(), readcn(), readHessian(), readLAMMPS(), readMDCASK(), readMDCASKJAIME(), readPOSCAR(), readRASMOLXYZ(), readRchain(), readXYZ(), redefinepbc(), refreshneighborlist, relabelatom(), relax(), relax_by_group(), removeellipsoid(), removefixedatoms(), removeoverlapatoms(), removerectbox(), replacefreeatom(), restoreH(), reversefixedatoms(), SYWindow::reversergb(), reversespecies(), RHtoS(), rotate(), rotate_com(), run(), runcommand(), runMC(), runMCSWITCH(), runMDSWITCH(), runTAMC(), saveH(), saverot(), scaleH(), scaleVel(), setconfig1(), setconfig2(), setFFSfilecounter(), setfilecounter(), setfixedatomsgroup(), setfixedatomsspecies(), setgroupcomvel(), setH(), shiftbox(), SHtoR(), splicecn(), statedistance(), step(), strelax(), switchconfig(), SYWindow::testcolor(), testpotential(), translate_com(), win, wintogglepause(), writeatomeyecfgfile(), writeatomtv(), writeavgcnfile(), writeENERGY(), writeFFScnfile(), writefinalcnfile(), writeFORCE(), writeintercnfile(), writeLAMMPS(), writeMDCASK(), writeMDCASKXYZ(), writePINYMD(), writePOSCAR(), writePOSITION(), writepovray(), SYWindow::writeps(), writeRASMOLXYZ(), writeRchain(), and zipfiles.
Referenced by VaspBox::exec(), SWFrame::exec(), BKSFrame::exec(), RODSFrame::exec(), MEAMFrame::exec(), LJDIMERFrame::exec(), LJBONDFrame::exec(), LJ2Frame::exec(), FSFrame::exec(), EAMFrame::exec(), BMBFrame::exec(), and ALGLUEFrame::exec().
| void MDFrame::extendbox | ( | ) |
Referenced by exec().
| int MDFrame::FFSprocess | ( | ) |
Definition at line 322 of file ffs.cpp.
References _Lam_array, _Lam_check, FFS0_check, FFS_i, FFS_i_minus, FFS_Pp, FFScn_weight, FFSoption, FFSpruning, N_lgst_cluster, step0, totalsteps, and zipfiles.
| void MDFrame::findcore | ( | ) |
Referenced by exec().
| void MDFrame::fix_constrainedatoms | ( | ) |
Referenced by exec().
| void MDFrame::fixallatoms | ( | ) |
Referenced by exec().
| void MDFrame::fixatoms_by_group | ( | double * | ) |
Referenced by exec().
| void MDFrame::fixatoms_by_ID | ( | ) |
Referenced by exec().
| void MDFrame::fixatoms_by_pos_topol | ( | ) |
Referenced by exec().
| void MDFrame::fixatoms_by_position | ( | ) |
Referenced by exec().
| void MDFrame::fixatoms_by_species | ( | double * | ) |
Referenced by exec().
| void MDFrame::fortranrelax | ( | ) |
Referenced by exec().
| void MDFrame::freeallatoms | ( | ) |
Referenced by BMBFrame::dope_Yttria(), and exec().
| void MDFrame::GAUSSpotential | ( | ) |
| void MDFrame::Gear6_init | ( | ) |
Definition at line 731 of file integrators.cpp.
References _NP, MAXNHCLEN, npold, Realloc, s2, s2real, s3, s4, s5, zetaNHC, zetaNHC2, zetaNHC3, zetaNHC4, zetaNHC5, zetaNHCa, and zetaNHCv.
Referenced by NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), and NVTC_Gear6().
| void MDFrame::GnuPlotHistogram | ( | ) |
Referenced by exec().
| void MDFrame::HApotential | ( | ) |
| void MDFrame::HApotential_energyonly | ( | ) |
| void MDFrame::I12potential | ( | ) |
| void MDFrame::I12potential_energyonly | ( | ) |
| void MDFrame::initparser | ( | ) | [virtual] |
Reimplemented in ALGLUEFrame, BMBFrame, EAMFrame, FSFrame, LJ2Frame, LJBONDFrame, LJDIMERFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, RODSFrame, BKSFrame, SWFrame, SWFrame, and VaspBox.
Definition at line 85 of file md.cpp.
References _ATOMCHARGE, _ATOMMASS, _BENDMOMENT, _BENDSIM, _BOXDAMP, _CHAINLENGTH, _constrainedMD, _current_NIC, _current_NNM, _Dexx, _DOUBLET, _DVIRIAL_Dexx, _ECOH, _ECSPRING, _ENABLE_FEXT, _EPOT, _EPOT0, _EPOT_BOX, _EPOT_Ewald, _EPOT_Ewald_Real, _EPOT_Ewald_Rec, _EPOT_Ewald_Self, _ESTRAIN, _EXTPRESSADD, _EXTSTRESS, _EXTSTRESSMUL, _F_COM, _GAUSS_EPSILON, _GAUSS_RC, _GAUSS_SIGMA, _GH, _H0, _HELM, _HELMP, _HPRECOND, _I12_EPSILON, _I12_RC, _I12_SIGMA, _KATOM, _KBOX, _LAMBDA0, _LAMBDA1, _NIC, _NIMAGES, _NNM, _NNM_plot, _NP, _NP0, _NPfixed, _NPfree, _OMEGA, _P_COM, _PSTRESS, _PTHETA_COM, _RANDSEED, _REFPOTENTIAL, _RLIST, _SAVEMEMORY, _SHEARRATE, _SIGMA, _SKIN, _SWITCHFREQ, _SWITCHFUNC, _T, _TDES, _TIMESTEP, _TORQUE, _TORSIONSIM, _TOTPRESSURE, _TOTSTRESS, _TOTSTRESSinMPa, _VACUUMRATIO, _VH, _VIRIAL_Ewald, _VIRIAL_Ewald_Real, _VIRIAL_Ewald_Rec, _WALLMASS, _WAVG, _WTOT, _XPRECOND, _YPRECOND, _ZPRECOND, allocmultiple, annealspec, applyshear, atomcolor, atomeyeexe, atomeyepath, atomeyerepeat, atomradius, autowritegiffreq, backgroundcolor, bendspec, Organizer::bindvar(), bondcolor, bondlength, bondradius, CE_Kc, coloratoms, colornames, command, conj_dfpred, conj_fevalmax, conj_fixatoms, conj_fixbox, conj_fixboxvec, conj_fixdir, conj_fixshape, conj_ftol, conj_g2res, conj_itmax, constrainatoms, constrainF, constrainS, constrainS_inst, continue_curstep, crystalstructure, curstep, dEdlambda, dH, DOUBLE, element, ensemble_type, equilsteps, Ewald_Alpha, Ewald_CE_or_PME, Ewald_option_Alpha, Ewald_precision, Ewald_Rcut, Ewald_time_ratio, extforce, FFS0_check, FFS_i, FFS_i_minus, FFS_i_plus, FFS_Pp, FFScn_weight, FFScnfile, FFSfilecounter, FFSoption, FFSpruning, filecounter, finalcnfile, fixatomcolor, fixedatomenergypartition, forcemul, fortranexe, fortranpath, highlightcolor, implementation_type, incnfile, input, INT, integrator_type, intercfgfile, intercnfile, L_for_QLM, latticeconst, latticesize, MAXCOLORS, MAXSPECIES, MC_accept_ratio, MC_atom, MC_dfrac, MC_dN_freq, MC_dr, MC_dV_freq, MC_dVmax, MC_mu_ext, MC_P_ext, MC_switchoffatoms, MDCASKpot, myname, N_lgst_cluster, N_lgst_index, N_lgst_skin, N_lgst_skin_index, N_solid_P, NCS, nebspec, NHChainLen, NHMass, nspecies, outpropfile, output_dat, output_fmt, output_str, plot_atom_info, plot_color_axis, plot_color_bar, plot_color_windows, plot_limits, plot_map_pbc, plotfreq, PME_bsp_n, PME_K1, PME_K2, PME_K3, potfile, Principal_Inertia, printfreq, QLM_cutoff, Rc_for_QLM, rc_plot, readparallelnebcn, rotateangles, runavgposition, s, savecfg, savecfgfreq, savecn, savecnfreq, saveFFScn, saveprop, savepropfreq, STRING, torquespec, totalsteps, vt2, win_height, win_width, writeall, writevelocity, wSKIN, zeta, zeta2, zeta3, zeta4, zeta5, zetaa, zetaNHC, zetaNHC2, zetaNHC3, zetaNHC4, zetaNHC5, zetaNHCa, zetaNHCv, zetav, and zipfiles.
Referenced by initvars().
| void MDFrame::initRchain | ( | ) |
Referenced by exec().
| void MDFrame::initvars | ( | ) | [virtual] |
Reimplemented in ALGLUEFrame, BMBFrame, EAMFrame, FSFrame, LJFrame, LJ2Frame, LJBONDFrame, LJDIMERFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, RODSFrame, SIEDIPFrame, BKSFrame, SWFrame, SWFrame, SWFrame, SWFrame, TersoffFrame, and VaspBox.
Definition at line 679 of file md.cpp.
References _H0, _SIGMA, atomcolor, atomeyerepeat, atomradius, bendspec, bondcolor, Matrix33::clear(), colornames, command, conj_fixboxvec, element, ensemble_type, extforce, finalcnfile, highlightcolor, incnfile, initparser(), integrator_type, intercfgfile, intercnfile, MAXCOLORS, MAXNHCLEN, MAXSPECIES, MDCASKpot, NHMass, outpropfile, potfile, and torquespec.
| void MDFrame::initvelocity | ( | ) |
Referenced by exec().
| virtual void MDFrame::integrator | ( | ) | [virtual] |
| int MDFrame::interpCN | ( | double | s | ) |
Referenced by exec().
| void MDFrame::makebendhandle | ( | ) |
Referenced by exec().
| void MDFrame::makecrystal | ( | ) |
Referenced by exec().
| void MDFrame::makecut | ( | ) |
Referenced by exec().
| void MDFrame::makecylinder | ( | ) |
Referenced by exec().
| void MDFrame::makedipole | ( | ) |
Referenced by exec().
| void MDFrame::makedislcylinder | ( | ) |
Referenced by exec().
| void MDFrame::makedislocation | ( | ) |
Referenced by exec().
| void MDFrame::makedisloop | ( | ) |
Referenced by exec().
| void MDFrame::makegrainboundary | ( | ) |
Referenced by exec().
| void MDFrame::maketorquehandle | ( | ) |
Referenced by exec().
| void MDFrame::makewave | ( | ) |
Referenced by exec().
| void MDFrame::markremovefixedatoms | ( | ) |
Referenced by BMBFrame::dope_Yttria(), and exec().
| void MDFrame::MCperturbevelocity | ( | ) |
Referenced by exec().
| int MDFrame::MCstep | ( | ) |
| int MDFrame::MCstep_dN | ( | ) |
| int MDFrame::MCstep_dN_fracatom | ( | ) |
| int MDFrame::MCstep_dV | ( | ) |
| int MDFrame::MCstep_dV_fracatom | ( | ) |
| int MDFrame::MCstep_fracatom | ( | ) |
| int MDFrame::MCstep_moveatom | ( | ) |
| int MDFrame::MCstep_moveatom_fracatom | ( | ) |
| int MDFrame::MCSWITCHstep | ( | double | lambda | ) |
| void MDFrame::moveatom | ( | ) |
Referenced by exec().
| void MDFrame::movefixedatoms | ( | ) |
Referenced by exec().
| void MDFrame::movegroup | ( | ) |
Referenced by exec().
| void MDFrame::moveRchain | ( | int | , | |
| int | ||||
| ) |
Referenced by exec().
| void MDFrame::multieval | ( | ) |
Referenced by exec().
| void MDFrame::multiplyvelocity | ( | ) |
Referenced by exec().
| void MDFrame::NbrList_free | ( | ) |
| void MDFrame::NbrList_freecell | ( | ) |
| void MDFrame::NbrList_freelinklist | ( | ) |
| void MDFrame::NbrList_init | ( | int | , | |
| int | ||||
| ) |
| void MDFrame::NbrList_initcell | ( | int | , | |
| int | , | |||
| int | , | |||
| int | ||||
| ) |
| void MDFrame::NbrList_initlinklist | ( | int | ) |
| bool MDFrame::NbrList_needrefresh | ( | ) |
| void MDFrame::NbrList_print | ( | ) |
Referenced by exec().
| virtual void MDFrame::NbrList_reconstruct | ( | int | iatom = -1 |
) | [virtual] |
Reimplemented in MEAMFrame.
| void MDFrame::NbrList_reconstruct_use_cell_list | ( | int | iatom = -1 |
) |
| void MDFrame::NbrList_reconstruct_use_link_list | ( | int | iatom = -1 |
) |
| void MDFrame::NbrList_refresh | ( | ) |
| void MDFrame::NbrListPlot_init | ( | int | , | |
| int | ||||
| ) |
| void MDFrame::NbrListPlot_reconstruct | ( | ) |
Referenced by exec().
| void MDFrame::nebrelax | ( | ) |
Referenced by exec().
| void MDFrame::NPH_Gear6 | ( | ) |
Definition at line 310 of file integrators.cpp.
References _ATOMMASS, _BOXDAMP, _F, _GH, _NP, _SR, _TIMESTEP, _VH, _VSR, _WALLMASS, calcprop(), call_potential(), conj_fixboxvec, F02, F12, F32, F42, F52, fixed, Gear6_init(), h2real, Matrix33::inv(), MASSCONVERT, npold, s2, s2real, s3, s4, s5, species, and Matrix33::tran().
| void MDFrame::NPH_VVerlet | ( | int | nstep | ) |
Definition at line 1082 of file integrators.cpp.
References _NP, _SR, _VH, _VSR, conj_fixboxvec, fixed, npold, Realloc, s2, step0, VVerlet_Get_h2(), and VVerlet_Get_s2().
| void MDFrame::NPH_VVerlet_Explicit_1 | ( | int | nstep | ) |
Definition at line 1145 of file integrators.cpp.
References _NP, _SR, _VH, _VSR, conj_fixboxvec, Matrix33::eye(), fixed, Matrix33::inv(), npold, Realloc, s2, Matrix33::set(), step0, Matrix33::tran(), VVerlet_Get_h2(), and VVerlet_Get_s2().
| void MDFrame::NPT_Gear6 | ( | ) |
Definition at line 415 of file integrators.cpp.
References _ATOMMASS, _BOXDAMP, _F, _GH, _NP, _SR, _T, _TDES, _TIMESTEP, _VH, _VSR, _WALLMASS, calcprop(), call_potential(), conj_fixboxvec, F02, F12, F32, F42, F52, fixed, Gear6_init(), h2real, Matrix33::inv(), MASSCONVERT, npold, s2, s2real, s3, s4, s5, species, Matrix33::tran(), vt2, zeta, zeta2, zeta3, zeta4, zeta5, zetaa, and zetav.
| void MDFrame::NPT_VVerlet_Explicit_1 | ( | int | nstep | ) |
Definition at line 1233 of file integrators.cpp.
| void MDFrame::NPT_VVerlet_Explicit_2 | ( | int | nstep | ) |
Definition at line 1238 of file integrators.cpp.
| void MDFrame::NPT_VVerlet_Implicit | ( | int | nstep | ) |
Definition at line 1228 of file integrators.cpp.
| void MDFrame::NPTC_Gear6 | ( | ) |
Definition at line 539 of file integrators.cpp.
References _ATOMMASS, _BOXDAMP, _F, _GH, _KATOM, _NP, _NPfree, _SR, _TDES, _TIMESTEP, _VH, _VSR, _WALLMASS, calcprop(), call_potential(), conj_fixboxvec, F02, F12, F32, F42, F52, fixed, Gear6_init(), h2real, Matrix33::inv(), KB, MASSCONVERT, MAXNHCLEN, NHChainLen, NHMass, npold, s2, s2real, s3, s4, s5, species, SQR, Matrix33::tran(), zetaNHC, zetaNHC2, zetaNHC3, zetaNHC4, zetaNHC5, zetaNHCa, and zetaNHCv.
| void MDFrame::NVE_Gear6 | ( | ) |
Definition at line 28 of file integrators.cpp.
References _ATOMMASS, _F, _NP, _SR, _TIMESTEP, _VSR, calcprop(), call_potential(), F02, F12, F32, F42, F52, fixed, Gear6_init(), Matrix33::inv(), MASSCONVERT, npold, s2, s2real, s3, s4, s5, and species.
| void MDFrame::NVE_VVerlet | ( | int | nstep | ) |
| void MDFrame::NVT_Gear6 | ( | ) |
Definition at line 91 of file integrators.cpp.
References _ATOMMASS, _F, _KATOM, _NP, _NPfree, _SR, _T, _TDES, _TIMESTEP, _VSR, calcprop(), call_potential(), F02, F12, F32, F42, F52, fixed, Gear6_init(), Matrix33::inv(), KB, MASSCONVERT, NHMass, npold, s2, s2real, s3, s4, s5, species, vt2, zeta, zeta2, zeta3, zeta4, zeta5, zetaa, and zetav.
| void MDFrame::NVT_VVerlet_Explicit_1 | ( | int | nstep | ) |
| void MDFrame::NVT_VVerlet_Explicit_2 | ( | int | nstep | ) |
| void MDFrame::NVT_VVerlet_Implicit | ( | int | nstep | ) |
| void MDFrame::NVTC_Gear6 | ( | ) |
Definition at line 186 of file integrators.cpp.
References _ATOMMASS, _F, _KATOM, _NP, _NPfree, _SR, _TDES, _TIMESTEP, _VSR, calcprop(), call_potential(), F02, F12, F32, F42, F52, fixed, Gear6_init(), Matrix33::inv(), KB, MASSCONVERT, MAXNHCLEN, NHChainLen, NHMass, npold, s2, s2real, s3, s4, s5, species, SQR, zetaNHC, zetaNHC2, zetaNHC3, zetaNHC4, zetaNHC5, zetaNHCa, and zetaNHCv.
| void MDFrame::NVTC_VVerlet_Explicit | ( | int | nstep | ) |
| int MDFrame::openFFScnfile | ( | ) |
Referenced by exec().
| int MDFrame::openintercnfile | ( | ) |
Referenced by exec().
| int MDFrame::openpropfile | ( | ) |
Referenced by exec().
| virtual void MDFrame::openwin | ( | ) | [virtual] |
Referenced by exec().
| int MDFrame::openwindow | ( | int | w, | |
| int | h, | |||
| const char * | n | |||
| ) |
| void MDFrame::pbcshiftatom | ( | ) |
Referenced by exec().
| void MDFrame::perturbevelocity | ( | ) |
Referenced by exec().
| void MDFrame::PME | ( | ) |
Definition at line 597 of file ewald.cpp.
References _EPOT_Ewald, _EPOT_Ewald_Real, _EPOT_Ewald_Rec, _EPOT_Ewald_Self, _EPOT_IND_Ewald, _EPOT_IND_Ewald_Real, _EPOT_IND_Ewald_Rec, _F_Ewald, _F_Ewald_Real, _F_Ewald_Rec, _NP, _VIRIAL_Ewald, _VIRIAL_Ewald_Real, _VIRIAL_Ewald_Rec, CE_Real(), and PME_Rec().
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), exec(), and BKSFrame::potential().
| void MDFrame::PME_cal_bsp_Bm | ( | int | mi, | |
| int | Ki | |||
| ) |
Definition at line 801 of file ewald.cpp.
References M_PI, PME_bsp_Mk, PME_bsp_n, PME_R_bsp_Bm, and SQR.
Referenced by PME_init().
| double MDFrame::PME_cal_bsp_Cm | ( | int | m1, | |
| int | m2, | |||
| int | m3 | |||
| ) |
Definition at line 837 of file ewald.cpp.
References Ewald_Alpha, Ewald_cell_V, Ewald_H_L1, Ewald_H_L2, Ewald_H_L3, M_PI, PME_K1, PME_K2, PME_K3, and SQR.
Referenced by PME_init(), and PME_Rec().
| void MDFrame::PME_cal_bsp_fac | ( | ) |
Definition at line 734 of file ewald.cpp.
References PME_bsp_fac, and PME_bsp_n.
Referenced by PME_init().
| void MDFrame::PME_cal_bsp_Mk | ( | ) |
Definition at line 755 of file ewald.cpp.
References PME_bsp_Mk, PME_bsp_n, and PME_cal_bsp_Mu().
Referenced by PME_init().
| double MDFrame::PME_cal_bsp_Mu | ( | int | n, | |
| double | u | |||
| ) |
Definition at line 770 of file ewald.cpp.
References PME_bsp_fac.
Referenced by PME_cal_bsp_Mk(), and PME_Rec().
| void MDFrame::PME_clear | ( | ) |
Definition at line 1124 of file ewald.cpp.
References _UR, PME_BC, PME_bsp_fac, PME_bsp_Mk, PME_CONV, PME_d1MU1, PME_d1MU2, PME_d1MU3, PME_d2MU1, PME_d2MU2, PME_d2MU3, PME_fft_plan1, PME_fft_plan2, PME_IQ, PME_m1, PME_m1mod, PME_m1s, PME_m2, PME_m2mod, PME_m2s, PME_m3, PME_m3mod, PME_m3s, PME_MU1, PME_MU2, PME_MU3, PME_Q, PME_x1, PME_x2, and PME_x3.
Referenced by exec().
| void MDFrame::PME_init | ( | ) |
Definition at line 616 of file ewald.cpp.
References _NP, _UR, Ewald_Alpha, Ewald_Rcut, PME_B, PME_BC, PME_bsp_fac, PME_bsp_Mk, PME_bsp_n, PME_C, PME_cal_bsp_Bm(), PME_cal_bsp_Cm(), PME_cal_bsp_fac(), PME_cal_bsp_Mk(), PME_CONV, PME_d1MU1, PME_d1MU2, PME_d1MU3, PME_d2MU1, PME_d2MU2, PME_d2MU3, PME_fft_plan1, PME_fft_plan2, PME_IQ, PME_K1, PME_K123, PME_K123d, PME_K123S, PME_K1d, PME_K2, PME_K23, PME_K23S, PME_K2d, PME_K3, PME_K3d, PME_K3S, PME_m1, PME_m1mod, PME_m1s, PME_m2, PME_m2mod, PME_m2s, PME_m3, PME_m3mod, PME_m3s, PME_MU1, PME_MU2, PME_MU3, PME_Q, PME_R_bsp_Bm, PME_x1, PME_x2, PME_x3, Realloc, and SQR.
Referenced by Ewald_init().
| void MDFrame::PME_Rec | ( | ) |
Definition at line 864 of file ewald.cpp.
References _ATOMCHARGE, _EPOT_Ewald_Rec, _EPOT_IND_Ewald_Rec, _F_Ewald_Rec, _NP, _SR, _UR, _VIRIAL_Ewald_Rec, Vector3::clear(), Matrix33::clear(), conj_fixbox, Ewald_Alpha, Ewald_cell_V, Ewald_H_L1, Ewald_H_L2, Ewald_H_L3, fixed, int(), M_PI, P_SQRT_CLMB, PME_B, PME_BC, PME_bsp_n, PME_C, PME_cal_bsp_Cm(), PME_cal_bsp_Mu(), PME_CONV, PME_d1MU1, PME_d1MU2, PME_d1MU3, PME_d2MU1, PME_d2MU2, PME_d2MU3, PME_eREC, PME_fft_plan1, PME_fft_plan2, PME_int_mod, PME_IQ, PME_K1, PME_K123d, PME_K1d, PME_K2, PME_K23, PME_K23S, PME_K2d, PME_K3, PME_K3d, PME_K3S, PME_m1, PME_m1mod, PME_m1s, PME_m2, PME_m2mod, PME_m2s, PME_m3, PME_m3mod, PME_m3s, PME_MU1, PME_MU2, PME_MU3, PME_Q, PME_sREC, PME_x1, PME_x2, PME_x3, species, SQR, Vector3::x, Vector3::y, and Vector3::z.
Referenced by PME().
| virtual void MDFrame::potential | ( | ) | [virtual] |
Reimplemented in ALGLUEFrame, BMBFrame, EAMFrame, FSFrame, LJFrame, LJ2Frame, LJBONDFrame, LJDIMERFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, MEAMFrame, RODSFrame, SIEDIPFrame, BKSFrame, SWFrame, SWFrame, SWFrame, SWFrame, TersoffFrame, and VaspBox.
| virtual double MDFrame::potential_energyonly | ( | int | iatom | ) | [virtual] |
| virtual void MDFrame::potential_energyonly | ( | ) | [virtual] |
| static void MDFrame::potential_wrapper | ( | int * | n, | |
| double | x[], | |||
| double * | f, | |||
| double | df[] | |||
| ) | [static] |
| static void MDFrame::potential_wrapper_c | ( | int | n, | |
| double | x[], | |||
| double * | f, | |||
| double | df[] | |||
| ) | [static] |
| void MDFrame::printatoms_in_sphere | ( | ) |
Referenced by exec().
| void MDFrame::printResult | ( | ) |
| void MDFrame::R0toR | ( | ) |
| void MDFrame::randomposition | ( | ) |
Referenced by exec().
| int MDFrame::readcn | ( | ) |
Referenced by exec().
| void MDFrame::readHessian | ( | ) |
Referenced by exec().
| int MDFrame::readLAMMPS | ( | ) |
Referenced by exec().
| int MDFrame::readMDCASK | ( | ) |
Referenced by exec().
| int MDFrame::readMDCASKJAIME | ( | ) |
Referenced by exec().
| int MDFrame::readPOSCAR | ( | ) |
Referenced by exec().
| void MDFrame::readRASMOLXYZ | ( | char * | fname | ) |
Referenced by exec().
| int MDFrame::readRchain | ( | ) |
Referenced by exec().
| int MDFrame::readXYZ | ( | ) |
Referenced by exec().
| void MDFrame::redefinepbc | ( | ) |
Referenced by exec().
| void MDFrame::relabelatom | ( | ) |
Referenced by exec().
| int MDFrame::relax | ( | ) |
Referenced by exec().
| void MDFrame::relax_by_group | ( | double * | ) |
Referenced by exec().
| void MDFrame::removeellipsoid | ( | ) |
Referenced by exec().
| void MDFrame::removefixedatoms | ( | ) |
Referenced by BMBFrame::dope_Yttria(), and exec().
| void MDFrame::removeoverlapatoms | ( | ) |
Referenced by exec().
| void MDFrame::removerectbox | ( | ) |
Referenced by exec().
| void MDFrame::removetorquehandle | ( | ) |
| void MDFrame::replacefreeatom | ( | ) |
Referenced by exec().
| void MDFrame::restoreH | ( | ) |
Referenced by exec().
| void MDFrame::reversefixedatoms | ( | ) |
Referenced by exec().
| void MDFrame::reversespecies | ( | ) |
Referenced by exec().
| void MDFrame::RHtoS | ( | ) |
Referenced by exec(), RODSFrame::final_structure(), and RODSFrame::init_structure().
| void MDFrame::rotate | ( | ) |
Referenced by exec().
| void MDFrame::rotate_com | ( | ) |
Referenced by exec().
| void MDFrame::RtoR0 | ( | ) |
| virtual void MDFrame::run | ( | ) | [virtual] |
Referenced by exec().
| void MDFrame::runcommand | ( | ) |
Definition at line 656 of file md.cpp.
References command, ncom, Organizer::nolog, and LFile::SubHomeDir().
Referenced by exec().
| int MDFrame::runMC | ( | ) |
Referenced by exec().
| int MDFrame::runMCSWITCH | ( | ) |
Referenced by exec().
| int MDFrame::runMDSWITCH | ( | ) |
Referenced by exec().
| int MDFrame::runTAMC | ( | ) |
Referenced by exec().
| void MDFrame::saveH | ( | ) |
Referenced by exec().
| virtual void MDFrame::saveintercn | ( | int | ) | [virtual] |
| void MDFrame::saverot | ( | ) |
Referenced by exec().
| void MDFrame::scaleH | ( | ) |
Referenced by exec().
| void MDFrame::scaleVel | ( | ) |
Referenced by exec().
| void MDFrame::setconfig1 | ( | ) |
Referenced by exec().
| void MDFrame::setconfig2 | ( | ) |
Referenced by exec().
| int MDFrame::setFFSfilecounter | ( | ) |
Referenced by exec().
| int MDFrame::setfilecounter | ( | ) |
Referenced by exec().
| void MDFrame::setfixbufferatoms | ( | ) |
| void MDFrame::setfixedatomsgroup | ( | ) |
Referenced by exec().
| void MDFrame::setfixedatomsspecies | ( | ) |
Referenced by exec().
| void MDFrame::setgroupcomvel | ( | ) |
Referenced by exec().
| void MDFrame::setH | ( | ) |
Referenced by exec().
| void MDFrame::shiftbox | ( | ) |
Referenced by exec().
| void MDFrame::SHtoR | ( | ) |
| void MDFrame::splicecn | ( | ) |
Referenced by exec().
| int MDFrame::statedistance | ( | ) |
Referenced by exec().
| void MDFrame::strelax | ( | ) |
Referenced by exec().
| double MDFrame::SWITCH_Find_Lambda | ( | ) |
| void MDFrame::switchconfig | ( | ) |
Referenced by exec().
| void MDFrame::SWITCHpotential | ( | double | lambda | ) |
| void MDFrame::SWITCHpotential_energyonly | ( | double | lambda | ) |
| virtual void MDFrame::SWITCHpotential_user | ( | double | lambda | ) | [virtual] |
Reimplemented in LJDIMERFrame, and SWFrame.
| virtual void MDFrame::SWITCHpotential_user_energyonly | ( | double | lambda | ) | [virtual] |
| void MDFrame::testpotential | ( | ) |
Referenced by exec().
| void MDFrame::translate_com | ( | ) |
Referenced by exec().
| void MDFrame::VVerlet_Get_h2 | ( | ) |
Definition at line 1272 of file integrators.cpp.
References _ATOMMASS, _BOXDAMP, _GH, _TIMESTEP, _VH, _WALLMASS, calcprop(), conj_fixboxvec, and MASSCONVERT.
Referenced by NPH_VVerlet(), and NPH_VVerlet_Explicit_1().
| void MDFrame::VVerlet_Get_s2 | ( | ) |
Definition at line 1246 of file integrators.cpp.
References _ATOMMASS, _F, _NP, _TIMESTEP, AVO, calcprop(), call_potential(), EV, fixed, Matrix33::inv(), s2, and species.
Referenced by NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NVE_VVerlet(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), and NVTC_VVerlet_Explicit().
| void MDFrame::VVerlet_Get_Tinst | ( | ) |
Definition at line 1306 of file integrators.cpp.
References _ATOMMASS, _KATOM, _NP, _NPfree, _T, _TIMESTEP, _VR, _VSR, fixed, KB, MASSCONVERT, Vector3::norm2(), and species.
Referenced by NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), and VVerlet_NHCINT().
| void MDFrame::VVerlet_NHCINT | ( | ) |
Definition at line 1332 of file integrators.cpp.
References _KATOM, _NP, _NPfree, _TDES, _TIMESTEP, _VSR, KB, NHChainLen, NHMass, SQR, VVerlet_Get_Tinst(), zetaNHC, zetaNHCa, and zetaNHCv.
Referenced by NVTC_VVerlet_Explicit().
| virtual void MDFrame::winplot | ( | int | ) | [virtual] |
| virtual void MDFrame::winplot | ( | ) | [virtual] |
| void MDFrame::wintogglepause | ( | ) |
Referenced by exec().
| virtual void MDFrame::writeatomeyecfgfile | ( | char * | fname | ) | [virtual] |
Referenced by exec().
| void MDFrame::writeatomtv | ( | char * | fname | ) |
Referenced by exec().
| int MDFrame::writeavgcnfile | ( | int | zip = 1, |
|
| bool | bg = true | |||
| ) |
Referenced by exec().
| void MDFrame::writeENERGY | ( | char * | fname | ) |
Referenced by exec().
| int MDFrame::writeFFScnfile | ( | int | zip = 1, |
|
| bool | bg = false | |||
| ) |
Referenced by exec().
| int MDFrame::writefinalcnfile | ( | int | zip = 1, |
|
| bool | bg = true | |||
| ) |
Referenced by exec().
| void MDFrame::writeFORCE | ( | char * | fname | ) |
Referenced by exec().
| void MDFrame::writefortraninifile | ( | char * | fname | ) |
| int MDFrame::writeintercnfile | ( | int | zip = 1, |
|
| bool | bg = false | |||
| ) |
Referenced by exec().
| int MDFrame::writeLAMMPS | ( | ) |
Referenced by exec().
| int MDFrame::writeMDCASK | ( | ) |
Referenced by exec().
| void MDFrame::writeMDCASKXYZ | ( | char * | fname | ) |
Referenced by exec().
| void MDFrame::writePINYMD | ( | char * | fname | ) |
Referenced by exec().
| int MDFrame::writePOSCAR | ( | ) |
Referenced by exec().
| void MDFrame::writePOSITION | ( | char * | fname | ) |
Referenced by exec().
| void MDFrame::writepovray | ( | char * | fname | ) |
Referenced by exec().
| void MDFrame::writeRASMOLXYZ | ( | char * | fname | ) |
Referenced by exec().
| int MDFrame::writeRchain | ( | ) |
Referenced by exec().
Member Data Documentation
| double MDFrame::_ATOMCHARGE[MAXSPECIES] |
Definition at line 296 of file md.h.
Referenced by CE_Real(), CE_Rec(), Ewald_init(), initparser(), and PME_Rec().
| double MDFrame::_ATOMMASS[MAXSPECIES] |
Definition at line 295 of file md.h.
Referenced by initparser(), MDFrame(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), NVTC_Gear6(), MEAMFrame::read_files(), VVerlet_Get_h2(), VVerlet_Get_s2(), and VVerlet_Get_Tinst().
| double MDFrame::_ATOMTCPL |
| double MDFrame::_BENDMOMENT |
| double * MDFrame::_BENDMOMENT_IND |
| double MDFrame::_BOXDAMP |
Definition at line 301 of file md.h.
Referenced by initparser(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), and VVerlet_Get_h2().
| double MDFrame::_BOXTCPL |
| class Vector3 MDFrame::_COM |
| double MDFrame::_Dexx |
| double MDFrame::_ECOH |
| double MDFrame::_ECSPRING |
| double MDFrame::_EPOT |
Definition at line 284 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), BMBFrame::born_meyer_buckingham_Ewald(), SIEDIPFrame::edip(), FSFrame::finnis_sinclair(), initparser(), EAMFrame::kraeam(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), MEAMFrame::MEAM(), BKSFrame::potential(), VaspBox::readoutcarstress(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), RODSFrame::rods_potential(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), TersoffFrame::tersoff(), and VaspBox::writeZXCGR().
| double MDFrame::_EPOT0 |
| double MDFrame::_EPOT0_ext |
| double MDFrame::_EPOT_BOX |
| double MDFrame::_EPOT_Ewald |
Definition at line 442 of file md.h.
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), CE(), initparser(), PME(), and BKSFrame::potential().
| double MDFrame::_EPOT_Ewald_Real |
| double MDFrame::_EPOT_Ewald_Rec |
| double MDFrame::_EPOT_Ewald_Self |
| double * MDFrame::_EPOT_IND |
Definition at line 284 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), BMBFrame::born_meyer_buckingham_Ewald(), SIEDIPFrame::edip(), FSFrame::finnis_sinclair(), EAMFrame::kraeam(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), MEAMFrame::MEAM(), RODSFrame::plot(), BKSFrame::potential(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), RODSFrame::rods_potential(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), and TersoffFrame::tersoff().
| double* MDFrame::_EPOT_IND_Ewald |
Definition at line 435 of file md.h.
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), CE(), Ewald_init(), PME(), and BKSFrame::potential().
| double * MDFrame::_EPOT_IND_Ewald_Real |
| double * MDFrame::_EPOT_IND_Ewald_Rec |
| double* MDFrame::_EPOT_RMV |
Definition at line 285 of file md.h.
Referenced by SWFrame::stillinger_weber(), and SWFrame::stillinger_weber_energyonly().
| double MDFrame::_ESTRAIN |
| double MDFrame::_EXTPRESSADD |
| class Matrix33 MDFrame::_EXTSTRESS |
Definition at line 350 of file md.h.
Referenced by VaspBox::calgh(), initparser(), and VaspBox::scalebox().
| double MDFrame::_EXTSTRESSMUL |
| class Vector3* MDFrame::_F |
Definition at line 269 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), BMBFrame::born_meyer_buckingham_Ewald(), MEAMFrame::dscrfor(), SIEDIPFrame::edip(), FSFrame::finnis_sinclair(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), LJDIMERFrame::lennard_jones_dimer_constrained(), MEAMFrame::MEAM(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), NVTC_Gear6(), RODSFrame::plot(), BKSFrame::potential(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), RODSFrame::rods_potential(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), TersoffFrame::tersoff(), and VVerlet_Get_s2().
| class Vector3 * MDFrame::_F0 |
Definition at line 434 of file md.h.
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), CE(), Ewald_init(), PME(), and BKSFrame::potential().
| class Vector3 ** MDFrame::_Fc |
| class Vector3* MDFrame::_Fext |
Definition at line 271 of file md.h.
Referenced by RODSFrame::Alloc(), and RODSFrame::rods_potential().
| double MDFrame::_GAUSS_EPSILON |
| double MDFrame::_GAUSS_RC |
| double MDFrame::_GAUSS_SIGMA |
| class Matrix33 MDFrame::_GH |
Definition at line 367 of file md.h.
Referenced by initparser(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), and VVerlet_Get_h2().
| class Matrix33 _H MDFrame::_H0 |
| double MDFrame::_HELM |
| double MDFrame::_HELMP |
| double MDFrame::_HPRECOND |
| double MDFrame::_I12_EPSILON |
| double MDFrame::_I12_RC |
| double MDFrame::_I12_SIGMA |
| double MDFrame::_KATOM |
Definition at line 294 of file md.h.
Referenced by initparser(), NPTC_Gear6(), NVT_Gear6(), NVT_VVerlet_Implicit(), NVTC_Gear6(), VVerlet_Get_Tinst(), and VVerlet_NHCINT().
| double MDFrame::_KBOX |
| int* MDFrame::_Lam_array |
| int * MDFrame::_Lam_check |
| double MDFrame::_LAMBDA |
| double MDFrame::_LAMBDA0 |
| double MDFrame::_LAMBDA1 |
| double* MDFrame::_nebinterp |
| int MDFrame::_NIC |
| int MDFrame::_NNM |
Definition at line 315 of file md.h.
Referenced by ALGLUEFrame::al_glue(), initparser(), MEAMFrame::NbrList_translate(), and MEAMFrame::screen().
| int MDFrame::_NP |
Definition at line 262 of file md.h.
Referenced by ALGLUEFrame::al_glue(), RODSFrame::Alloc(), LJBONDFrame::Alloc(), FSFrame::Alloc(), EAMFrame::Alloc(), ALGLUEFrame::Alloc(), allocQLM(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), BMBFrame::born_meyer_buckingham_Ewald(), calcrystalorder(), CE(), CE_enumKV(), CE_fillSinCosTables(), CE_init(), CE_Real(), CE_Rec(), BMBFrame::dope_Yttria(), MEAMFrame::dscreen(), MEAMFrame::dscrfor(), SIEDIPFrame::edip(), Ewald_init(), RODSFrame::final_structure(), LJDIMERFrame::find_dimer_indices(), FSFrame::finnis_sinclair(), Gear6_init(), RODSFrame::init_structure(), initparser(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), LJBONDFrame::makelipids(), MEAMFrame::MEAM(), MEAMFrame::NbrList_translate(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVE_VVerlet(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), RODSFrame::plot(), PME(), PME_init(), PME_Rec(), BKSFrame::potential(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), RODSFrame::rods_potential(), MEAMFrame::screen(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), TersoffFrame::tersoff(), VVerlet_Get_s2(), VVerlet_Get_Tinst(), VVerlet_NHCINT(), and RODSFrame::zero_com_rotation().
| int MDFrame::_NP0 |
| int MDFrame::_NPfree |
Definition at line 264 of file md.h.
Referenced by initparser(), NPTC_Gear6(), NVT_Gear6(), NVTC_Gear6(), VVerlet_Get_Tinst(), and VVerlet_NHCINT().
| double MDFrame::_OMEGA |
| class Matrix33 MDFrame::_PSTRESS |
| double MDFrame::_PTHETA_COM |
| double * MDFrame::_QL |
Definition at line 406 of file md.h.
Referenced by allocQLM(), calcrystalorder(), DFS(), and DFS1().
| double* MDFrame::_QLM |
| class Vector3* MDFrame::_R |
Definition at line 266 of file md.h.
Referenced by RODSFrame::connect_nodes(), RODSFrame::final_structure(), RODSFrame::init_structure(), MEAMFrame::MEAM(), RODSFrame::plot(), RODSFrame::rods_potential(), SWFrame::stillinger_weber(), and RODSFrame::zero_com_rotation().
| class Vector3* MDFrame::_R0 |
| class Vector3** MDFrame::_Rc |
| double MDFrame::_RLIST |
Definition at line 313 of file md.h.
Referenced by Ewald_init(), ALGLUEFrame::initglue(), LJBONDFrame::initLJ(), initparser(), VaspBox::initvars(), TersoffFrame::initvars(), SWFrame::initvars(), BKSFrame::initvars(), SIEDIPFrame::initvars(), RODSFrame::initvars(), LJDIMERFrame::initvars(), LJBONDFrame::initvars(), LJ2Frame::initvars(), LJFrame::initvars(), EAMFrame::readeam(), MEAMFrame::readMEAM(), FSFrame::readpot(), and SWFrame::stillinger_weber().
| class Matrix33 MDFrame::_SIGMA |
| double MDFrame::_SKIN |
Definition at line 313 of file md.h.
Referenced by Ewald_init(), ALGLUEFrame::initglue(), LJBONDFrame::initLJ(), initparser(), TersoffFrame::initvars(), SWFrame::initvars(), BKSFrame::initvars(), SIEDIPFrame::initvars(), RODSFrame::initvars(), LJDIMERFrame::initvars(), LJBONDFrame::initvars(), LJ2Frame::initvars(), LJFrame::initvars(), EAMFrame::readeam(), MEAMFrame::readMEAM(), FSFrame::readpot(), and SWFrame::stillinger_weber().
| class Vector3 * MDFrame::_SR |
Definition at line 266 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), calcrystalorder(), CE_fillSinCosTables(), CE_Real(), DFS(), DFS1(), MEAMFrame::dscreen(), MEAMFrame::dscrfor(), SIEDIPFrame::edip(), exec(), FSFrame::finnis_sinclair(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), LJDIMERFrame::lennard_jones_dimer_constrained(), LJBONDFrame::makelipids(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVE_VVerlet(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), RODSFrame::plot(), PME_Rec(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), MEAMFrame::screen(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), TersoffFrame::tersoff(), and RODSFrame::zero_com_rotation().
| class Vector3* MDFrame::_SR1 |
| class Vector3 * MDFrame::_SR2 |
| class Vector3 * MDFrame::_SR3 |
| class Vector3* MDFrame::_SRA |
| double MDFrame::_T |
Definition at line 298 of file md.h.
Referenced by initparser(), NPT_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), and VVerlet_Get_Tinst().
| double MDFrame::_TDES |
Definition at line 298 of file md.h.
Referenced by initparser(), NPT_Gear6(), NPTC_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), and VVerlet_NHCINT().
| double MDFrame::_TIMESTEP |
Definition at line 297 of file md.h.
Referenced by initparser(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), VVerlet_Get_h2(), VVerlet_Get_s2(), VVerlet_Get_Tinst(), and VVerlet_NHCINT().
| double* MDFrame::_TOPOL |
Definition at line 289 of file md.h.
Referenced by calcrystalorder(), DFS(), DFS1(), RODSFrame::plot(), and SWFrame::stillinger_weber().
| double MDFrame::_TORQUE |
| double * MDFrame::_TORQUE_IND |
| double MDFrame::_TOTPRESSURE |
| class Matrix33 MDFrame::_TOTSTRESS |
| double MDFrame::_VACUUMRATIO |
| class Matrix33 _VIRIAL MDFrame::_VH |
Definition at line 282 of file md.h.
Referenced by initparser(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), and VVerlet_Get_h2().
Definition at line 436 of file md.h.
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), CE(), initparser(), PME(), and BKSFrame::potential().
| class Matrix33* MDFrame::_VIRIAL_IND |
Definition at line 283 of file md.h.
Referenced by MEAMFrame::dscrfor(), MEAMFrame::kraMEAM(), MEAMFrame::MEAM(), MEAMFrame::rhoMEAM(), and SWFrame::stillinger_weber().
| class Vector3* MDFrame::_VR |
Definition at line 268 of file md.h.
Referenced by VVerlet_Get_Tinst(), and RODSFrame::zero_com_rotation().
| class Vector3 * MDFrame::_VSR |
Definition at line 268 of file md.h.
Referenced by LJDIMERFrame::lennard_jones_dimer_constrained(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVE_VVerlet(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), VVerlet_Get_Tinst(), VVerlet_NHCINT(), and RODSFrame::zero_com_rotation().
| double MDFrame::_WALLMASS |
Definition at line 295 of file md.h.
Referenced by initparser(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), and VVerlet_Get_h2().
| double MDFrame::_WAVG |
| double MDFrame::_WTOT |
| double MDFrame::_XPRECOND |
| double MDFrame::_YPRECOND |
| double MDFrame::_ZPRECOND |
Definition at line 528 of file md.h.
Referenced by RODSFrame::Alloc(), LJBONDFrame::Alloc(), FSFrame::Alloc(), EAMFrame::Alloc(), ALGLUEFrame::Alloc(), and initparser().
| double MDFrame::annealspec[10] |
| char MDFrame::atomcolor[MAXSPECIES][30] |
| char MDFrame::atomeyeexe[100] |
| char MDFrame::atomeyepath[100] |
| int MDFrame::atomeyerepeat[4] |
| double MDFrame::atomradius[MAXSPECIES] |
| class AVGCNFile MDFrame::avgcn |
| char MDFrame::backgroundcolor[30] |
| double MDFrame::bendspec[4] |
| char MDFrame::bondcolor[30] |
| double MDFrame::bondlength |
| double MDFrame::bondradius |
| clock_t MDFrame::CE_eREAL |
| clock_t MDFrame::CE_eREC |
| double MDFrame::CE_iREAL |
| double MDFrame::CE_iREC |
| double MDFrame::CE_Kc |
| struct MDFrame::K_rec * MDFrame::CE_KV |
Referenced by CE_clear(), CE_enumKV(), and CE_Rec().
| int MDFrame::CE_Mka |
Definition at line 447 of file md.h.
Referenced by CE_enumKV(), CE_fillSinCosTables(), and CE_init().
| int MDFrame::CE_Mkb |
Definition at line 447 of file md.h.
Referenced by CE_enumKV(), CE_fillSinCosTables(), and CE_init().
| int MDFrame::CE_Mkc |
Definition at line 447 of file md.h.
Referenced by CE_enumKV(), CE_fillSinCosTables(), and CE_init().
| int MDFrame::CE_MKV |
| int MDFrame::CE_nKV |
Definition at line 452 of file md.h.
Referenced by CE_clear(), CE_enumKV(), CE_fillSinCosTables(), and CE_Rec().
Definition at line 452 of file md.h.
Referenced by CE_enumKV(), CE_fillSinCosTables(), and CE_Rec().
Definition at line 452 of file md.h.
Referenced by CE_enumKV(), CE_fillSinCosTables(), and CE_Rec().
| clock_t MDFrame::CE_sREAL |
| clock_t MDFrame::CE_sREC |
| double MDFrame::CE_tREAL |
| double MDFrame::CE_tREC |
| char* MDFrame::cell_mem |
| int**** MDFrame::celllist |
| double* MDFrame::color_ind |
| char MDFrame::colornames[MAXCOLORS][30] |
| unsigned MDFrame::colors[MAXCOLORS+15] |
| char MDFrame::command[MAXCMDLEN] |
| double MDFrame::conj_dfpred |
| double MDFrame::conj_f |
Definition at line 361 of file md.h.
Referenced by initparser(), initvars(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), and VVerlet_Get_h2().
| double MDFrame::conj_ftol |
| double MDFrame::conj_g2res |
| double* MDFrame::conj_space |
| double MDFrame::constrain_dist |
| int MDFrame::constrainatoms[MAXCONSTRAINATOMS] |
| double MDFrame::constrainF |
| double MDFrame::constrainS |
| double MDFrame::constrainS_inst |
| char MDFrame::crystalstructure[30] |
| int MDFrame::curstep |
| double MDFrame::dEdlambda |
Definition at line 388 of file md.h.
Referenced by initparser(), LJDIMERFrame::lennard_jones_dimer_constrained(), and SWFrame::stillinger_weber_switch_3body().
| class Matrix33 MDFrame::dH |
| double MDFrame::dlambdadt |
| class Vector3 MDFrame::dscom12 |
| char MDFrame::element[MAXSPECIES][10] |
Definition at line 279 of file md.h.
Referenced by initparser(), initvars(), MEAMFrame::read_files(), and MEAMFrame::rhoMEAM().
| char MDFrame::ensemble_type[100] |
| double MDFrame::Ewald_Alpha |
Definition at line 443 of file md.h.
Referenced by CE_init(), CE_Real(), CE_Rec(), Ewald_init(), initparser(), PME_cal_bsp_Cm(), PME_init(), and PME_Rec().
Definition at line 437 of file md.h.
Referenced by BMBFrame::born_meyer_buckingham_Ewald(), Ewald_init(), initparser(), and BKSFrame::potential().
| double MDFrame::Ewald_cell_V |
Definition at line 444 of file md.h.
Referenced by CE_enumKV(), CE_Rec(), Ewald_init(), PME_cal_bsp_Cm(), and PME_Rec().
| double MDFrame::Ewald_H_L1 |
Definition at line 444 of file md.h.
Referenced by CE_enumKV(), CE_Rec(), Ewald_init(), PME_cal_bsp_Cm(), and PME_Rec().
| double MDFrame::Ewald_H_L2 |
Definition at line 444 of file md.h.
Referenced by CE_enumKV(), CE_Rec(), Ewald_init(), PME_cal_bsp_Cm(), and PME_Rec().
| double MDFrame::Ewald_H_L3 |
Definition at line 444 of file md.h.
Referenced by CE_enumKV(), CE_Rec(), Ewald_init(), PME_cal_bsp_Cm(), and PME_Rec().
| double MDFrame::Ewald_precision |
| double MDFrame::Ewald_qSQRsum |
| double MDFrame::Ewald_Rcut |
Definition at line 439 of file md.h.
Referenced by BMBFrame::born_meyer_buckingham(), CE_Real(), Ewald_init(), initparser(), and PME_init().
| double MDFrame::Ewald_time_ratio |
| double MDFrame::extforce[100] |
| int MDFrame::FFS_i |
| double MDFrame::FFS_Pp |
| double MDFrame::FFScn_weight |
| char MDFrame::FFScnfile[200] |
| class CNFile initcn intercn FFScn MDFrame::finalcn |
| char MDFrame::finalcnfile[200] |
| class LAMMPSFile initlammps MDFrame::finallammps |
| class MDCASKconFile initmdcaskcon MDFrame::finalmdcaskcon |
| class MDCASKinputFile initmdcaskinput MDFrame::finalmdcaskinput |
| class POSCARFile initposcar MDFrame::finalposcar |
| bool MDFrame::firsttime |
| char MDFrame::fixatomcolor[30] |
| int* MDFrame::fixed |
Definition at line 274 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BMBFrame::born_meyer_buckingham(), CE_Real(), CE_Rec(), BMBFrame::dope_Yttria(), MEAMFrame::dscreen(), MEAMFrame::dscrfor(), SIEDIPFrame::edip(), Ewald_init(), FSFrame::finnis_sinclair(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), MEAMFrame::NbrList_translate(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVE_VVerlet(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), RODSFrame::plot(), PME_Rec(), MEAMFrame::rhoMEAM(), RODSFrame::rods_potential(), MEAMFrame::screen(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), TersoffFrame::tersoff(), VVerlet_Get_s2(), VVerlet_Get_Tinst(), and RODSFrame::zero_com_rotation().
Definition at line 532 of file md.h.
Referenced by FSFrame::finnis_sinclair(), initparser(), SWFrame::stillinger_weber(), and SWFrame::stillinger_weber_energyonly().
| double MDFrame::forcemul |
| char MDFrame::fortranexe[100] |
| char MDFrame::fortranpath[100] |
| int* MDFrame::group |
| class Matrix33 h2 h3 h4 h5 MDFrame::h2real |
| double* MDFrame::hes |
| int * MDFrame::hesind |
| int MDFrame::heslen |
| char MDFrame::highlightcolor[30] |
| int* MDFrame::image |
| char MDFrame::incnfile[200] |
Definition at line 514 of file md.h.
Referenced by exec(), initparser(), TersoffFrame::initvars(), SWFrame::initvars(), SIEDIPFrame::initvars(), initvars(), and FSFrame::initvars().
| double MDFrame::input[20000] |
Definition at line 507 of file md.h.
Referenced by assign_Lam(), BMBFrame::dope_Yttria(), exec(), initparser(), LJBONDFrame::linklipids(), LJBONDFrame::makelipids(), MDFrame(), and MEAMFrame::printpairpot().
| char MDFrame::integrator_type[100] |
| char MDFrame::intercfgfile[200] |
| char MDFrame::intercnfile[200] |
| double MDFrame::latticeconst[3] |
| double MDFrame::latticesize[3][4] |
| int* MDFrame::link_head |
| int * MDFrame::link_list |
| double MDFrame::MC_accept_ratio |
| int MDFrame::MC_atom |
| double MDFrame::MC_dfrac |
| double MDFrame::MC_dVmax |
| double MDFrame::MC_fracatom |
| double MDFrame::MC_Lambda3 |
| double MDFrame::MC_mu_ext |
| double MDFrame::MC_P_ext |
| int MDFrame::MC_switchoffatoms[10] |
| char MDFrame::MDCASKpot[50] |
| char MDFrame::myname[200] |
Definition at line 411 of file md.h.
Referenced by calcrystalorder(), FFSprocess(), and initparser().
| double MDFrame::N_lgst_index |
| double MDFrame::N_lgst_skin |
| double MDFrame::N_lgst_skin_index |
| int MDFrame::ncom |
| int MDFrame::NCS |
| int MDFrame::nebspec[10] |
Definition at line 336 of file md.h.
Referenced by initparser(), NPTC_Gear6(), NVTC_Gear6(), and VVerlet_NHCINT().
| double MDFrame::NHMass[MAXNHCLEN] |
Definition at line 339 of file md.h.
Referenced by initparser(), initvars(), NPTC_Gear6(), NVT_Gear6(), NVTC_Gear6(), and VVerlet_NHCINT().
| int** MDFrame::nindex |
Definition at line 317 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), calcrystalorder(), CE_Real(), DFS(), DFS1(), MEAMFrame::dscreen(), MEAMFrame::dscrfor(), SIEDIPFrame::edip(), FSFrame::finnis_sinclair(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), MEAMFrame::NbrList_translate(), MEAMFrame::read_files(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), MEAMFrame::screen(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), and TersoffFrame::tersoff().
| char * MDFrame::nindex_mem |
| int** MDFrame::nindex_plot |
| char* MDFrame::nindex_plot_mem |
| int* MDFrame::nn |
Definition at line 316 of file md.h.
Referenced by ALGLUEFrame::al_glue(), BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), calcrystalorder(), CE_Real(), DFS(), DFS1(), MEAMFrame::dscreen(), MEAMFrame::dscrfor(), SIEDIPFrame::edip(), FSFrame::finnis_sinclair(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), LJFrame::lennard_jones(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), MEAMFrame::NbrList_translate(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), MEAMFrame::screen(), SWFrame::stillinger_weber(), SWFrame::stillinger_weber_energyonly(), and TersoffFrame::tersoff().
| int* MDFrame::nn_plot |
| int MDFrame::npold |
Definition at line 335 of file md.h.
Referenced by Gear6_init(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVE_VVerlet(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), and NVTC_VVerlet_Explicit().
| char MDFrame::outpropfile[200] |
| double MDFrame::output_dat[2000] |
| char MDFrame::output_fmt[10000] |
| char MDFrame::output_str[10000] |
| class PropFile MDFrame::pf |
| double MDFrame::plot_color_bar[10] |
| double MDFrame::plot_color_windows[100] |
| int MDFrame::plot_highlight_atoms[10000] |
| double MDFrame::plot_limits[10] |
| double* MDFrame::PME_B |
| double* MDFrame::PME_BC |
| double* MDFrame::PME_bsp_fac |
Definition at line 475 of file md.h.
Referenced by PME_cal_bsp_fac(), PME_cal_bsp_Mu(), PME_clear(), and PME_init().
| double* MDFrame::PME_bsp_Mk |
Definition at line 474 of file md.h.
Referenced by PME_cal_bsp_Bm(), PME_cal_bsp_Mk(), PME_clear(), and PME_init().
Definition at line 458 of file md.h.
Referenced by initparser(), PME_cal_bsp_Bm(), PME_cal_bsp_fac(), PME_cal_bsp_Mk(), PME_init(), and PME_Rec().
| double* MDFrame::PME_C |
| double* MDFrame::PME_CONV |
| double* MDFrame::PME_d1MU1 |
| double * MDFrame::PME_d1MU2 |
| double * MDFrame::PME_d1MU3 |
| double* MDFrame::PME_d2MU1 |
| double * MDFrame::PME_d2MU2 |
| double * MDFrame::PME_d2MU3 |
| clock_t MDFrame::PME_eREC |
| fftw_plan MDFrame::PME_fft_plan1 |
| fftw_plan MDFrame::PME_fft_plan2 |
| double MDFrame::PME_iREC |
| int MDFrame::PME_K1 |
Definition at line 460 of file md.h.
Referenced by initparser(), PME_cal_bsp_Cm(), PME_init(), and PME_Rec().
| double MDFrame::PME_K123d |
| double MDFrame::PME_K1d |
| int MDFrame::PME_K2 |
Definition at line 460 of file md.h.
Referenced by initparser(), PME_cal_bsp_Cm(), PME_init(), and PME_Rec().
| int MDFrame::PME_K23 |
| double MDFrame::PME_K2d |
| int MDFrame::PME_K3 |
Definition at line 460 of file md.h.
Referenced by initparser(), PME_cal_bsp_Cm(), PME_init(), and PME_Rec().
| double MDFrame::PME_K3d |
| int MDFrame::PME_K3S |
| int* MDFrame::PME_m1 |
| int* MDFrame::PME_m1mod |
| int* MDFrame::PME_m1s |
| int * MDFrame::PME_m2 |
| int * MDFrame::PME_m2mod |
| int * MDFrame::PME_m2s |
| int * MDFrame::PME_m3 |
| int * MDFrame::PME_m3mod |
| int * MDFrame::PME_m3s |
| double* MDFrame::PME_MU1 |
| double * MDFrame::PME_MU2 |
| double * MDFrame::PME_MU3 |
| double* MDFrame::PME_Q |
| clock_t MDFrame::PME_sREC |
| double MDFrame::PME_tREC |
| double* MDFrame::PME_x1 |
| double * MDFrame::PME_x2 |
| double * MDFrame::PME_x3 |
| char MDFrame::potfile[100] |
Definition at line 520 of file md.h.
Referenced by initparser(), initvars(), EAMFrame::initvars(), EAMFrame::readeam(), and FSFrame::readpot().
| double MDFrame::QLM_cutoff |
| int* MDFrame::QLM_mark |
Definition at line 414 of file md.h.
Referenced by allocQLM(), calcrystalorder(), DFS(), and DFS1().
| int* MDFrame::QLM_solid |
Definition at line 415 of file md.h.
Referenced by allocQLM(), calcrystalorder(), DFS(), and DFS1().
| double MDFrame::Rc_for_QLM |
Definition at line 412 of file md.h.
Referenced by calcrystalorder(), DFS(), DFS1(), and initparser().
| double MDFrame::rc_plot |
| double MDFrame::rotateangles[5] |
Definition at line 332 of file md.h.
Referenced by MEAMFrame::dscrfor(), SIEDIPFrame::edip(), Gear6_init(), MEAMFrame::kraMEAM(), NPH_Gear6(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVE_VVerlet(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), RODSFrame::plot(), and VVerlet_Get_s2().
Definition at line 332 of file md.h.
Referenced by Gear6_init(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), and NVTC_Gear6().
Definition at line 332 of file md.h.
Referenced by MEAMFrame::dscrfor(), SIEDIPFrame::edip(), Gear6_init(), MEAMFrame::kraMEAM(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), and NVTC_Gear6().
Definition at line 332 of file md.h.
Referenced by Gear6_init(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), and NVTC_Gear6().
Definition at line 332 of file md.h.
Referenced by Gear6_init(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), and NVTC_Gear6().
| int MDFrame::savecfg |
| int MDFrame::savecn |
| int* MDFrame::species |
Definition at line 276 of file md.h.
Referenced by BKSFrame::bks_mod(), BMBFrame::born_meyer_buckingham(), CE_Real(), CE_Rec(), BMBFrame::dope_Yttria(), MEAMFrame::dscreen(), MEAMFrame::dscrfor(), Ewald_init(), LJDIMERFrame::find_dimer_indices(), EAMFrame::kraeam(), MEAMFrame::kraMEAM(), LJ2Frame::lennard_jones_2(), LJBONDFrame::lennard_jones_bond(), LJDIMERFrame::lennard_jones_dimer(), LJBONDFrame::makelipids(), MEAMFrame::MEAM(), NPH_Gear6(), NPT_Gear6(), NPTC_Gear6(), NVE_Gear6(), NVT_Gear6(), NVTC_Gear6(), RODSFrame::plot(), PME_Rec(), EAMFrame::rhoeam(), MEAMFrame::rhoMEAM(), MEAMFrame::screen(), SWFrame::stillinger_weber(), TersoffFrame::tersoff(), VVerlet_Get_s2(), and VVerlet_Get_Tinst().
| int MDFrame::step0 |
Definition at line 377 of file md.h.
Referenced by FFSprocess(), NPH_VVerlet(), NPH_VVerlet_Explicit_1(), NVE_VVerlet(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), NVT_VVerlet_Implicit(), and NVTC_VVerlet_Explicit().
| class Vector3* MDFrame::storedr |
| double MDFrame::torquespec[3] |
| double MDFrame::vt2 |
Definition at line 302 of file md.h.
Referenced by initparser(), NPT_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), and NVT_VVerlet_Implicit().
| int MDFrame::wSKIN |
| double MDFrame::zeta |
Definition at line 302 of file md.h.
Referenced by initparser(), NPT_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), and NVT_VVerlet_Implicit().
| double MDFrame::zeta2 |
| double MDFrame::zeta3 |
| double MDFrame::zeta4 |
| double MDFrame::zeta5 |
| double MDFrame::zetaa |
Definition at line 302 of file md.h.
Referenced by initparser(), NPT_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), and NVT_VVerlet_Implicit().
| double MDFrame::zetaNHC[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), and VVerlet_NHCINT().
| double MDFrame::zetaNHC2[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), and NVTC_Gear6().
| double MDFrame::zetaNHC3[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), and NVTC_Gear6().
| double MDFrame::zetaNHC4[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), and NVTC_Gear6().
| double MDFrame::zetaNHC5[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), and NVTC_Gear6().
| double MDFrame::zetaNHCa[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), and VVerlet_NHCINT().
| double MDFrame::zetaNHCv[MAXNHCLEN] |
Definition at line 337 of file md.h.
Referenced by Gear6_init(), initparser(), NPTC_Gear6(), NVTC_Gear6(), NVTC_VVerlet_Explicit(), and VVerlet_NHCINT().
| double MDFrame::zetav |
Definition at line 302 of file md.h.
Referenced by initparser(), NPT_Gear6(), NVT_Gear6(), NVT_VVerlet_Explicit_1(), NVT_VVerlet_Explicit_2(), and NVT_VVerlet_Implicit().
The documentation for this class was generated from the following files:
- My Documents/Codes/MD++.svn/trunk/src/md.h
- My Documents/Codes/MD++.svn/trunk/src/ewald.cpp
- My Documents/Codes/MD++.svn/trunk/src/ffs.cpp
- My Documents/Codes/MD++.svn/trunk/src/integrators.cpp
- My Documents/Codes/MD++.svn/trunk/src/md.cpp
