Gromacs
2018.8
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#include "gromacs/utility/basedefinitions.h"
Declares enumerated types used throughout the code.
Macros | |
#define | ETCOUPLTYPE(e) enum_name(e, etcNR, etcoupl_names) |
Macro for selecting t coupling string. | |
#define | ETC_ANDERSEN(e) (((e) == etcANDERSENMASSIVE) || ((e) == etcANDERSEN)) |
Return whether this is andersen coupling. | |
#define | EPCOUPLTYPE(e) enum_name(e, epcNR, epcoupl_names) |
Macro to return the correct pcoupling string. | |
#define | EREFSCALINGTYPE(e) enum_name(e, erscNR, erefscaling_names) |
Macro to select correct coordinate scaling string. | |
#define | EPCOUPLTYPETYPE(e) enum_name(e, epctNR, epcoupltype_names) |
Macro to select the right string for pcoupl type. | |
#define | ECUTSCHEME(e) enum_name(e, ecutsNR, ecutscheme_names) |
Macro to select the right string for cutoff scheme. | |
#define | INTMODIFIER(e) enum_name(e, eintmodNR, eintmod_names) |
Macro to select the correct string for modifiers. | |
#define | EELTYPE(e) enum_name(e, eelNR, eel_names) |
Macro for correct string for Coulomb treatment. | |
#define | EEL_RF(e) ((e) == eelRF || (e) == eelGRF || (e) == eelRF_NEC_UNSUPPORTED || (e) == eelRF_ZERO ) |
Macro telling us whether we use reaction field. | |
#define | EEL_PME(e) ((e) == eelPME || (e) == eelPMESWITCH || (e) == eelPMEUSER || (e) == eelPMEUSERSWITCH || (e) == eelP3M_AD) |
Macro telling us whether we use PME. | |
#define | EEL_PME_EWALD(e) (EEL_PME(e) || (e) == eelEWALD) |
Macro telling us whether we use PME or full Ewald. | |
#define | EEL_FULL(e) (EEL_PME_EWALD(e) || (e) == eelPOISSON) |
Macro telling us whether we use full electrostatics of any sort. | |
#define | EEL_USER(e) ((e) == eelUSER || (e) == eelPMEUSER || (e) == (eelPMEUSERSWITCH)) |
Macro telling us whether we use user defined electrostatics. | |
#define | EVDWTYPE(e) enum_name(e, evdwNR, evdw_names) |
Macro for selecting correct string for VdW treatment. | |
#define | ELJPMECOMBNAMES(e) enum_name(e, eljpmeNR, eljpme_names) |
Macro for correct LJPME comb rule name. | |
#define | EVDW_PME(e) ((e) == evdwPME) |
Macro to tell us whether we use LJPME. | |
#define | ENS(e) enum_name(e, ensNR, ens_names) |
Macro for correct NS algorithm. | |
#define | EI(e) enum_name(e, eiNR, ei_names) |
Macro returning integrator string. | |
#define | EI_VV(e) ((e) == eiVV || (e) == eiVVAK) |
Do we use velocity Verlet. | |
#define | EI_MD(e) ((e) == eiMD || EI_VV(e)) |
Do we use molecular dynamics. | |
#define | EI_SD(e) ((e) == eiSD1) |
Do we use stochastic dynamics. | |
#define | EI_RANDOM(e) (EI_SD(e) || (e) == eiBD) |
Do we use any stochastic integrator. | |
#define | EI_DYNAMICS(e) (EI_MD(e) || EI_RANDOM(e)) |
Do we use any type of dynamics. | |
#define | EI_ENERGY_MINIMIZATION(e) ((e) == eiSteep || (e) == eiCG || (e) == eiLBFGS) |
Or do we use minimization. | |
#define | EI_TPI(e) ((e) == eiTPI || (e) == eiTPIC) |
Do we apply test particle insertion. | |
#define | EI_STATE_VELOCITY(e) (EI_MD(e) || EI_SD(e)) |
Do we deal with particle velocities. | |
#define | ECONSTRTYPE(e) enum_name(e, econtNR, econstr_names) |
Macro to select the correct string. | |
#define | EDISRETYPE(e) enum_name(e, edrNR, edisre_names) |
Macro to select the right disre algorithm string. | |
#define | EDISREWEIGHTING(e) enum_name(e, edrwNR, edisreweighting_names) |
Macro corresponding to dr weighting. | |
#define | ECOMBNAME(e) enum_name(e, eCOMB_NR, ecomb_names) |
Macro to select the comb rule string. | |
#define | ENBFNAME(e) enum_name(e, eNBF_NR, enbf_names) |
Macro for correct VdW potential string. | |
#define | ESIMTEMP(e) enum_name(e, esimtempNR, esimtemp_names) |
Macro for correct tempering string. | |
#define | EFEPTYPE(e) enum_name(e, efepNR, efep_names) |
Macro corresponding to FEP string. | |
#define | ELAMSTATS_EXPANDED(e) ((e) > elamstatsNO) |
Macro telling us whether we use expanded ensemble. | |
#define | EWL(e) ((e) == elamstatsWL || (e) == elamstatsWWL) |
Macro telling us whether we use some kind of Wang-Landau. | |
#define | SEPDHDLFILETYPE(e) enum_name(e, esepdhdlfileNR, separate_dhdl_file_names) |
Monster macro for DHDL file selection. | |
#define | DHDLDERIVATIVESTYPE(e) enum_name(e, edhdlderivativesNR, dhdl_derivatives_names) |
YAMM (Yet another monster macro) | |
#define | ESOLTYPE(e) enum_name(e, esolNR, esol_names) |
Macro lest we print the wrong solvent model string. | |
#define | EDISPCORR(e) enum_name(e, edispcNR, edispc_names) |
Macro for dispcorr string. | |
#define | ECOM(e) enum_name(e, ecmNR, ecm_names) |
Macro for COM removal string. | |
#define | EANNEAL(e) enum_name(e, eannNR, eann_names) |
And macro for simulated annealing string. | |
#define | EIMPLICITSOL(e) enum_name(e, eisNR, eis_names) |
Macro for implicit solvent string. | |
#define | EGBALGORITHM(e) enum_name(e, egbNR, egb_names) |
Macro for GB string. | |
#define | ESAALGORITHM(e) enum_name(e, esaNR, esa_names) |
brief Macro for SA algorithm string. | |
#define | EWALLTYPE(e) enum_name(e, ewtNR, ewt_names) |
Macro for wall type string. | |
#define | EPULLTYPE(e) enum_name(e, epullNR, epull_names) |
Macro for pulling string. | |
#define | EPULLGEOM(e) enum_name(e, epullgNR, epullg_names) |
Macro for pull group string. | |
#define | EROTGEOM(e) enum_name(e, erotgNR, erotg_names) |
Macro for rot group names. | |
#define | EROTORIGIN(e) enum_name(e, erotgOriginNR, erotg_originnames) |
Macro for rot group origin names. | |
#define | EROTFIT(e) enum_name(e, erotgFitNR, erotg_fitnames) |
Macro for rot group fit names. | |
#define | ESWAPTYPE(e) enum_name(e, eSwapTypesNR, eSwapTypes_names) |
Macro for swapping string. | |
#define | EQMMETHOD(e) enum_name(e, eQMmethodNR, eQMmethod_names) |
Macro to pick QMMM method name. | |
#define | EQMBASIS(e) enum_name(e, eQMbasisNR, eQMbasis_names) |
Macro to pick right basis function string. | |
#define | EQMMMSCHEME(e) enum_name(e, eQMMMschemeNR, eQMMMscheme_names) |
Macro to pick QMMMM scheme name. | |
Enumerations | |
enum | eCompartment { eCompA, eCompB, eCompNR } |
The two compartments for CompEL setups. | |
enum | eChannel { eChan0, eChan1, eChanNR } |
The channels that define with their COM the compartment boundaries in CompEL setups. More... | |
enum | { etcNO, etcBERENDSEN, etcNOSEHOOVER, etcYES, etcANDERSEN, etcANDERSENMASSIVE, etcVRESCALE, etcNR } |
Temperature coupling type. More... | |
enum | { epcNO, epcBERENDSEN, epcPARRINELLORAHMAN, epcISOTROPIC, epcMTTK, epcNR } |
Pressure coupling types. More... | |
enum | { efbposresZERO, efbposresSPHERE, efbposresCYLINDER, efbposresX, efbposresY, efbposresZ, efbposresCYLINDERX, efbposresCYLINDERY, efbposresCYLINDERZ, efbposresNR } |
Flat-bottom posres geometries. | |
enum | { erscNO, erscALL, erscCOM, erscNR } |
Relative coordinate scaling type for position restraints. | |
enum | { etrtNONE, etrtNHC, etrtBAROV, etrtBARONHC, etrtNHC2, etrtBAROV2, etrtBARONHC2, etrtVELOCITY1, etrtVELOCITY2, etrtPOSITION, etrtSKIPALL, etrtNR } |
Trotter decomposition extended variable parts. | |
enum | { ettTSEQ0, ettTSEQ1, ettTSEQ2, ettTSEQ3, ettTSEQ4, ettTSEQMAX } |
Sequenced parts of the trotter decomposition. | |
enum | { epctISOTROPIC, epctSEMIISOTROPIC, epctANISOTROPIC, epctSURFACETENSION, epctNR } |
Pressure coupling type. | |
enum | { ecutsVERLET, ecutsGROUP, ecutsNR } |
\brief Cutoff scheme | |
enum | eintmod { eintmodPOTSHIFT_VERLET, eintmodPOTSHIFT, eintmodNONE, eintmodPOTSWITCH, eintmodEXACTCUTOFF, eintmodFORCESWITCH, eintmodNR } |
Coulomb / VdW interaction modifiers. More... | |
enum | { eelCUT, eelRF, eelGRF, eelPME, eelEWALD, eelP3M_AD, eelPOISSON, eelSWITCH, eelSHIFT, eelUSER, eelGB_NOTUSED, eelRF_NEC_UNSUPPORTED, eelENCADSHIFT, eelPMEUSER, eelPMESWITCH, eelPMEUSERSWITCH, eelRF_ZERO, eelNR } |
Cut-off treatment for Coulomb. More... | |
enum | { eewg3D, eewg3DC, eewgNR } |
Ewald geometry. | |
enum | { evdwCUT, evdwSWITCH, evdwSHIFT, evdwUSER, evdwENCADSHIFT, evdwPME, evdwNR } |
Van der Waals interaction treatment. | |
enum | { eljpmeGEOM, eljpmeLB, eljpmeNR } |
Type of long-range VdW treatment of combination rules. | |
enum | { ensGRID, ensSIMPLE, ensNR } |
Neighborsearching algorithm. | |
enum | { eiMD, eiSteep, eiCG, eiBD, eiSD2_REMOVED, eiNM, eiLBFGS, eiTPI, eiTPIC, eiSD1, eiVV, eiVVAK, eiNR } |
Integrator algorithm. More... | |
enum | { econtLINCS, econtSHAKE, econtNR } |
Constraint algorithm. | |
enum | { edrNone, edrSimple, edrEnsemble, edrNR } |
Distance restraint refinement algorithm. | |
enum | { edrwConservative, edrwEqual, edrwNR } |
Distance restraints weighting type. | |
enum | { eCOMB_NONE, eCOMB_GEOMETRIC, eCOMB_ARITHMETIC, eCOMB_GEOM_SIG_EPS, eCOMB_NR } |
Combination rule algorithm. | |
enum | { eNBF_NONE, eNBF_LJ, eNBF_BHAM, eNBF_NR } |
Van der Waals potential. | |
enum | { esimtempGEOMETRIC, esimtempEXPONENTIAL, esimtempLINEAR, esimtempNR } |
Simulated tempering methods. | |
enum | { efepNO, efepYES, efepSTATIC, efepSLOWGROWTH, efepEXPANDED, efepNR } |
Free energy perturbation type. More... | |
enum | { efptFEP, efptMASS, efptCOUL, efptVDW, efptBONDED, efptRESTRAINT, efptTEMPERATURE, efptNR } |
Free energy pertubation coupling types. | |
enum | { edHdLPrintEnergyNO, edHdLPrintEnergyTOTAL, edHdLPrintEnergyPOTENTIAL, edHdLPrintEnergyYES, edHdLPrintEnergyNR } |
What to print for free energy calculations. More... | |
enum | { elamstatsNO, elamstatsMETROPOLIS, elamstatsBARKER, elamstatsMINVAR, elamstatsWL, elamstatsWWL, elamstatsNR } |
How the lambda weights are calculated. More... | |
enum | { elmcmoveNO, elmcmoveMETROPOLIS, elmcmoveBARKER, elmcmoveGIBBS, elmcmoveMETGIBBS, elmcmoveNR } |
How moves in lambda are calculated. More... | |
enum | { elmceqNO, elmceqYES, elmceqWLDELTA, elmceqNUMATLAM, elmceqSTEPS, elmceqSAMPLES, elmceqRATIO, elmceqNR } |
How we decide whether weights have reached equilibrium. More... | |
enum | { esepdhdlfileYES, esepdhdlfileNO, esepdhdlfileNR } |
separate_dhdl_file selection More... | |
enum | { edhdlderivativesYES, edhdlderivativesNO, edhdlderivativesNR } |
dhdl_derivatives selection \ More... | |
enum | { esolNO, esolSPC, esolTIP4P, esolNR } |
Solvent model. More... | |
enum | { edispcNO, edispcEnerPres, edispcEner, edispcAllEnerPres, edispcAllEner, edispcNR } |
Dispersion correction. | |
enum | { ecmLINEAR, ecmANGULAR, ecmNO, ecmLINEAR_ACCELERATION_CORRECTION, ecmNR } |
Center of mass motion removal algorithm. | |
enum | { eannNO, eannSINGLE, eannPERIODIC, eannNR } |
Algorithm for simulated annealing. | |
enum | { eisNO, eisGBSA, eisNR } |
Implicit solvent algorithms. | |
enum | { egbSTILL, egbHCT, egbOBC, egbNR } |
Algorithms for calculating GB radii. | |
enum | { esaAPPROX, esaNO, esaSTILL, esaNR } |
Surface area algorithm for implicit solvent. | |
enum | { ewt93, ewt104, ewtTABLE, ewt126, ewtNR } |
Wall types. | |
enum | { epullUMBRELLA, epullCONSTRAINT, epullCONST_F, epullFLATBOTTOM, epullFLATBOTTOMHIGH, epullEXTERNAL, epullNR } |
Pulling algorithm. | |
enum | { epullgDIST, epullgDIR, epullgCYL, epullgDIRPBC, epullgDIRRELATIVE, epullgANGLE, epullgDIHEDRAL, epullgANGLEAXIS, epullgNR } |
Control of pull groups. | |
enum | { erotgISO, erotgISOPF, erotgPM, erotgPMPF, erotgRM, erotgRMPF, erotgRM2, erotgRM2PF, erotgFLEX, erotgFLEXT, erotgFLEX2, erotgFLEX2T, erotgNR } |
Enforced rotation groups. | |
enum | { erotgFitRMSD, erotgFitNORM, erotgFitPOT, erotgFitNR } |
Rotation group fitting type. | |
enum | eSwaptype { eswapNO, eswapX, eswapY, eswapZ, eSwapTypesNR } |
Direction along which ion/water swaps happen. More... | |
enum | { eGrpSplit0, eGrpSplit1, eGrpSolvent, eSwapFixedGrpNR } |
Swap group splitting type. More... | |
enum | { eQMmethodAM1, eQMmethodPM3, eQMmethodRHF, eQMmethodUHF, eQMmethodDFT, eQMmethodB3LYP, eQMmethodMP2, eQMmethodCASSCF, eQMmethodB3LYPLAN, eQMmethodDIRECT, eQMmethodNR } |
QMMM methods. | |
enum | { eQMbasisSTO3G, eQMbasisSTO3G2, eQMbasis321G, eQMbasis321Gp, eQMbasis321dGp, eQMbasis621G, eQMbasis631G, eQMbasis631Gp, eQMbasis631dGp, eQMbasis6311G, eQMbasisNR } |
QMMM basis function for QM part. | |
enum | { eQMMMschemenormal, eQMMMschemeoniom, eQMMMschemeNR } |
QMMM scheme. | |
enum | gmx_nblist_kernel_geometry { GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_GEOMETRY_WATER3_PARTICLE, GMX_NBLIST_GEOMETRY_WATER3_WATER3, GMX_NBLIST_GEOMETRY_WATER4_PARTICLE, GMX_NBLIST_GEOMETRY_WATER4_WATER4, GMX_NBLIST_GEOMETRY_CG_CG, GMX_NBLIST_GEOMETRY_NR } |
Neighborlist geometry type. More... | |
enum | gmx_nbkernel_elec { GMX_NBKERNEL_ELEC_NONE, GMX_NBKERNEL_ELEC_COULOMB, GMX_NBKERNEL_ELEC_REACTIONFIELD, GMX_NBKERNEL_ELEC_CUBICSPLINETABLE, GMX_NBKERNEL_ELEC_GENERALIZEDBORN, GMX_NBKERNEL_ELEC_EWALD, GMX_NBKERNEL_ELEC_NR } |
Types of electrostatics calculations. More... | |
enum | gmx_nbkernel_vdw { GMX_NBKERNEL_VDW_NONE, GMX_NBKERNEL_VDW_LENNARDJONES, GMX_NBKERNEL_VDW_BUCKINGHAM, GMX_NBKERNEL_VDW_CUBICSPLINETABLE, GMX_NBKERNEL_VDW_LJEWALD, GMX_NBKERNEL_VDW_NR } |
Types of vdw calculations available. More... | |
enum | gmx_nblist_interaction_type { GMX_NBLIST_INTERACTION_STANDARD, GMX_NBLIST_INTERACTION_FREE_ENERGY, GMX_NBLIST_INTERACTION_NR } |
Types of interactions inside the neighborlist. | |
Functions | |
const char * | enum_name (int index, int max_index, const char *names[]) |
Return a string from a list of strings. More... | |
Variables | |
const char * | yesno_names [2+1] |
Boolean strings no or yes. | |
const char * | etcoupl_names [etcNR+1] |
Strings corresponding to temperatyre coupling types. | |
const char * | epcoupl_names [epcNR+1] |
String corresponding to pressure coupling algorithm. | |
const char * | erefscaling_names [erscNR+1] |
String corresponding to relativ coordinate scaling. | |
const char * | epcoupltype_names [epctNR+1] |
String corresponding to pressure coupling type. | |
const char * | ecutscheme_names [ecutsNR+1] |
String corresponding to cutoff scheme. | |
const char * | eintmod_names [eintmodNR+1] |
String corresponding to interaction modifiers. | |
const char * | eel_names [eelNR+1] |
String corresponding to Coulomb treatment. | |
const char * | eewg_names [eewgNR+1] |
String corresponding to Ewald geometry. | |
const char * | evdw_names [evdwNR+1] |
String corresponding to Van der Waals treatment. | |
const char * | eljpme_names [eljpmeNR+1] |
String for LJPME combination rule treatment. | |
const char * | ens_names [ensNR+1] |
String corresponding to neighborsearching. | |
const char * | ei_names [eiNR+1] |
Name of the integrator algorithm. | |
const char * | econstr_names [econtNR+1] |
String corresponding to constraint algorithm. | |
const char * | edisre_names [edrNR+1] |
String corresponding to distance restraint algorithm. | |
const char * | edisreweighting_names [edrwNR+1] |
String corresponding to distance restraint weighting. | |
const char * | ecomb_names [eCOMB_NR+1] |
String for combination rule algorithm. | |
const char * | enbf_names [eNBF_NR+1] |
String corresponding to Van der Waals potential. | |
const char * | esimtemp_names [esimtempNR+1] |
String corresponding to simulated tempering. | |
const char * | efep_names [efepNR+1] |
String corresponding to FEP type. | |
const char * | efpt_names [efptNR+1] |
String for FEP coupling type. | |
const char * | efpt_singular_names [efptNR+1] |
Long names for FEP coupling type. | |
const char * | edHdLPrintEnergy_names [edHdLPrintEnergyNR+1] |
String corresponding to printing of free energy. | |
const char * | elamstats_names [elamstatsNR+1] |
String corresponding to lambda weights. | |
const char * | elmcmove_names [elmcmoveNR+1] |
String corresponding to lambda moves. | |
const char * | elmceq_names [elmceqNR+1] |
String corresponding to equilibrium algorithm. | |
const char * | separate_dhdl_file_names [esepdhdlfileNR+1] |
String corresponding to separate DHDL file selection. | |
const char * | dhdl_derivatives_names [edhdlderivativesNR+1] |
String for DHDL derivatives. | |
const char * | esol_names [esolNR+1] |
String corresponding to solvent type. | |
const char * | edispc_names [edispcNR+1] |
String corresponding to dispersion corrections. | |
const char * | ecm_names [ecmNR+1] |
String corresponding to COM removal. | |
const char * | eann_names [eannNR+1] |
String for simulated annealing. | |
const char * | eis_names [eisNR+1] |
String corresponding to implicit solvent. | |
const char * | egb_names [egbNR+1] |
String for GB algorithm name. | |
const char * | esa_names [esaNR+1] |
String corresponding to surface area algorithm. | |
const char * | ewt_names [ewtNR+1] |
String corresponding to wall type. | |
const char * | epull_names [epullNR+1] |
String for pulling algorithm. | |
const char * | epullg_names [epullgNR+1] |
String for pull groups. | |
const char * | erotg_names [erotgNR+1] |
Rotation group names. | |
const char * | erotg_originnames [erotgNR+1] |
String for rotation group origin names. | |
const char * | erotg_fitnames [erotgFitNR+1] |
String corresponding to rotation group fitting. | |
const char * | eSwapTypes_names [eSwapTypesNR+1] |
Names for swapping. | |
const char * | eSwapFixedGrp_names [eSwapFixedGrpNR+1] |
String for swap group splitting. | |
const char * | eQMmethod_names [eQMmethodNR+1] |
String corresponding to QMMM methods. | |
const char * | eQMbasis_names [eQMbasisNR+1] |
Name for QMMM basis function. | |
const char * | eQMMMscheme_names [eQMMMschemeNR+1] |
QMMMM scheme names. | |
const char * | gmx_nblist_geometry_names [GMX_NBLIST_GEOMETRY_NR+1] |
String corresponding to nblist geometry names. | |
const char * | gmx_nbkernel_elec_names [GMX_NBKERNEL_ELEC_NR+1] |
String corresponding to electrostatics kernels. | |
const char * | gmx_nbkernel_vdw_names [GMX_NBKERNEL_VDW_NR+1] |
String corresponding to VdW kernels. | |
const char * | gmx_nblist_interaction_names [GMX_NBLIST_INTERACTION_NR+1] |
String corresponding to interactions in neighborlist code. | |
anonymous enum |
Free energy perturbation type.
efepNO, there are no evaluations at other states. efepYES, treated equivalently to efepSTATIC. efepSTATIC, then lambdas do not change during the simulation. efepSLOWGROWTH, then the states change monotonically throughout the simulation. efepEXPANDED, then expanded ensemble simulations are occuring.
anonymous enum |
What to print for free energy calculations.
Printing the energy to the free energy dhdl file. YES is an alias to TOTAL, and will be converted in readir, so we never have to account for it in code.
anonymous enum |
How the lambda weights are calculated.
elamstatsMETROPOLIS - using the metropolis criteria elamstatsBARKER - using the Barker critera for transition weights, also called unoptimized Bennett elamstatsMINVAR - using Barker + minimum variance for weights elamstatsWL - Wang-Landu (using visitation counts) elamstatsWWL - Weighted Wang-Landau (using optimized Gibbs weighted visitation counts)
anonymous enum |
How moves in lambda are calculated.
elmovemcMETROPOLIS - using the Metropolis criteria, and 50% up and down elmovemcBARKER - using the Barker criteria, and 50% up and down elmovemcGIBBS - computing the transition using the marginalized probabilities of the lambdas elmovemcMETGIBBS - computing the transition using the metropolized version of Gibbs (Monte Carlo Strategies in Scientific computing, Liu, p. 134)
anonymous enum |
How we decide whether weights have reached equilibrium.
elmceqNO - never stop, weights keep going elmceqYES - fix the weights from the beginning; no movement elmceqWLDELTA - stop when the WL-delta falls below a certain level elmceqNUMATLAM - stop when we have a certain number of samples at every step elmceqSTEPS - stop when we've run a certain total number of steps elmceqSAMPLES - stop when we've run a certain total number of samples elmceqRATIO - stop when the ratio of samples (lowest to highest) is sufficiently large
anonymous enum |
separate_dhdl_file selection
NOTE: YES is the first one. Do NOT interpret this one as a gmx_bool
anonymous enum |
dhdl_derivatives selection \
NOTE: YES is the first one. Do NOT interpret this one as a gmx_bool
anonymous enum |
Solvent model.
Distinguishes classical water types with 3 or 4 particles
anonymous enum |
Swap group splitting type.
These are just the fixed groups we need for any setup. In t_swap's grp entry after that follows the variable number of swap groups.
anonymous enum |
Temperature coupling type.
yes is an alias for berendsen
anonymous enum |
Pressure coupling types.
isotropic is an alias for berendsen
anonymous enum |
Cut-off treatment for Coulomb.
eelNOTUSED1 used to be GB, but to enable generalized born with different forms of electrostatics (RF, switch, etc.) in the future it is now selected separately (through the implicit_solvent option).
anonymous enum |
Integrator algorithm.
eiSD2 has been removed, but we keep a renamed enum entry, so we can refuse to do MD with such .tpr files. eiVV is normal velocity verlet eiVVAK uses 1/2*(KE(t-dt/2)+KE(t+dt/2)) as the kinetic energy, and the half step kinetic energy for temperature control
enum eChannel |
The channels that define with their COM the compartment boundaries in CompEL setups.
In principle one could also use modified setups with more than two channels.
enum eintmod |
Coulomb / VdW interaction modifiers.
grompp replaces eintmodPOTSHIFT_VERLET by eintmodPOTSHIFT or eintmodNONE. Exactcutoff is only used by Reaction-field-zero, and is not user-selectable.
enum eSwaptype |
Direction along which ion/water swaps happen.
Part of "Computational Electrophysiology" (CompEL) setups
enum gmx_nbkernel_elec |
Types of electrostatics calculations.
Types of electrostatics calculations available inside nonbonded kernels. Note that these do NOT necessarily correspond to the user selections in the MDP file; many interactions for instance map to tabulated kernels.
enum gmx_nbkernel_vdw |
Types of vdw calculations available.
Types of vdw calculations available inside nonbonded kernels. Note that these do NOT necessarily correspond to the user selections in the MDP file; many interactions for instance map to tabulated kernels.
Neighborlist geometry type.
Kernels will compute interactions between two particles, 3-center water, 4-center water or coarse-grained beads.
const char* enum_name | ( | int | index, |
int | max_index, | ||
const char * | names[] | ||
) |
Return a string from a list of strings.
If index if within 0 .. max_index-1 returns the corresponding string or "no name defined" otherwise, in other words this is a range-check that does not crash.
[in] | index | The index in the array |
[in] | max_index | The length of the array |
[in] | names | The array |