| version 1.1464 | version 1.1465 |
|---|
| |
| /***************************************************************************** | /***************************************************************************** |
| * $Source: /home/cvs/namd/cvsroot/namd2/src/SimParameters.C,v $ | * $Source: /home/cvs/namd/cvsroot/namd2/src/SimParameters.C,v $ |
| * $Author: jim $ | * $Author: jim $ |
| * $Date: 2016/09/05 18:25:43 $ | * $Date: 2016/09/07 18:09:59 $ |
| * $Revision: 1.1464 $ | * $Revision: 1.1465 $ |
| *****************************************************************************/ | *****************************************************************************/ |
| | |
| /** \file SimParameters.C | /** \file SimParameters.C |
| |
| fixedAtomsOn = atobool(value); | fixedAtomsOn = atobool(value); |
| return; | return; |
| } | } |
| // SCRIPT_PARSE_BOOL("extraBonds", extraBondsOn) | |
| // SCRIPT_PARSE_STRING("binCoordinates", binCoordinateFilename) | |
| | |
| //fepb | //fepb |
| // SCRIPT_PARSE_BOOL("alch", alchOn) | if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) { |
| | alchOn = atobool(value); |
| | if ( alchOn && ! alchOnAtStartup ) { |
| | NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script."); |
| | } |
| | ComputeNonbondedUtil::select(); |
| | return; |
| | } |
| SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps) | SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps) |
| | |
| if ( ! strncasecmp(param,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) { | if ( ! strncasecmp(param,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) { |
| |
| //fepb | //fepb |
| alchFepOn = FALSE; | alchFepOn = FALSE; |
| alchThermIntOn = FALSE; | alchThermIntOn = FALSE; |
| | alchOnAtStartup = alchOn; |
| | |
| if (alchOn) { | if (alchOn) { |
| if (vdwForceSwitching && (alchFepWCARepuOn || alchFepWCADispOn)) { | if (vdwForceSwitching && (alchFepWCARepuOn || alchFepWCADispOn)) { |
| |
| NAMD_die("Sorry, combined LES with FEP or TI is not implemented.\n"); | NAMD_die("Sorry, combined LES with FEP or TI is not implemented.\n"); |
| if ( alchOn && alchThermIntOn && lesOn ) | if ( alchOn && alchThermIntOn && lesOn ) |
| NAMD_die("Sorry, combined LES and TI is not implemented.\n"); | NAMD_die("Sorry, combined LES and TI is not implemented.\n"); |
| if ( alchDecouple && (! (alchFepOn || alchThermIntOn) ) ) { | if ( alchDecouple && !alchOn ) { |
| iout << iWARN << "Alchemical decoupling was requested but \ | iout << iWARN << "Alchemical decoupling was requested but \ |
| alchemical free energy calculation is not active. Setting \ | alchemical free energy calculation is not active. Setting \ |
| alchDecouple to off.\n" << endi; | alchDecouple to off.\n" << endi; |
| alchDecouple = FALSE; | alchDecouple = FALSE; |
| } | } |
| if ( alchBondDecouple && (! (alchFepOn || alchThermIntOn) ) ) { | if ( alchBondDecouple && !alchOn ) { |
| iout << iWARN << "Alchemical bond decoupling was requested but \ | iout << iWARN << "Alchemical bond decoupling was requested but \ |
| alchemical free energy calculation is not active. Setting \ | alchemical free energy calculation is not active. Setting \ |
| alchBondDecouple to off.\n" << endi; | alchBondDecouple to off.\n" << endi; |
| |
| if ( lesOn && ( lesFactor < 1 || lesFactor > 255 ) ) { | if ( lesOn && ( lesFactor < 1 || lesFactor > 255 ) ) { |
| NAMD_die("lesFactor must be positive and less than 256"); | NAMD_die("lesFactor must be positive and less than 256"); |
| } | } |
| if ((pairInteractionOn && alchFepOn) || (pairInteractionOn && lesOn) || (pairInteractionOn && alchThermIntOn) ) | if ((pairInteractionOn && alchOn) || (pairInteractionOn && lesOn)) |
| NAMD_die("Sorry, pair interactions may not be calculated when LES, FEP or TI is enabled."); | NAMD_die("Sorry, pair interactions may not be calculated when LES, FEP or TI is enabled."); |
| | |
| // Drude model | // Drude model |