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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <cmath> |
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#include "simError.h" |
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#include "parse_me.h" |
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#include "MakeStamps.hpp" |
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#include "Globals.hpp" |
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#include "SimInfo.hpp" |
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// quick case asignments |
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#include "sysBuild.hpp" |
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#include "bilayerSys.hpp" |
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|
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// this routine is defined in BASS_interface.cpp |
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extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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|
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|
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// case asignments |
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#define BILAYER 1 |
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char* program_name; |
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bassInfo bsInfo; |
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void usage(void); |
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char current_flag; |
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char* out_prefix; |
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char* in_name; |
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char* id; |
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|
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includeLinked* headInc; |
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includeLinked* prevInc; |
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includeLinked* currInc; |
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|
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// initialize simError |
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initSimError(); |
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MakeStamps* the_stamps = NULL; |
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Globals* the_globals = NULL; |
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Component** the_components = NULL; |
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LinkedMolStamp* headStamp = NULL; |
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LinkedMolStamp* currStamp; |
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|
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// initialize all functions and variables |
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|
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program_name = argv[0]; /*save the program name in case we need it*/ |
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initSimError(); |
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program_name = argv[0]; |
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sysType = -1; |
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have_prefix = 0; |
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isRandom = 0; |
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in_name = NULL; |
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headInc = NULL; |
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|
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bsInfo.includes = NULL; |
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bsInfo.componentsNmol = NULL; |
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bsInfo.compStamps = NULL; |
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bsInfo.havePressure = 0; |
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bsInfo.haveTauBarostat = 0; |
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bsInfo.haveTauThermostat = 0; |
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bsInfo.haveQmass = 0; |
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|
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headStamp = new LinkedMolStamp(); |
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the_stamps = new MakeStamps(); |
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the_globals = new Globals(); |
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set_interface_stamps( the_stamps, the_globals ); |
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|
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// parse command line arguments |
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|
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for( i = 1; i < argc; i++){ |
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|
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if(argv[i][0] =='-'){ |
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simError(); |
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usage(); |
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} |
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|
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sysType = BILAYER; |
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|
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i++; |
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if( i>=argc ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for bilayer\n"); |
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painCave.isFatal = 0; |
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simError(); |
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usage(); |
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} |
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strcpy( bsInfo.lipidName, argv[i] ); |
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|
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i++; |
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if( i>=argc ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for bilayer\n"); |
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painCave.isFatal = 0; |
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simError(); |
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usage(); |
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} |
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strcpy( bsInfo.waterName, argv[i] ); |
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|
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} |
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else{ |
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done = 1; |
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break; |
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|
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case 'I': |
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// -I <include> => the include file. |
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|
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i++; |
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if( headInc == NULL ){ |
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headInc = new includeLinked; |
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headInc->next = NULL; |
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strcpy( headInc->name, argv[i] ); |
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} |
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else{ |
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prevInc = headInc; |
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currInc = headInc->next; |
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while( currInc != NULL ){ |
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prevInc = currInc; |
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currInc = prevInc->next; |
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} |
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currInc = new includeLinked; |
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currInc->next = NULL; |
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strcpy( currInc->name, argv[i] ); |
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prevInc->next = currInc; |
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} |
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|
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done = 1; |
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break; |
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|
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case 'h': |
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// -h => give the usage |
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|
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default: |
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sprintf(painCave.errMsg, |
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"Bad option \"-%s\"\n", current_flag); |
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"Bad option \"-%c\"\n", current_flag); |
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painCave.isFatal = 0; |
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simError(); |
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usage(); |
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} |
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|
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if(in_name == NULL){ |
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sprintf( painCave.errMsg, |
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"No input bass file was specified.\n"); |
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painCave.isFatal = 0; |
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simError(); |
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usage(); |
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} |
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|
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if( sysType < 0 ){ |
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sprintf( painCave.errMsg, |
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"No system type was specified.\n"); |
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painCave.isFatal = 0; |
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simError(); |
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usage(); |
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} |
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// if no output prefix is given default to "donkey". |
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|
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if( !have_prefix ){ |
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out_prefix = strdup( "donkey" ); |
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} |
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|
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// set command line info into the bassInfo struct |
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|
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bsInfo.outPrefix = out_prefix; |
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bsInfo.includes = headInc; |
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|
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|
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// open and parse the bass file. |
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|
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set_interface_stamps( the_stamps, the_globals ); |
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yacc_BASS( in_name ); |
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|
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// set the easy ones first |
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bsInfo.targetTemp = the_globals->getTargetTemp(); |
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bsInfo.dt = the_globals->getDt(); |
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bsInfo.runTime = the_globals->getRunTime(); |
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|
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// get the ones we know are there, yet still may need some work. |
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bsInfo.nComponents = the_globals->getNComponents(); |
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strcpy( bsInfo.forceField, the_globals->getForceField() ); |
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|
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// get the ensemble: |
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strcpy( bsInfo.ensemble, the_globals->getEnsemble() ); |
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if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) { |
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|
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if (the_globals->haveTargetPressure()){ |
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bsInfo.targetPressure = the_globals->getTargetPressure(); |
263 |
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bsInfo.havePressure = 1; |
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} |
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else { |
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sprintf( painCave.errMsg, |
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"sysBuild error: If you use the constant pressure\n" |
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" ensemble, you must set targetPressure.\n" |
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" This was found in the BASS file.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (the_globals->haveTauThermostat()){ |
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bsInfo.tauThermostat = the_globals->getTauThermostat(); |
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bsInfo.haveTauThermostat = 1;; |
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} |
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else if (the_globals->haveQmass()){ |
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bsInfo.Qmass = the_globals->getQmass(); |
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bsInfo.haveQmass = 1; |
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} |
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else { |
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sprintf( painCave.errMsg, |
284 |
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"sysBuild error: If you use one of the constant temperature\n" |
285 |
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" ensembles, you must set either tauThermostat or qMass.\n" |
286 |
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" Neither of these was found in the BASS file.\n"); |
287 |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (the_globals->haveTauBarostat()){ |
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bsInfo.tauBarostat = the_globals->getTauBarostat(); |
293 |
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bsInfo.haveTauBarostat = 1; |
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} |
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else { |
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sprintf( painCave.errMsg, |
297 |
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"sysBuild error: If you use the constant pressure\n" |
298 |
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" ensemble, you must set tauBarostat.\n" |
299 |
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" This was found in the BASS file.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) { |
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|
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if (the_globals->haveTauThermostat()){ |
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bsInfo.tauThermostat = the_globals->getTauThermostat(); |
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bsInfo.haveTauThermostat = 1; |
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} |
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else if (the_globals->haveQmass()){ |
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bsInfo.Qmass = the_globals->getQmass(); |
313 |
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bsInfo.haveQmass = 1; |
314 |
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} |
315 |
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else { |
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sprintf( painCave.errMsg, |
317 |
+ |
"sysBuild error: If you use one of the constant temperature\n" |
318 |
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" ensembles, you must set either tauThermostat or qMass.\n" |
319 |
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" Neither of these was found in the BASS file.\n"); |
320 |
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painCave.isFatal = 1; |
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simError(); |
322 |
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} |
323 |
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|
324 |
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} |
325 |
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else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) { |
326 |
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|
327 |
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// nothing special for now |
328 |
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} |
329 |
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else { |
330 |
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sprintf( painCave.errMsg, |
331 |
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"sysBuild Warning. Unrecognized Ensemble -> %s, " |
332 |
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"reverting to NVE for this simulation.\n", |
333 |
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bsInfo.ensemble ); |
334 |
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painCave.isFatal = 0; |
335 |
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simError(); |
336 |
+ |
strcpy( bsInfo.ensemble, "NVE" ); |
337 |
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} |
338 |
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|
339 |
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|
340 |
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// get the components and calculate the tot_nMol and indvidual n_mol |
341 |
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|
342 |
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the_components = the_globals->getComponents(); |
343 |
+ |
bsInfo.componentsNmol = new int[bsInfo.nComponents]; |
344 |
+ |
bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents]; |
345 |
+ |
bsInfo.totNmol = 0; |
346 |
+ |
for( i=0; i<bsInfo.nComponents; i++ ){ |
347 |
+ |
|
348 |
+ |
if( !the_components[i]->haveNMol() ){ |
349 |
+ |
// we have a problem |
350 |
+ |
sprintf( painCave.errMsg, |
351 |
+ |
"sysBuild Error. No component NMol" |
352 |
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" given. Cannot calculate the number of atoms.\n" ); |
353 |
+ |
painCave.isFatal = 1; |
354 |
+ |
simError(); |
355 |
+ |
} |
356 |
+ |
|
357 |
+ |
bsInfo.totNmol += the_components[i]->getNMol(); |
358 |
+ |
bsInfo.componentsNmol[i] = the_components[i]->getNMol(); |
359 |
+ |
} |
360 |
+ |
|
361 |
+ |
// make an array of molecule stamps that match the components used. |
362 |
+ |
// also extract the used stamps out into a separate linked list |
363 |
|
|
364 |
+ |
for( i=0; i<bsInfo.nComponents; i++ ){ |
365 |
+ |
|
366 |
+ |
id = the_components[i]->getType(); |
367 |
+ |
bsInfo.compStamps[i] = NULL; |
368 |
+ |
|
369 |
+ |
// check to make sure the component isn't already in the list |
370 |
+ |
|
371 |
+ |
bsInfo.compStamps[i] = headStamp->match( id ); |
372 |
+ |
if( bsInfo.compStamps[i] == NULL ){ |
373 |
+ |
|
374 |
+ |
// extract the component from the list; |
375 |
+ |
|
376 |
+ |
currStamp = the_stamps->extractMolStamp( id ); |
377 |
+ |
if( currStamp == NULL ){ |
378 |
+ |
sprintf( painCave.errMsg, |
379 |
+ |
"sysBuild error: Component \"%s\" was not found in the " |
380 |
+ |
"list of declared molecules\n", |
381 |
+ |
id ); |
382 |
+ |
painCave.isFatal = 1; |
383 |
+ |
simError(); |
384 |
+ |
} |
385 |
+ |
|
386 |
+ |
headStamp->add( currStamp ); |
387 |
+ |
bsInfo.compStamps[i] = headStamp->match( id ); |
388 |
+ |
} |
389 |
+ |
} |
390 |
+ |
|
391 |
+ |
// get and set the boxSize |
392 |
+ |
|
393 |
+ |
if( the_globals->haveBox() ){ |
394 |
+ |
bsInfo.boxX = the_globals->getBox(); |
395 |
+ |
bsInfo.boxY = the_globals->getBox(); |
396 |
+ |
bsInfo.boxZ = the_globals->getBox(); |
397 |
+ |
} |
398 |
+ |
else if( the_globals->haveDensity() ){ |
399 |
+ |
|
400 |
+ |
double vol; |
401 |
+ |
vol = (double)bsInfo.totNmol / the_globals->getDensity(); |
402 |
+ |
bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) ); |
403 |
+ |
bsInfo.boxY = bsInfo.boxX; |
404 |
+ |
bsInfo.boxZ = bsInfo.boxY; |
405 |
+ |
} |
406 |
+ |
else{ |
407 |
+ |
if( !the_globals->haveBoxX() ){ |
408 |
+ |
sprintf( painCave.errMsg, |
409 |
+ |
"sysBuild error, no periodic BoxX size given.\n" ); |
410 |
+ |
painCave.isFatal = 1; |
411 |
+ |
simError(); |
412 |
+ |
} |
413 |
+ |
bsInfo.boxX = the_globals->getBoxX(); |
414 |
+ |
|
415 |
+ |
if( !the_globals->haveBoxY() ){ |
416 |
+ |
sprintf( painCave.errMsg, |
417 |
+ |
"sysBuild error, no periodic BoxY size given.\n" ); |
418 |
+ |
painCave.isFatal = 1; |
419 |
+ |
simError(); |
420 |
+ |
} |
421 |
+ |
bsInfo.boxY = the_globals->getBoxY(); |
422 |
+ |
|
423 |
+ |
if( !the_globals->haveBoxZ() ){ |
424 |
+ |
sprintf( painCave.errMsg, |
425 |
+ |
"SimSetup error, no periodic BoxZ size given.\n" ); |
426 |
+ |
painCave.isFatal = 1; |
427 |
+ |
simError(); |
428 |
+ |
} |
429 |
+ |
bsInfo.boxZ = the_globals->getBoxZ(); |
430 |
+ |
} |
431 |
|
|
432 |
+ |
|
433 |
+ |
//************************************************************ |
434 |
+ |
// that should be all we need from bass. now to switch to the |
435 |
+ |
// appropriate system builder. |
436 |
+ |
// *********************************************************** |
437 |
+ |
|
438 |
+ |
|
439 |
+ |
switch( sysType ){ |
440 |
+ |
|
441 |
+ |
case BILAYER: |
442 |
+ |
|
443 |
+ |
buildBilayer( isRandom ); |
444 |
+ |
break; |
445 |
+ |
|
446 |
+ |
default: |
447 |
+ |
sprintf( painCave.errMsg, |
448 |
+ |
"Unknown system type: %d\n", sysType ); |
449 |
+ |
painCave.isFatal = 1; |
450 |
+ |
simError(); |
451 |
+ |
} |
452 |
|
|
453 |
+ |
|
454 |
+ |
|
455 |
+ |
// clean up memory; |
456 |
+ |
|
457 |
+ |
if( headStamp!= NULL ) delete headStamp; |
458 |
+ |
if( the_stamps != NULL ) delete the_stamps; |
459 |
+ |
if( the_globals != NULL ) delete the_globals; |
460 |
+ |
if( the_components != NULL ) delete[] the_components; |
461 |
|
|
462 |
+ |
if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol; |
463 |
+ |
if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps; |
464 |
+ |
if( bsInfo.includes != NULL ){ |
465 |
+ |
prevInc = bsInfo.includes; |
466 |
+ |
while( prevInc != NULL ){ |
467 |
+ |
currInc = prevInc->next; |
468 |
+ |
delete prevInc; |
469 |
+ |
prevInc = currInc; |
470 |
+ |
} |
471 |
+ |
} |
472 |
+ |
|
473 |
|
return 0; |
474 |
|
} |
475 |
|
|
488 |
|
" ------\n" |
489 |
|
" -h Display this message\n" |
490 |
|
" -o <prefix> The output prefix\n" |
491 |
+ |
" -I <include> File name that should be included at the top of the\n" |
492 |
+ |
" output bass file.\n" |
493 |
|
" -r toggle the random option\n" |
494 |
|
"\n" |
495 |
|
" long:\n" |
496 |
|
" -----\n" |
497 |
< |
" --bilayer Tries to build a basic bilayer with the specified number\n" |
498 |
< |
" of lipids in the input bass file. The bilayer will be\n" |
499 |
< |
" surrounded by the number of solvent molecules given\n" |
500 |
< |
" in the bass file.\n" |
501 |
< |
" -note: combined with \"-r\" the simulation will start in\n" |
502 |
< |
" an FCC lattice with randomly assigned latice\n" |
166 |
< |
" for all atoms involved.\n" |
497 |
> |
" --bilayer <lipid> <water> Tries to build a basic bilayer with the specified number\n" |
498 |
> |
" of lipids in the input bass file. The bilayer will be\n" |
499 |
> |
" surrounded by the number of solvent molecules given\n" |
500 |
> |
" in the bass file.\n" |
501 |
> |
" -note: combined with \"-r\" the simulation will start\n" |
502 |
> |
" the lipids randomly oriented in a sea of waters.\n" |
503 |
|
"\n" |
504 |
|
"\n", |
505 |
|
program_name); |