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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 <iostream> |
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|
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#include "cmdline.h" |
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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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|
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#include "sysBuild.hpp" |
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#include "latticeBuilder.hpp" |
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#include "bilayerSys.hpp" |
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#include "nanoBuilder.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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#define NANOPARTICLE 2 |
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|
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char* program_name; |
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bassInfo bsInfo; |
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void usage(void); |
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int grabCmdArgs(void); |
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|
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|
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|
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|
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int have_prefix; |
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char* out_prefix; |
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char* in_name; |
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int isRandom; |
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includeLinked* headInc; |
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includeLinked* prevInc; |
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includeLinked* currInc; |
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gengetopt_args_info args_info; |
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|
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|
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int main( int argc, char* argv[]){ |
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|
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int i,j,k; |
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int sysType; |
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int done; |
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char current_flag; |
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// int have_prefix; |
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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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int hasErrors; |
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|
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// initialize all functions and variables |
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|
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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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|
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|
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// parse command line arguments |
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|
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if (cmdline_parser (argc, argv, &args_info) != 0) |
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exit(1) ; |
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|
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// Handle command line arguments. |
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sysType = grabCmdArgs(); |
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|
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// Keep me |
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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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cmdline_parser_print_help(); |
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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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cmdline_parser_print_help(); |
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} |
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|
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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(); |
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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, |
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"sysBuild error: If you use one of the constant temperature\n" |
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" ensembles, you must set either tauThermostat or qMass.\n" |
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" Neither of these 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->haveTauBarostat()){ |
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bsInfo.tauBarostat = the_globals->getTauBarostat(); |
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bsInfo.haveTauBarostat = 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 tauBarostat.\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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} |
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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(); |
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bsInfo.haveQmass = 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 one of the constant temperature\n" |
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" ensembles, you must set either tauThermostat or qMass.\n" |
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" Neither of these 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, "NVE") ) { |
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|
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// nothing special for now |
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} |
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else { |
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sprintf( painCave.errMsg, |
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"sysBuild Warning. Unrecognized Ensemble -> %s, " |
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"reverting to NVE for this simulation.\n", |
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bsInfo.ensemble ); |
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painCave.isFatal = 0; |
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simError(); |
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strcpy( bsInfo.ensemble, "NVE" ); |
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} |
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|
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|
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// get the components and calculate the tot_nMol and indvidual n_mol |
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|
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the_components = the_globals->getComponents(); |
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bsInfo.componentsNmol = new int[bsInfo.nComponents]; |
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bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents]; |
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bsInfo.totNmol = 0; |
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for( i=0; i<bsInfo.nComponents; i++ ){ |
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|
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if( !the_components[i]->haveNMol() ){ |
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// we have a problem |
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sprintf( painCave.errMsg, |
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"sysBuild Error. No component NMol" |
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" given. Cannot calculate the number of atoms.\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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bsInfo.totNmol += the_components[i]->getNMol(); |
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bsInfo.componentsNmol[i] = the_components[i]->getNMol(); |
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} |
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|
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// make an array of molecule stamps that match the components used. |
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// also extract the used stamps out into a separate linked list |
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|
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for( i=0; i<bsInfo.nComponents; i++ ){ |
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|
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id = the_components[i]->getType(); |
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bsInfo.compStamps[i] = NULL; |
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|
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// check to make sure the component isn't already in the list |
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|
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bsInfo.compStamps[i] = headStamp->match( id ); |
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if( bsInfo.compStamps[i] == NULL ){ |
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|
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// extract the component from the list; |
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|
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currStamp = the_stamps->extractMolStamp( id ); |
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if( currStamp == NULL ){ |
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sprintf( painCave.errMsg, |
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"sysBuild error: Component \"%s\" was not found in the " |
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"list of declared molecules\n", |
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id ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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headStamp->add( currStamp ); |
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bsInfo.compStamps[i] = headStamp->match( id ); |
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} |
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} |
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|
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// get and set the boxSize |
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|
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bsInfo.haveBox = false; |
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|
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std::cerr << "Box setting..."; |
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|
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std::cerr <<" haveBox= " << the_globals->haveBox() << "\n"; |
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|
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if( the_globals->haveBox() ){ |
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bsInfo.boxX = the_globals->getBox(); |
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bsInfo.boxY = the_globals->getBox(); |
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bsInfo.boxZ = the_globals->getBox(); |
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bsInfo.haveBox = true; |
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std::cerr<< "box=>yes\n"; |
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} |
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else if( the_globals->haveDensity() ){ |
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|
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double vol; |
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vol = (double)bsInfo.totNmol / the_globals->getDensity(); |
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bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) ); |
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bsInfo.boxY = bsInfo.boxX; |
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bsInfo.boxZ = bsInfo.boxY; |
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bsInfo.haveBox = true; |
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|
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std::cerr<< "dens=>yes\n"; |
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} |
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else{ |
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std::cerr<< "none.\n"; |
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} |
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|
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|
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// ************************************************************ |
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// that should be all we need from bass. now to switch to the |
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// appropriate system builder. |
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// *********************************************************** |
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|
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nanoBuilder* buildNano; |
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|
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switch( sysType ){ |
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|
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case BILAYER: |
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buildBilayer( isRandom ); |
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break; |
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|
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case NANOPARTICLE: |
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|
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buildNano = new nanoBuilder(hasErrors); |
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|
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buildNano->buildNanoParticle(); |
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|
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break; |
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|
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default: |
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sprintf( painCave.errMsg, |
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"Unknown system type: %d\n", sysType ); |
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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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|
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|
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// clean up memory; |
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|
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if( headStamp!= NULL ) delete headStamp; |
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if( the_stamps != NULL ) delete the_stamps; |
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if( the_globals != NULL ) delete the_globals; |
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// if( the_components != NULL ) delete[] the_components; |
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|
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if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol; |
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if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps; |
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if( bsInfo.includes != NULL ){ |
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prevInc = bsInfo.includes; |
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while( prevInc != NULL ){ |
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currInc = prevInc->next; |
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delete prevInc; |
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prevInc = currInc; |
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} |
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} |
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|
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return 0; |
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} |
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|
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|
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|
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/* Parses command line arguments. Returns systype. If systype is -1, |
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sysType was undefined. |
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*/ |
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int grabCmdArgs(){ |
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int sysType; |
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int i; |
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|
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sysType = -1; |
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|
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/* Handle model arguments first....*/ |
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|
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if (args_info.bilayer_given){ //Test for bilayer system. |
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sysType = BILAYER; |
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if ((args_info.water_given) && (args_info.lipid_given)){ |
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strcpy( bsInfo.lipidName, args_info.lipid_arg ); |
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strcpy( bsInfo.waterName, args_info.water_arg ); |
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} |
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else { |
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sprintf( painCave.errMsg, |
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"You must specify a lipid and water model for bilayer.\n" ); |
362 |
painCave.isFatal = 0; |
363 |
simError(); |
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cmdline_parser_print_help(); |
365 |
} |
366 |
} |
367 |
|
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// Test for nanoparticle system. |
369 |
if (args_info.nanoparticle_given){ |
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sysType = NANOPARTICLE; |
371 |
if (!args_info.core_given){ |
372 |
sprintf( painCave.errMsg, |
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"You must specify core model for nanoparticle.\n" ); |
374 |
painCave.isFatal = 0; |
375 |
simError(); |
376 |
cmdline_parser_print_help(); |
377 |
} |
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|
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// set core model |
380 |
strcpy( bsInfo.coreName, args_info.core_arg ); |
381 |
if (args_info.shell_given){ |
382 |
bsInfo.buildCoreShell = 1; |
383 |
strcpy( bsInfo.shellName, args_info.shell_arg ); |
384 |
|
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|
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} |
387 |
|
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// Check for vacancies. |
389 |
if (args_info.vacancies_given){ |
390 |
|
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if (!args_info.vacancyradius_given){ // Make sure that a vacancy radius was given. |
392 |
sprintf( painCave.errMsg, |
393 |
"You must specify a vacancy radius for building vacancies.\n" ); |
394 |
painCave.isFatal = 0; |
395 |
simError(); |
396 |
cmdline_parser_print_help(); |
397 |
} |
398 |
bsInfo.hasVacancies = 1; |
399 |
bsInfo.vacancyRadius = args_info.vacancyradius_arg; |
400 |
} |
401 |
else if (args_info.vacancyradius_given){ |
402 |
sprintf( painCave.errMsg, |
403 |
"You must specify vacancies=percent for vacancy radius.\n" ); |
404 |
painCave.isFatal = 0; |
405 |
simError(); |
406 |
cmdline_parser_print_help(); |
407 |
} |
408 |
|
409 |
if (args_info.randomparticle_given){ |
410 |
bsInfo.isRandomParticle = 1; |
411 |
bsInfo.soluteX = args_info.randomparticle_arg; |
412 |
} |
413 |
|
414 |
} |
415 |
/* ---------------Now do general arguments-----------------------*/ |
416 |
|
417 |
if (args_info.output_given){ //Output File (defaults to donkey if not specified. |
418 |
out_prefix = args_info.output_arg; |
419 |
have_prefix = 1; |
420 |
} |
421 |
|
422 |
if (args_info.include_given){ // Deal with multiple include files. |
423 |
for( i = 0; i < args_info.include_given;++i){ |
424 |
if( headInc == NULL ){ |
425 |
headInc = new includeLinked; |
426 |
headInc->next = NULL; |
427 |
strcpy( headInc->name, args_info.include_arg[i] ); |
428 |
} |
429 |
else{ |
430 |
prevInc = headInc; |
431 |
currInc = headInc->next; |
432 |
while( currInc != NULL ){ |
433 |
prevInc = currInc; |
434 |
currInc = prevInc->next; |
435 |
} |
436 |
currInc = new includeLinked; |
437 |
currInc->next = NULL; |
438 |
strcpy( currInc->name, args_info.include_arg[i] ); |
439 |
prevInc->next = currInc; |
440 |
} |
441 |
} |
442 |
} |
443 |
|
444 |
if (args_info.random_given){ // Random Particle |
445 |
isRandom = 1;; |
446 |
} |
447 |
|
448 |
if (args_info.inputs_num) { //Get input file name |
449 |
in_name = args_info.inputs[0]; |
450 |
cerr << in_name << "\n"; |
451 |
} |
452 |
else { |
453 |
sprintf( painCave.errMsg, |
454 |
"You must specify a input file name.\n" ); |
455 |
painCave.isFatal = 0; |
456 |
simError(); |
457 |
cmdline_parser_print_help(); |
458 |
|
459 |
} |
460 |
|
461 |
return sysType; |
462 |
} |
463 |
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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/*************************************************************************** |
474 |
* prints out the usage for the command line arguments, then exits. |
475 |
***************************************************************************/ |
476 |
|
477 |
void usage(){ |
478 |
(void)fprintf(stdout, |
479 |
"The proper usage is: %s [options] <input bass>\n" |
480 |
"\n" |
481 |
"Options:\n" |
482 |
"\n" |
483 |
" short:\n" |
484 |
" ------\n" |
485 |
" -h Display this message\n" |
486 |
" -o <prefix> The output prefix\n" |
487 |
" -I <include> File name that should be included at the top of the\n" |
488 |
" output bass file.\n" |
489 |
" -r toggle the random option\n" |
490 |
"\n" |
491 |
" long:\n" |
492 |
" -----\n" |
493 |
" --bilayer <lipid> <water> Tries to build a basic bilayer with the specified number\n" |
494 |
" of lipids in the input bass file. The bilayer will be\n" |
495 |
" surrounded by the number of solvent molecules given\n" |
496 |
" in the bass file.\n" |
497 |
" -note: combined with \"-r\" the simulation will start\n" |
498 |
" the lipids randomly oriented in a sea of waters.\n" |
499 |
"\n" |
500 |
"\n", |
501 |
program_name); |
502 |
exit(8); |
503 |
} |