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|
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#include <cstdlib> |
| 3 |
#include <cstdio> |
| 4 |
#include <cstring> |
| 5 |
#include <cmath> |
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#include <iostream> |
| 7 |
|
| 8 |
#include "cmdline.h" |
| 9 |
#include "simError.h" |
| 10 |
#include "parse_me.h" |
| 11 |
#include "MakeStamps.hpp" |
| 12 |
#include "Globals.hpp" |
| 13 |
#include "SimInfo.hpp" |
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|
| 15 |
#include "sysBuild.hpp" |
| 16 |
#include "bilayerSys.hpp" |
| 17 |
#include "nanoBuilder.hpp" |
| 18 |
|
| 19 |
// this routine is defined in BASS_interface.cpp |
| 20 |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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|
| 22 |
|
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// case asignments |
| 24 |
#define BILAYER 1 |
| 25 |
#define NANOPARTICLE 2 |
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|
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char* program_name; |
| 28 |
bassInfo bsInfo; |
| 29 |
void usage(void); |
| 30 |
void grabCmdArgs(void); |
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|
| 32 |
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, have_prefix, isRandom; |
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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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int hasVacancies; |
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int thisLatticeType; |
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int isRandomParticle; |
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double solute_X; |
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double vacancyFraction; |
| 46 |
double particleRadius; |
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|
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|
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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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MakeStamps* the_stamps = NULL; |
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Globals* the_globals = NULL; |
| 56 |
Component** the_components = NULL; |
| 57 |
LinkedMolStamp* headStamp = NULL; |
| 58 |
LinkedMolStamp* currStamp; |
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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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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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//Nanobuilder components. |
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bsInfo.latticeType = FCC_LATTICE_TYPE; // set lattice type to FCC. |
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bsInfo.hasVacancies = 0; //set vacancies to false. |
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bsInfo.buildCoreShell = 0; |
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|
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bsInfo.latticeSpacing = 0.0; |
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bsInfo.coreRadius = 0.0; |
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bsInfo.particleRadius = 0.0; |
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bsInfo.shellRadius = 0.0; |
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bsInfo.vacancyRadius = 0.0; |
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bsInfo.vacancyFraction = 0.0; |
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bsInfo.soluteX = 0.0; |
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|
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|
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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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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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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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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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|
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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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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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} |
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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 ) ); |
| 296 |
bsInfo.boxY = bsInfo.boxX; |
| 297 |
bsInfo.boxZ = bsInfo.boxY; |
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} |
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else{ |
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if( !the_globals->haveBoxX() ){ |
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sprintf( painCave.errMsg, |
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"sysBuild error, no periodic BoxX size given.\n" ); |
| 303 |
painCave.isFatal = 1; |
| 304 |
simError(); |
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} |
| 306 |
bsInfo.boxX = the_globals->getBoxX(); |
| 307 |
|
| 308 |
if( !the_globals->haveBoxY() ){ |
| 309 |
sprintf( painCave.errMsg, |
| 310 |
"sysBuild error, no periodic BoxY size given.\n" ); |
| 311 |
painCave.isFatal = 1; |
| 312 |
simError(); |
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} |
| 314 |
bsInfo.boxY = the_globals->getBoxY(); |
| 315 |
|
| 316 |
if( !the_globals->haveBoxZ() ){ |
| 317 |
sprintf( painCave.errMsg, |
| 318 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
| 319 |
painCave.isFatal = 1; |
| 320 |
simError(); |
| 321 |
} |
| 322 |
bsInfo.boxZ = the_globals->getBoxZ(); |
| 323 |
} |
| 324 |
|
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|
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//************************************************************ |
| 327 |
// that should be all we need from bass. now to switch to the |
| 328 |
// appropriate system builder. |
| 329 |
// *********************************************************** |
| 330 |
|
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|
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switch( sysType ){ |
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|
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case BILAYER: |
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|
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buildBilayer( isRandom ); |
| 337 |
break; |
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|
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case NANO: |
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|
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|
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break; |
| 343 |
|
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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; |
| 348 |
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; |
| 355 |
|
| 356 |
if( headStamp!= NULL ) delete headStamp; |
| 357 |
if( the_stamps != NULL ) delete the_stamps; |
| 358 |
if( the_globals != NULL ) delete the_globals; |
| 359 |
if( the_components != NULL ) delete[] the_components; |
| 360 |
|
| 361 |
if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol; |
| 362 |
if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps; |
| 363 |
if( bsInfo.includes != NULL ){ |
| 364 |
prevInc = bsInfo.includes; |
| 365 |
while( prevInc != NULL ){ |
| 366 |
currInc = prevInc->next; |
| 367 |
delete prevInc; |
| 368 |
prevInc = currInc; |
| 369 |
} |
| 370 |
} |
| 371 |
|
| 372 |
return 0; |
| 373 |
} |
| 374 |
|
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|
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|
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|
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|
| 379 |
void grabCmdArgs(){ |
| 380 |
|
| 381 |
|
| 382 |
/* Handle model arguments first....*/ |
| 383 |
|
| 384 |
if (args_info.bilayer_given){ //Test for bilayer system. |
| 385 |
sysType = BILAYER; |
| 386 |
if ((args_info.water_given) && (args_info.lipid_given)){ |
| 387 |
bsInfo.lipidName = args_info.lipid_arg; |
| 388 |
bsInfo.waterName = args_info.water_arg; |
| 389 |
} |
| 390 |
else { |
| 391 |
sprintf( painCave.errMsg, |
| 392 |
"You must specify a lipid and water model for bilayer.\n" ); |
| 393 |
painCave.isFatal = 0; |
| 394 |
simError(); |
| 395 |
cmdline_parser_print_help(); |
| 396 |
} |
| 397 |
} |
| 398 |
|
| 399 |
// Test for nanoparticle system. |
| 400 |
if (args_info.nanoparticle_given){ |
| 401 |
sysType = NANOPARTICLE; |
| 402 |
if (!core_given){ |
| 403 |
sprintf( painCave.errMsg, |
| 404 |
"You must specify core model for nanoparticle.\n" ); |
| 405 |
painCave.isFatal = 0; |
| 406 |
simError(); |
| 407 |
cmdline_parser_print_help(); |
| 408 |
} |
| 409 |
|
| 410 |
// set core model |
| 411 |
bsInfo.coreName = args_info.core_arg; |
| 412 |
if (args_info.shell_given){ |
| 413 |
bsInfo.buildCoreShell = 1; |
| 414 |
bsInfo.shellName = args_info.shell_arg; |
| 415 |
} |
| 416 |
|
| 417 |
// Check for vacancies. |
| 418 |
if (vacancies_given){ |
| 419 |
|
| 420 |
if (!vacancyradius_given){ // Make sure that a vacancy radius was given. |
| 421 |
sprintf( painCave.errMsg, |
| 422 |
"You must specify a vacancy radius for building vacancies.\n" ); |
| 423 |
painCave.isFatal = 0; |
| 424 |
simError(); |
| 425 |
cmdline_parser_print_help(); |
| 426 |
} |
| 427 |
bsInfo.hasVacancies = 1; |
| 428 |
bsInfo.vacancyRadius = arg_info.vacancyradius; |
| 429 |
} |
| 430 |
else if (vacancyradius_given){ |
| 431 |
sprintf( painCave.errMsg, |
| 432 |
"You must specify vacancies=% for vacancy radius.\n" ); |
| 433 |
painCave.isFatal = 0; |
| 434 |
simError(); |
| 435 |
cmdline_parser_print_help(); |
| 436 |
} |
| 437 |
|
| 438 |
if (arg_info.randomparticle_given){ |
| 439 |
isRandomParticle = 1; |
| 440 |
soluteX = arg_info.randomparticle_arg; |
| 441 |
} |
| 442 |
|
| 443 |
} |
| 444 |
/* ---------------Now do general arguments-----------------------*/ |
| 445 |
|
| 446 |
if (output_given){ //Output File (defaults to donkey if not specified. |
| 447 |
out_prefix = arg_info.output_arg; |
| 448 |
have_prefix = 1; |
| 449 |
} |
| 450 |
|
| 451 |
if (args_info.include_given){ // Deal with multiple include files. |
| 452 |
for( i = 0; i < args_info.include_given;++i){ |
| 453 |
if( headInc == NULL ){ |
| 454 |
headInc = new includeLinked; |
| 455 |
headInc->next = NULL; |
| 456 |
strcpy( headInc->name, args_info.include_arg[i] ); |
| 457 |
} |
| 458 |
else{ |
| 459 |
prevInc = headInc; |
| 460 |
currInc = headInc->next; |
| 461 |
while( currInc != NULL ){ |
| 462 |
prevInc = currInc; |
| 463 |
currInc = prevInc->next; |
| 464 |
} |
| 465 |
currInc = new includeLinked; |
| 466 |
currInc->next = NULL; |
| 467 |
strcpy( currInc->name, args_info.include_arg[i] ); |
| 468 |
prevInc->next = currInc; |
| 469 |
} |
| 470 |
} |
| 471 |
} |
| 472 |
|
| 473 |
if (args_info.random_given){ // Random Particle |
| 474 |
isRandom = 1;; |
| 475 |
} |
| 476 |
|
| 477 |
if (arg_info.inputs_num) { //Get input file name |
| 478 |
input_name = arg_info.inputs[1]; |
| 479 |
} |
| 480 |
else { |
| 481 |
sprintf( painCave.errMsg, |
| 482 |
"You must specify a input file name.\n" ); |
| 483 |
painCave.isFatal = 0; |
| 484 |
simError(); |
| 485 |
cmdline_parser_print_help(); |
| 486 |
|
| 487 |
} |
| 488 |
|
| 489 |
} |
| 490 |
|
| 491 |
|
| 492 |
|
| 493 |
|
| 494 |
|
| 495 |
|
| 496 |
|
| 497 |
|
| 498 |
|
| 499 |
|
| 500 |
/*************************************************************************** |
| 501 |
* prints out the usage for the command line arguments, then exits. |
| 502 |
***************************************************************************/ |
| 503 |
|
| 504 |
void usage(){ |
| 505 |
(void)fprintf(stdout, |
| 506 |
"The proper usage is: %s [options] <input bass>\n" |
| 507 |
"\n" |
| 508 |
"Options:\n" |
| 509 |
"\n" |
| 510 |
" short:\n" |
| 511 |
" ------\n" |
| 512 |
" -h Display this message\n" |
| 513 |
" -o <prefix> The output prefix\n" |
| 514 |
" -I <include> File name that should be included at the top of the\n" |
| 515 |
" output bass file.\n" |
| 516 |
" -r toggle the random option\n" |
| 517 |
"\n" |
| 518 |
" long:\n" |
| 519 |
" -----\n" |
| 520 |
" --bilayer <lipid> <water> Tries to build a basic bilayer with the specified number\n" |
| 521 |
" of lipids in the input bass file. The bilayer will be\n" |
| 522 |
" surrounded by the number of solvent molecules given\n" |
| 523 |
" in the bass file.\n" |
| 524 |
" -note: combined with \"-r\" the simulation will start\n" |
| 525 |
" the lipids randomly oriented in a sea of waters.\n" |
| 526 |
"\n" |
| 527 |
"\n", |
| 528 |
program_name); |
| 529 |
exit(8); |
| 530 |
} |
