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mmeineke |
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#include <iostream> |
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <math.h> |
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#include <string.h> |
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#include "QuickBass.hpp" |
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#include "latticeBuilder.hpp" |
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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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// 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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bassInfo bsInfo; |
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void parseBuildBass(char* in_name){ |
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int i; |
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char* id; |
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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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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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//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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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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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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// open and parse the bass file. |
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set_interface_stamps( the_stamps, the_globals ); |
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yacc_BASS( in_name ); |
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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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// 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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// 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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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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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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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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else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) { |
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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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else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) { |
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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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// get the components and calculate the tot_nMol and indvidual n_mol |
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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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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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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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// 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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for( i=0; i<bsInfo.nComponents; i++ ){ |
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id = the_components[i]->getType(); |
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bsInfo.compStamps[i] = NULL; |
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// check to make sure the component isn't already in the list |
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bsInfo.compStamps[i] = headStamp->match( id ); |
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if( bsInfo.compStamps[i] == NULL ){ |
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// extract the component from the list; |
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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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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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// get and set the boxSize |
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bsInfo.haveBox = false; |
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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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} |
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else if( the_globals->haveDensity() ){ |
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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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} |
