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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC vs.
Revision 1064 by tim, Tue Feb 24 15:44:45 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	//#include "ConjugateMinimizer.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14
15		#ifdef IS_MPI
16		#include "mpiBASS.h"
#	Line 14 | Line 19
19
20		// some defines for ensemble and Forcefield  cases
21
22	<	#define NVE_ENS   0
23	<	#define NVT_ENS   1
24	<	#define NPTi_ENS  2
25	<	#define NPTf_ENS  3
26	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
22	>	#define NVE_ENS        0
23	>	#define NVT_ENS        1
24	>	#define NPTi_ENS       2
25	>	#define NPTf_ENS       3
26	>	#define NPTxyz_ENS     4
27
28
29	<	#define FF_DUFF 0
30	<	#define FF_LJ   1
29	>	#define FF_DUFF  0
30	>	#define FF_LJ    1
31	>	#define FF_EAM   2
32	>	#define FF_H2O   3
33
34	+	using namespace std;
35
36	+	/**
37	+	* Check whether dividend is divisble by divisor or not
38	+	*/
39	+	bool isDivisible(double dividend, double divisor){
40	+	double tolerance = 0.000001;
41	+	double quotient;
42	+	double diff;
43	+	int intQuotient;
44	+
45	+	quotient = dividend / divisor;
46	+
47	+	if (quotient < 0)
48	+	quotient = -quotient;
49	+
50	+	intQuotient = int (quotient + tolerance);
51	+
52	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
53	+
54	+	if (diff <= tolerance)
55	+	return true;
56	+	else
57	+	return false;
58	+	}
59	+
60		SimSetup::SimSetup(){
61	+
62	+	initSuspend = false;
63	+	isInfoArray = 0;
64	+	nInfo = 1;
65	+
66		stamps = new MakeStamps();
67		globals = new Globals();
68	<
68	>
69	>
70		#ifdef IS_MPI
71	<	strcpy( checkPointMsg, "SimSetup creation successful" );
71	>	strcpy(checkPointMsg, "SimSetup creation successful");
72		MPIcheckPoint();
73		#endif // IS_MPI
74		}
#	Line 41 | Line 78 | void SimSetup::parseFile( char* fileName ){
78		delete globals;
79		}
80
81	<	void SimSetup::parseFile( char* fileName ){
81	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
82	>	info = the_info;
83	>	nInfo = theNinfo;
84	>	isInfoArray = 1;
85	>	initSuspend = true;
86	>	}
87
88	+
89	+	void SimSetup::parseFile(char* fileName){
90		#ifdef IS_MPI
91	<	if( worldRank == 0 ){
91	>	if (worldRank == 0){
92		#endif // is_mpi
93	<
93	>
94		inFileName = fileName;
95	<	set_interface_stamps( stamps, globals );
96	<
95	>	set_interface_stamps(stamps, globals);
96	>
97		#ifdef IS_MPI
98		mpiEventInit();
99		#endif
100
101	<	yacc_BASS( fileName );
101	>	yacc_BASS(fileName);
102
103		#ifdef IS_MPI
104		throwMPIEvent(NULL);
105		}
106	<	else receiveParse();
106	>	else{
107	>	receiveParse();
108	>	}
109		#endif
110
111		}
112
113		#ifdef IS_MPI
114		void SimSetup::receiveParse(void){
115	<
116	<	set_interface_stamps( stamps, globals );
117	<	mpiEventInit();
118	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
115	>	set_interface_stamps(stamps, globals);
116	>	mpiEventInit();
117	>	MPIcheckPoint();
118	>	mpiEventLoop();
119		}
120
121		#endif // is_mpi
122
123	<	void SimSetup::createSim( void ){
123	>	void SimSetup::createSim(void){
124
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
83	–	int i, j, k, globalAtomIndex;
84	–
125		// gather all of the information from the Bass file
126	<
126	>
127		gatherInfo();
128
129		// creation of complex system objects
130
131		sysObjectsCreation();
132
93	–
94	–
95	–	// initialize the arrays
96	–
97	–
98	–
99	–	makeMolecules();
100	–	info->identArray = new int[info->n_atoms];
101	–	for(i=0; i<info->n_atoms; i++){
102	–	info->identArray[i] = the_atoms[i]->getIdent();
103	–	}
104	–
105	–
133		// check on the post processing info
134	<
134	>
135		finalInfoCheck();
136
110	–
111	–
112	–
137		// initialize the system coordinates
138
139	<	initSystemCoords();
140	<
139	>	if ( !initSuspend ){
140	>	initSystemCoords();
141
142	+	if( !(globals->getUseInitTime()) )
143	+	info[0].currentTime = 0.0;
144	+	}
145	+
146		// make the output filenames
147
148		makeOutNames();
121	–
122	–
123	–
149
150	+	if (globals->haveMinimizer())
151	+	// make minimizer
152	+	makeMinimizer();
153	+	else
154	+	// make the integrator
155	+	makeIntegrator();
156
126	–
127	–
128	–
129	–
130	–	// make the integrator
131	–
132	–
133	–	NVT*  myNVT = NULL;
134	–	NPTi* myNPTi = NULL;
135	–	NPTf* myNPTf = NULL;
136	–	NPTim* myNPTim = NULL;
137	–	NPTfm* myNPTfm = NULL;
138	–
139	–	switch( ensembleCase ){
140	–
141	–	case NVE_ENS:
142	–	new NVE( info, the_ff );
143	–	break;
144	–
145	–	case NVT_ENS:
146	–	myNVT = new NVT( info, the_ff );
147	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
148	–
149	–	if (the_globals->haveTauThermostat())
150	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
151	–
152	–	else {
153	–	sprintf( painCave.errMsg,
154	–	"SimSetup error: If you use the NVT\n"
155	–	"    ensemble, you must set tauThermostat.\n");
156	–	painCave.isFatal = 1;
157	–	simError();
158	–	}
159	–	break;
160	–
161	–	case NPTi_ENS:
162	–	myNPTi = new NPTi( info, the_ff );
163	–	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164	–
165	–	if (the_globals->haveTargetPressure())
166	–	myNPTi->setTargetPressure(the_globals->getTargetPressure());
167	–	else {
168	–	sprintf( painCave.errMsg,
169	–	"SimSetup error: If you use a constant pressure\n"
170	–	"    ensemble, you must set targetPressure in the BASS file.\n");
171	–	painCave.isFatal = 1;
172	–	simError();
173	–	}
174	–
175	–	if( the_globals->haveTauThermostat() )
176	–	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
177	–	else{
178	–	sprintf( painCave.errMsg,
179	–	"SimSetup error: If you use an NPT\n"
180	–	"    ensemble, you must set tauThermostat.\n");
181	–	painCave.isFatal = 1;
182	–	simError();
183	–	}
184	–
185	–	if( the_globals->haveTauBarostat() )
186	–	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
187	–	else{
188	–	sprintf( painCave.errMsg,
189	–	"SimSetup error: If you use an NPT\n"
190	–	"    ensemble, you must set tauBarostat.\n");
191	–	painCave.isFatal = 1;
192	–	simError();
193	–	}
194	–	break;
195	–
196	–	case NPTf_ENS:
197	–	myNPTf = new NPTf( info, the_ff );
198	–	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199	–
200	–	if (the_globals->haveTargetPressure())
201	–	myNPTf->setTargetPressure(the_globals->getTargetPressure());
202	–	else {
203	–	sprintf( painCave.errMsg,
204	–	"SimSetup error: If you use a constant pressure\n"
205	–	"    ensemble, you must set targetPressure in the BASS file.\n");
206	–	painCave.isFatal = 1;
207	–	simError();
208	–	}
209	–
210	–	if( the_globals->haveTauThermostat() )
211	–	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
212	–	else{
213	–	sprintf( painCave.errMsg,
214	–	"SimSetup error: If you use an NPT\n"
215	–	"    ensemble, you must set tauThermostat.\n");
216	–	painCave.isFatal = 1;
217	–	simError();
218	–	}
219	–
220	–	if( the_globals->haveTauBarostat() )
221	–	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
222	–	else{
223	–	sprintf( painCave.errMsg,
224	–	"SimSetup error: If you use an NPT\n"
225	–	"    ensemble, you must set tauBarostat.\n");
226	–	painCave.isFatal = 1;
227	–	simError();
228	–	}
229	–	break;
230	–
231	–	case NPTim_ENS:
232	–	myNPTim = new NPTim( info, the_ff );
233	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234	–
235	–	if (the_globals->haveTargetPressure())
236	–	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	–	else {
238	–	sprintf( painCave.errMsg,
239	–	"SimSetup error: If you use a constant pressure\n"
240	–	"    ensemble, you must set targetPressure in the BASS file.\n");
241	–	painCave.isFatal = 1;
242	–	simError();
243	–	}
244	–
245	–	if( the_globals->haveTauThermostat() )
246	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	–	else{
248	–	sprintf( painCave.errMsg,
249	–	"SimSetup error: If you use an NPT\n"
250	–	"    ensemble, you must set tauThermostat.\n");
251	–	painCave.isFatal = 1;
252	–	simError();
253	–	}
254	–
255	–	if( the_globals->haveTauBarostat() )
256	–	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
257	–	else{
258	–	sprintf( painCave.errMsg,
259	–	"SimSetup error: If you use an NPT\n"
260	–	"    ensemble, you must set tauBarostat.\n");
261	–	painCave.isFatal = 1;
262	–	simError();
263	–	}
264	–	break;
265	–
266	–	case NPTfm_ENS:
267	–	myNPTfm = new NPTfm( info, the_ff );
268	–	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269	–
270	–	if (the_globals->haveTargetPressure())
271	–	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
272	–	else {
273	–	sprintf( painCave.errMsg,
274	–	"SimSetup error: If you use a constant pressure\n"
275	–	"    ensemble, you must set targetPressure in the BASS file.\n");
276	–	painCave.isFatal = 1;
277	–	simError();
278	–	}
279	–
280	–	if( the_globals->haveTauThermostat() )
281	–	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282	–	else{
283	–	sprintf( painCave.errMsg,
284	–	"SimSetup error: If you use an NPT\n"
285	–	"    ensemble, you must set tauThermostat.\n");
286	–	painCave.isFatal = 1;
287	–	simError();
288	–	}
289	–
290	–	if( the_globals->haveTauBarostat() )
291	–	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292	–	else{
293	–	sprintf( painCave.errMsg,
294	–	"SimSetup error: If you use an NPT\n"
295	–	"    ensemble, you must set tauBarostat.\n");
296	–	painCave.isFatal = 1;
297	–	simError();
298	–	}
299	–	break;
300	–
301	–	default:
302	–	sprintf( painCave.errMsg,
303	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
304	–	painCave.isFatal = 1;
305	–	simError();
306	–	}
307	–
308	–
157		#ifdef IS_MPI
158		mpiSim->mpiRefresh();
159		#endif
160
161		// initialize the Fortran
162
163	<
316	<	info->refreshSim();
317	<
318	<	if( !strcmp( info->mixingRule, "standard") ){
319	<	the_ff->initForceField( LB_MIXING_RULE );
320	<	}
321	<	else if( !strcmp( info->mixingRule, "explicit") ){
322	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
323	<	}
324	<	else{
325	<	sprintf( painCave.errMsg,
326	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
327	<	info->mixingRule );
328	<	painCave.isFatal = 1;
329	<	simError();
330	<	}
331	<
332	<
333	<	#ifdef IS_MPI
334	<	strcpy( checkPointMsg,
335	<	"Successfully intialized the mixingRule for Fortran." );
336	<	MPIcheckPoint();
337	<	#endif // is_mpi
163	>	initFortran();
164		}
165
166
167	<	void SimSetup::makeMolecules( void ){
168	<
167	>	void SimSetup::makeMolecules(void){
168	>	int k;
169		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	<	molInit info;
170	>	molInit molInfo;
171		DirectionalAtom* dAtom;
172		LinkedAssign* extras;
173		LinkedAssign* current_extra;
#	Line 354 | Line 180 | void SimSetup::makeMolecules( void ){
180		bend_set* theBends;
181		torsion_set* theTorsions;
182
357	–
183		//init the forceField paramters
184
185		the_ff->readParams();
186
187	<
187	>
188		// init the atoms
189
190	+	double phi, theta, psi;
191	+	double sux, suy, suz;
192	+	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
193		double ux, uy, uz, u, uSqr;
366	–
367	–	atomOffset = 0;
368	–	excludeOffset = 0;
369	–	for(i=0; i<info->n_mol; i++){
370	–
371	–	stampID = the_molecules[i].getStampID();
194
195	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
196	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
375	<	info.nBends    = comp_stamps[stampID]->getNBends();
376	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
377	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
195	>	for (k = 0; k < nInfo; k++){
196	>	the_ff->setSimInfo(&(info[k]));
197
198	<	info.myAtoms = &the_atoms[atomOffset];
199	<	info.myExcludes = &the_excludes[excludeOffset];
200	<	info.myBonds = new Bond*[info.nBonds];
201	<	info.myBends = new Bend*[info.nBends];
383	<	info.myTorsions = new Torsion*[info.nTorsions];
198	>	atomOffset = 0;
199	>	excludeOffset = 0;
200	>	for (i = 0; i < info[k].n_mol; i++){
201	>	stampID = info[k].molecules[i].getStampID();
202
203	<	theBonds = new bond_pair[info.nBonds];
204	<	theBends = new bend_set[info.nBends];
205	<	theTorsions = new torsion_set[info.nTorsions];
206	<
207	<	// make the Atoms
208	<
209	<	for(j=0; j<info.nAtoms; j++){
210	<
211	<	currentAtom = comp_stamps[stampID]->getAtom( j );
212	<	if( currentAtom->haveOrientation() ){
213	<
214	<	dAtom = new DirectionalAtom(j + atomOffset);
215	<	info->n_oriented++;
216	<	info.myAtoms[j] = dAtom;
217	<
218	<	ux = currentAtom->getOrntX();
219	<	uy = currentAtom->getOrntY();
220	<	uz = currentAtom->getOrntZ();
221	<
222	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
223	<
224	<	u = sqrt( uSqr );
225	<	ux = ux / u;
226	<	uy = uy / u;
227	<	uz = uz / u;
228	<
229	<	dAtom->setSUx( ux );
230	<	dAtom->setSUy( uy );
231	<	dAtom->setSUz( uz );
232	<	}
233	<	else{
234	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
235	<	}
236	<	info.myAtoms[j]->setType( currentAtom->getType() );
237	<
238	<	#ifdef IS_MPI
239	<
240	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
241	<
242	<	#endif // is_mpi
243	<	}
244	<
245	<	// make the bonds
246	<	for(j=0; j<info.nBonds; j++){
247	<
248	<	currentBond = comp_stamps[stampID]->getBond( j );
249	<	theBonds[j].a = currentBond->getA() + atomOffset;
250	<	theBonds[j].b = currentBond->getB() + atomOffset;
251	<
252	<	exI = theBonds[j].a;
253	<	exJ = theBonds[j].b;
254	<
255	<	// exclude_I must always be the smaller of the pair
256	<	if( exI > exJ ){
257	<	tempEx = exI;
258	<	exI = exJ;
259	<	exJ = tempEx;
260	<	}
261	<	#ifdef IS_MPI
262	<	tempEx = exI;
263	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
264	<	tempEx = exJ;
265	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
266	<
267	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
203	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
204	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
205	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
206	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
207	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
208	>
209	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
210	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
211	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
212	>	molInfo.myBends = new Bend * [molInfo.nBends];
213	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
214	>
215	>	theBonds = new bond_pair[molInfo.nBonds];
216	>	theBends = new bend_set[molInfo.nBends];
217	>	theTorsions = new torsion_set[molInfo.nTorsions];
218	>
219	>	// make the Atoms
220	>
221	>	for (j = 0; j < molInfo.nAtoms; j++){
222	>	currentAtom = comp_stamps[stampID]->getAtom(j);
223	>	if (currentAtom->haveOrientation()){
224	>	dAtom = new DirectionalAtom((j + atomOffset),
225	>	info[k].getConfiguration());
226	>	info[k].n_oriented++;
227	>	molInfo.myAtoms[j] = dAtom;
228	>
229	>	// Directional Atoms have standard unit vectors which are oriented
230	>	// in space using the three Euler angles.  We assume the standard
231	>	// unit vector was originally along the z axis below.
232	>
233	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
234	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
235	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
236	>
237	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
238	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239	>	Axz = sin(theta) * sin(psi);
240	>
241	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243	>	Ayz = sin(theta) * cos(psi);
244	>
245	>	Azx = sin(phi) * sin(theta);
246	>	Azy = -cos(phi) * sin(theta);
247	>	Azz = cos(theta);
248	>
249	>	sux = 0.0;
250	>	suy = 0.0;
251	>	suz = 1.0;
252	>
253	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
254	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
255	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
256	>
257	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258	>
259	>	u = sqrt(uSqr);
260	>	ux = ux / u;
261	>	uy = uy / u;
262	>	uz = uz / u;
263	>
264	>	dAtom->setSUx(ux);
265	>	dAtom->setSUy(uy);
266	>	dAtom->setSUz(uz);
267	>	}
268	>	else{
269	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
270	>	info[k].getConfiguration());
271	>	}
272	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
273	>
274	>	#ifdef IS_MPI
275	>
276	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
277	>
278	>	#endif // is_mpi
279	>	}
280	>
281	>	// make the bonds
282	>	for (j = 0; j < molInfo.nBonds; j++){
283	>	currentBond = comp_stamps[stampID]->getBond(j);
284	>	theBonds[j].a = currentBond->getA() + atomOffset;
285	>	theBonds[j].b = currentBond->getB() + atomOffset;
286	>
287	>	exI = theBonds[j].a;
288	>	exJ = theBonds[j].b;
289	>
290	>	// exclude_I must always be the smaller of the pair
291	>	if (exI > exJ){
292	>	tempEx = exI;
293	>	exI = exJ;
294	>	exJ = tempEx;
295	>	}
296	>	#ifdef IS_MPI
297	>	tempEx = exI;
298	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	>	tempEx = exJ;
300	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301	>
302	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
303	>	#else  // isn't MPI
304	>
305	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306	>	#endif  //is_mpi
307	>	}
308	>	excludeOffset += molInfo.nBonds;
309	>
310	>	//make the bends
311	>	for (j = 0; j < molInfo.nBends; j++){
312	>	currentBend = comp_stamps[stampID]->getBend(j);
313	>	theBends[j].a = currentBend->getA() + atomOffset;
314	>	theBends[j].b = currentBend->getB() + atomOffset;
315	>	theBends[j].c = currentBend->getC() + atomOffset;
316	>
317	>	if (currentBend->haveExtras()){
318	>	extras = currentBend->getExtras();
319	>	current_extra = extras;
320	>
321	>	while (current_extra != NULL){
322	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
323	>	switch (current_extra->getType()){
324	>	case 0:
325	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
326	>	theBends[j].isGhost = 1;
327	>	break;
328	>
329	>	case 1:
330	>	theBends[j].ghost = (int) current_extra->getDouble() +
331	>	atomOffset;
332	>	theBends[j].isGhost = 1;
333	>	break;
334	>
335	>	default:
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: ghostVectorSource was neither a "
338	>	"double nor an int.\n"
339	>	"-->Bend[%d] in %s\n",
340	>	j, comp_stamps[stampID]->getID());
341	>	painCave.isFatal = 1;
342	>	simError();
343	>	}
344	>	}
345	>	else{
346	>	sprintf(painCave.errMsg,
347	>	"SimSetup Error: unhandled bend assignment:\n"
348	>	"    -->%s in Bend[%d] in %s\n",
349	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353	>
354	>	current_extra = current_extra->getNext();
355	>	}
356	>	}
357	>
358	>	if (!theBends[j].isGhost){
359	>	exI = theBends[j].a;
360	>	exJ = theBends[j].c;
361	>	}
362	>	else{
363	>	exI = theBends[j].a;
364	>	exJ = theBends[j].b;
365	>	}
366	>
367	>	// exclude_I must always be the smaller of the pair
368	>	if (exI > exJ){
369	>	tempEx = exI;
370	>	exI = exJ;
371	>	exJ = tempEx;
372	>	}
373	>	#ifdef IS_MPI
374	>	tempEx = exI;
375	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
376	>	tempEx = exJ;
377	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
378	>
379	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
380		#else  // isn't MPI
381	<
452	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
381	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
382		#endif  //is_mpi
454	–	}
455	–	excludeOffset += info.nBonds;
456	–
457	–	//make the bends
458	–	for(j=0; j<info.nBends; j++){
459	–
460	–	currentBend = comp_stamps[stampID]->getBend( j );
461	–	theBends[j].a = currentBend->getA() + atomOffset;
462	–	theBends[j].b = currentBend->getB() + atomOffset;
463	–	theBends[j].c = currentBend->getC() + atomOffset;
464	–
465	–	if( currentBend->haveExtras() ){
466	–
467	–	extras = currentBend->getExtras();
468	–	current_extra = extras;
469	–
470	–	while( current_extra != NULL ){
471	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	–
473	–	switch( current_extra->getType() ){
474	–
475	–	case 0:
476	–	theBends[j].ghost =
477	–	current_extra->getInt() + atomOffset;
478	–	theBends[j].isGhost = 1;
479	–	break;
480	–
481	–	case 1:
482	–	theBends[j].ghost =
483	–	(int)current_extra->getDouble() + atomOffset;
484	–	theBends[j].isGhost = 1;
485	–	break;
486	–
487	–	default:
488	–	sprintf( painCave.errMsg,
489	–	"SimSetup Error: ghostVectorSource was neither a "
490	–	"double nor an int.\n"
491	–	"-->Bend[%d] in %s\n",
492	–	j, comp_stamps[stampID]->getID() );
493	–	painCave.isFatal = 1;
494	–	simError();
495	–	}
496	–	}
497	–
498	–	else{
499	–
500	–	sprintf( painCave.errMsg,
501	–	"SimSetup Error: unhandled bend assignment:\n"
502	–	"    -->%s in Bend[%d] in %s\n",
503	–	current_extra->getlhs(),
504	–	j, comp_stamps[stampID]->getID() );
505	–	painCave.isFatal = 1;
506	–	simError();
507	–	}
508	–
509	–	current_extra = current_extra->getNext();
510	–	}
383		}
384	<
513	<	if( !theBends[j].isGhost ){
514	<
515	<	exI = theBends[j].a;
516	<	exJ = theBends[j].c;
517	<	}
518	<	else{
519	<
520	<	exI = theBends[j].a;
521	<	exJ = theBends[j].b;
522	<	}
523	<
524	<	// exclude_I must always be the smaller of the pair
525	<	if( exI > exJ ){
526	<	tempEx = exI;
527	<	exI = exJ;
528	<	exJ = tempEx;
529	<	}
530	<	#ifdef IS_MPI
531	<	tempEx = exI;
532	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
533	<	tempEx = exJ;
534	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
535	<
536	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
537	<	#else  // isn't MPI
538	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
539	<	#endif  //is_mpi
540	<	}
541	<	excludeOffset += info.nBends;
384	>	excludeOffset += molInfo.nBends;
385
386	<	for(j=0; j<info.nTorsions; j++){
387	<
388	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
389	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
549	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
550	<
551	<	exI = theTorsions[j].a;
552	<	exJ = theTorsions[j].d;
386	>	for (j = 0; j < molInfo.nTorsions; j++){
387	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
388	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
389	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
390	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
391	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
392
393	<	// exclude_I must always be the smaller of the pair
394	<	if( exI > exJ ){
395	<	tempEx = exI;
396	<	exI = exJ;
397	<	exJ = tempEx;
398	<	}
393	>	exI = theTorsions[j].a;
394	>	exJ = theTorsions[j].d;
395	>
396	>	// exclude_I must always be the smaller of the pair
397	>	if (exI > exJ){
398	>	tempEx = exI;
399	>	exI = exJ;
400	>	exJ = tempEx;
401	>	}
402		#ifdef IS_MPI
403	<	tempEx = exI;
404	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
405	<	tempEx = exJ;
406	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
407	<
408	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
403	>	tempEx = exI;
404	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
405	>	tempEx = exJ;
406	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
407	>
408	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
409		#else  // isn't MPI
410	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
410	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
411		#endif  //is_mpi
412	<	}
413	<	excludeOffset += info.nTorsions;
412	>	}
413	>	excludeOffset += molInfo.nTorsions;
414
573	–
574	–	// send the arrays off to the forceField for init.
415
416	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
577	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
578	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
416	>	// send the arrays off to the forceField for init.
417
418	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
419	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
420	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
421	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
422	+	theTorsions);
423
582	–	the_molecules[i].initialize( info );
424
425	+	info[k].molecules[i].initialize(molInfo);
426
427	<	atomOffset += info.nAtoms;
428	<	delete[] theBonds;
429	<	delete[] theBends;
430	<	delete[] theTorsions;
427	>
428	>	atomOffset += molInfo.nAtoms;
429	>	delete[] theBonds;
430	>	delete[] theBends;
431	>	delete[] theTorsions;
432	>	}
433		}
434
435		#ifdef IS_MPI
436	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
436	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
437		MPIcheckPoint();
438		#endif // is_mpi
439
440		// clean up the forcefield
441	+
442		the_ff->calcRcut();
443		the_ff->cleanMe();
599	–
444		}
445
446	<	void SimSetup::initFromBass( void ){
603	<
446	>	void SimSetup::initFromBass(void){
447		int i, j, k;
448		int n_cells;
449		double cellx, celly, cellz;
#	Line 609 | Line 452 | void SimSetup::initFromBass( void ){
452		int n_extra;
453		int have_extra, done;
454
455	<	temp1 = (double)tot_nmol / 4.0;
456	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
457	<	temp3 = ceil( temp2 );
455	>	double vel[3];
456	>	vel[0] = 0.0;
457	>	vel[1] = 0.0;
458	>	vel[2] = 0.0;
459
460	<	have_extra =0;
461	<	if( temp2 < temp3 ){ // we have a non-complete lattice
462	<	have_extra =1;
460	>	temp1 = (double) tot_nmol / 4.0;
461	>	temp2 = pow(temp1, (1.0 / 3.0));
462	>	temp3 = ceil(temp2);
463
464	<	n_cells = (int)temp3 - 1;
465	<	cellx = info->boxLx / temp3;
466	<	celly = info->boxLy / temp3;
467	<	cellz = info->boxLz / temp3;
468	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
469	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
470	<	n_per_extra = (int)ceil( temp1 );
464	>	have_extra = 0;
465	>	if (temp2 < temp3){
466	>	// we have a non-complete lattice
467	>	have_extra = 1;
468	>
469	>	n_cells = (int) temp3 - 1;
470	>	cellx = info[0].boxL[0] / temp3;
471	>	celly = info[0].boxL[1] / temp3;
472	>	cellz = info[0].boxL[2] / temp3;
473	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
474	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
475	>	n_per_extra = (int) ceil(temp1);
476
477	<	if( n_per_extra > 4){
478	<	sprintf( painCave.errMsg,
479	<	"SimSetup error. There has been an error in constructing"
480	<	" the non-complete lattice.\n" );
477	>	if (n_per_extra > 4){
478	>	sprintf(painCave.errMsg,
479	>	"SimSetup error. There has been an error in constructing"
480	>	" the non-complete lattice.\n");
481		painCave.isFatal = 1;
482		simError();
483		}
484		}
485		else{
486	<	n_cells = (int)temp3;
487	<	cellx = info->boxLx / temp3;
488	<	celly = info->boxLy / temp3;
489	<	cellz = info->boxLz / temp3;
486	>	n_cells = (int) temp3;
487	>	cellx = info[0].boxL[0] / temp3;
488	>	celly = info[0].boxL[1] / temp3;
489	>	cellz = info[0].boxL[2] / temp3;
490		}
491
492		current_mol = 0;
#	Line 645 | Line 494 | void SimSetup::initFromBass( void ){
494		current_comp = 0;
495		current_atom_ndx = 0;
496
497	<	for( i=0; i < n_cells ; i++ ){
498	<	for( j=0; j < n_cells; j++ ){
499	<	for( k=0; k < n_cells; k++ ){
497	>	for (i = 0; i < n_cells ; i++){
498	>	for (j = 0; j < n_cells; j++){
499	>	for (k = 0; k < n_cells; k++){
500	>	makeElement(i * cellx, j * celly, k * cellz);
501
502	<	makeElement( i * cellx,
653	<	j * celly,
654	<	k * cellz );
502	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
503
504	<	makeElement( i * cellx + 0.5 * cellx,
657	<	j * celly + 0.5 * celly,
658	<	k * cellz );
504	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
505
506	<	makeElement( i * cellx,
661	<	j * celly + 0.5 * celly,
662	<	k * cellz + 0.5 * cellz );
663	<
664	<	makeElement( i * cellx + 0.5 * cellx,
665	<	j * celly,
666	<	k * cellz + 0.5 * cellz );
506	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
507		}
508		}
509		}
510
511	<	if( have_extra ){
511	>	if (have_extra){
512		done = 0;
513
514		int start_ndx;
515	<	for( i=0; i < (n_cells+1) && !done; i++ ){
516	<	for( j=0; j < (n_cells+1) && !done; j++ ){
515	>	for (i = 0; i < (n_cells + 1) && !done; i++){
516	>	for (j = 0; j < (n_cells + 1) && !done; j++){
517	>	if (i < n_cells){
518	>	if (j < n_cells){
519	>	start_ndx = n_cells;
520	>	}
521	>	else
522	>	start_ndx = 0;
523	>	}
524	>	else
525	>	start_ndx = 0;
526
527	<	if( i < n_cells ){
527	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
528	>	makeElement(i * cellx, j * celly, k * cellz);
529	>	done = (current_mol >= tot_nmol);
530
531	<	if( j < n_cells ){
532	<	start_ndx = n_cells;
533	<	}
534	<	else start_ndx = 0;
535	<	}
685	<	else start_ndx = 0;
531	>	if (!done && n_per_extra > 1){
532	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
533	>	k * cellz);
534	>	done = (current_mol >= tot_nmol);
535	>	}
536
537	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
537	>	if (!done && n_per_extra > 2){
538	>	makeElement(i * cellx, j * celly + 0.5 * celly,
539	>	k * cellz + 0.5 * cellz);
540	>	done = (current_mol >= tot_nmol);
541	>	}
542
543	<	makeElement( i * cellx,
544	<	j * celly,
545	<	k * cellz );
546	<	done = ( current_mol >= tot_nmol );
547	<
548	<	if( !done && n_per_extra > 1 ){
695	<	makeElement( i * cellx + 0.5 * cellx,
696	<	j * celly + 0.5 * celly,
697	<	k * cellz );
698	<	done = ( current_mol >= tot_nmol );
699	<	}
700	<
701	<	if( !done && n_per_extra > 2){
702	<	makeElement( i * cellx,
703	<	j * celly + 0.5 * celly,
704	<	k * cellz + 0.5 * cellz );
705	<	done = ( current_mol >= tot_nmol );
706	<	}
707	<
708	<	if( !done && n_per_extra > 3){
709	<	makeElement( i * cellx + 0.5 * cellx,
710	<	j * celly,
711	<	k * cellz + 0.5 * cellz );
712	<	done = ( current_mol >= tot_nmol );
713	<	}
714	<	}
543	>	if (!done && n_per_extra > 3){
544	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
545	>	k * cellz + 0.5 * cellz);
546	>	done = (current_mol >= tot_nmol);
547	>	}
548	>	}
549		}
550		}
551		}
552
553	<
554	<	for( i=0; i<info->n_atoms; i++ ){
721	<	info->atoms[i]->set_vx( 0.0 );
722	<	info->atoms[i]->set_vy( 0.0 );
723	<	info->atoms[i]->set_vz( 0.0 );
553	>	for (i = 0; i < info[0].n_atoms; i++){
554	>	info[0].atoms[i]->setVel(vel);
555		}
556		}
557
558	<	void SimSetup::makeElement( double x, double y, double z ){
728	<
558	>	void SimSetup::makeElement(double x, double y, double z){
559		int k;
560		AtomStamp* current_atom;
561		DirectionalAtom* dAtom;
562		double rotMat[3][3];
563	+	double pos[3];
564
565	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
566	<
567	<	current_atom = comp_stamps[current_comp]->getAtom( k );
568	<	if( !current_atom->havePosition() ){
569	<	sprintf( painCave.errMsg,
570	<	"SimSetup:initFromBass error.\n"
571	<	"\tComponent %s, atom %s does not have a position specified.\n"
572	<	"\tThe initialization routine is unable to give a start"
573	<	" position.\n",
743	<	comp_stamps[current_comp]->getID(),
744	<	current_atom->getType() );
565	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
566	>	current_atom = comp_stamps[current_comp]->getAtom(k);
567	>	if (!current_atom->havePosition()){
568	>	sprintf(painCave.errMsg,
569	>	"SimSetup:initFromBass error.\n"
570	>	"\tComponent %s, atom %s does not have a position specified.\n"
571	>	"\tThe initialization routine is unable to give a start"
572	>	" position.\n",
573	>	comp_stamps[current_comp]->getID(), current_atom->getType());
574		painCave.isFatal = 1;
575		simError();
576		}
577
578	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
579	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
580	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
578	>	pos[0] = x + current_atom->getPosX();
579	>	pos[1] = y + current_atom->getPosY();
580	>	pos[2] = z + current_atom->getPosZ();
581
582	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
582	>	info[0].atoms[current_atom_ndx]->setPos(pos);
583
584	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
584	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
585	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
586
587		rotMat[0][0] = 1.0;
588		rotMat[0][1] = 0.0;
#	Line 766 | Line 596 | void SimSetup::makeElement( double x, double y, double
596		rotMat[2][1] = 0.0;
597		rotMat[2][2] = 1.0;
598
599	<	dAtom->setA( rotMat );
599	>	dAtom->setA(rotMat);
600		}
601
602		current_atom_ndx++;
#	Line 775 | Line 605 | void SimSetup::makeElement( double x, double y, double
605		current_mol++;
606		current_comp_mol++;
607
608	<	if( current_comp_mol >= components_nmol[current_comp] ){
779	<
608	>	if (current_comp_mol >= components_nmol[current_comp]){
609		current_comp_mol = 0;
610		current_comp++;
611		}
612		}
613
614
615	<	void SimSetup::gatherInfo( void ){
615	>	void SimSetup::gatherInfo(void){
616	>	int i;
617
618		ensembleCase = -1;
619		ffCase = -1;
620
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
621		// set the easy ones first
796	–	info->target_temp = the_globals->getTargetTemp();
797	–	info->dt = the_globals->getDt();
798	–	info->run_time = the_globals->getRunTime();
799	–	n_components = the_globals->getNComponents();
622
623	+	for (i = 0; i < nInfo; i++){
624	+	info[i].target_temp = globals->getTargetTemp();
625	+	info[i].dt = globals->getDt();
626	+	info[i].run_time = globals->getRunTime();
627	+	}
628	+	n_components = globals->getNComponents();
629
630	+
631		// get the forceField
632
633	<	strcpy( force_field, the_globals->getForceField() );
633	>	strcpy(force_field, globals->getForceField());
634
635	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
636	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
635	>	if (!strcasecmp(force_field, "DUFF")){
636	>	ffCase = FF_DUFF;
637	>	}
638	>	else if (!strcasecmp(force_field, "LJ")){
639	>	ffCase = FF_LJ;
640	>	}
641	>	else if (!strcasecmp(force_field, "EAM")){
642	>	ffCase = FF_EAM;
643	>	}
644	>	else if (!strcasecmp(force_field, "WATER")){
645	>	ffCase = FF_H2O;
646	>	}
647		else{
648	<	sprintf( painCave.errMsg,
649	<	"SimSetup Error. Unrecognized force field -> %s\n",
650	<	force_field );
651	<	painCave.isFatal = 1;
813	<	simError();
648	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
649	>	force_field);
650	>	painCave.isFatal = 1;
651	>	simError();
652		}
653
654	<	// get the ensemble
654	>	// get the ensemble
655
656	<	strcpy( ensemble, the_globals->getEnsemble() );
656	>	strcpy(ensemble, globals->getEnsemble());
657
658	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
821	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
822	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
823	<	ensembleCase = NPTi_ENS;
824	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
825	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
826	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
827	<	else{
828	<	sprintf( painCave.errMsg,
829	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
830	<	"reverting to NVE for this simulation.\n",
831	<	ensemble );
832	<	painCave.isFatal = 0;
833	<	simError();
834	<	strcpy( ensemble, "NVE" );
658	>	if (!strcasecmp(ensemble, "NVE")){
659		ensembleCase = NVE_ENS;
660	<	}
661	<	strcpy( info->ensemble, ensemble );
662	<
663	<	// get the mixing rule
660	>	}
661	>	else if (!strcasecmp(ensemble, "NVT")){
662	>	ensembleCase = NVT_ENS;
663	>	}
664	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
665	>	ensembleCase = NPTi_ENS;
666	>	}
667	>	else if (!strcasecmp(ensemble, "NPTf")){
668	>	ensembleCase = NPTf_ENS;
669	>	}
670	>	else if (!strcasecmp(ensemble, "NPTxyz")){
671	>	ensembleCase = NPTxyz_ENS;
672	>	}
673	>	else{
674	>	sprintf(painCave.errMsg,
675	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
676	>	"\treverting to NVE for this simulation.\n",
677	>	ensemble);
678	>	painCave.isFatal = 0;
679	>	simError();
680	>	strcpy(ensemble, "NVE");
681	>	ensembleCase = NVE_ENS;
682	>	}
683
684	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
685	<	info->usePBC = the_globals->getPBC();
686	<
687	<
684	>	for (i = 0; i < nInfo; i++){
685	>	strcpy(info[i].ensemble, ensemble);
686	>
687	>	// get the mixing rule
688	>
689	>	strcpy(info[i].mixingRule, globals->getMixingRule());
690	>	info[i].usePBC = globals->getPBC();
691	>	}
692	>
693		// get the components and calculate the tot_nMol and indvidual n_mol
694	<
695	<	the_components = the_globals->getComponents();
694	>
695	>	the_components = globals->getComponents();
696		components_nmol = new int[n_components];
697
698
699	<	if( !the_globals->haveNMol() ){
699	>	if (!globals->haveNMol()){
700		// we don't have the total number of molecules, so we assume it is
701		// given in each component
702
703		tot_nmol = 0;
704	<	for( i=0; i<n_components; i++ ){
705	<
706	<	if( !the_components[i]->haveNMol() ){
707	<	// we have a problem
708	<	sprintf( painCave.errMsg,
709	<	"SimSetup Error. No global NMol or component NMol"
710	<	" given. Cannot calculate the number of atoms.\n" );
711	<	painCave.isFatal = 1;
864	<	simError();
704	>	for (i = 0; i < n_components; i++){
705	>	if (!the_components[i]->haveNMol()){
706	>	// we have a problem
707	>	sprintf(painCave.errMsg,
708	>	"SimSetup Error. No global NMol or component NMol given.\n"
709	>	"\tCannot calculate the number of atoms.\n");
710	>	painCave.isFatal = 1;
711	>	simError();
712		}
713
714		tot_nmol += the_components[i]->getNMol();
#	Line 869 | Line 716 | void SimSetup::gatherInfo( void ){
716		}
717		}
718		else{
719	<	sprintf( painCave.errMsg,
720	<	"SimSetup error.\n"
721	<	"\tSorry, the ability to specify total"
722	<	" nMols and then give molfractions in the components\n"
723	<	"\tis not currently supported."
724	<	" Please give nMol in the components.\n" );
719	>	sprintf(painCave.errMsg,
720	>	"SimSetup error.\n"
721	>	"\tSorry, the ability to specify total"
722	>	" nMols and then give molfractions in the components\n"
723	>	"\tis not currently supported."
724	>	" Please give nMol in the components.\n");
725		painCave.isFatal = 1;
726		simError();
727		}
728
729	<	// set the status, sample, and thermal kick times
730	<
731	<	if( the_globals->haveSampleTime() ){
732	<	info->sampleTime = the_globals->getSampleTime();
733	<	info->statusTime = info->sampleTime;
734	<	info->thermalTime = info->sampleTime;
729	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
730	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
731	>	sprintf(painCave.errMsg,
732	>	"Sample time is not divisible by dt.\n"
733	>	"\tThis will result in samples that are not uniformly\n"
734	>	"\tdistributed in time.  If this is a problem, change\n"
735	>	"\tyour sampleTime variable.\n");
736	>	painCave.isFatal = 0;
737	>	simError();
738		}
889	–	else{
890	–	info->sampleTime = the_globals->getRunTime();
891	–	info->statusTime = info->sampleTime;
892	–	info->thermalTime = info->sampleTime;
893	–	}
739
740	<	if( the_globals->haveStatusTime() ){
741	<	info->statusTime = the_globals->getStatusTime();
740	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
741	>	sprintf(painCave.errMsg,
742	>	"Status time is not divisible by dt.\n"
743	>	"\tThis will result in status reports that are not uniformly\n"
744	>	"\tdistributed in time.  If this is a problem, change \n"
745	>	"\tyour statusTime variable.\n");
746	>	painCave.isFatal = 0;
747	>	simError();
748		}
749
750	<	if( the_globals->haveThermalTime() ){
751	<	info->thermalTime = the_globals->getThermalTime();
752	<	}
750	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
751	>	sprintf(painCave.errMsg,
752	>	"Thermal time is not divisible by dt.\n"
753	>	"\tThis will result in thermalizations that are not uniformly\n"
754	>	"\tdistributed in time.  If this is a problem, change \n"
755	>	"\tyour thermalTime variable.\n");
756	>	painCave.isFatal = 0;
757	>	simError();
758	>	}
759
760	<	// check for the temperature set flag
760	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
761	>	sprintf(painCave.errMsg,
762	>	"Reset time is not divisible by dt.\n"
763	>	"\tThis will result in integrator resets that are not uniformly\n"
764	>	"\tdistributed in time.  If this is a problem, change\n"
765	>	"\tyour resetTime variable.\n");
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769
770	<	if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();
770	>	// set the status, sample, and thermal kick times
771
772	<	// get some of the tricky things that may still be in the globals
772	>	for (i = 0; i < nInfo; i++){
773	>	if (globals->haveSampleTime()){
774	>	info[i].sampleTime = globals->getSampleTime();
775	>	info[i].statusTime = info[i].sampleTime;
776	>	info[i].thermalTime = info[i].sampleTime;
777	>	}
778	>	else{
779	>	info[i].sampleTime = globals->getRunTime();
780	>	info[i].statusTime = info[i].sampleTime;
781	>	info[i].thermalTime = info[i].sampleTime;
782	>	}
783
784	<	double boxVector[3];
785	<	if( the_globals->haveBox() ){
911	<	boxVector[0] = the_globals->getBox();
912	<	boxVector[1] = the_globals->getBox();
913	<	boxVector[2] = the_globals->getBox();
914	<
915	<	info->setBox( boxVector );
916	<	}
917	<	else if( the_globals->haveDensity() ){
918	<
919	<	double vol;
920	<	vol = (double)tot_nmol / the_globals->getDensity();
921	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
922	<	boxVector[1] = boxVector[0];
923	<	boxVector[2] = boxVector[0];
924	<
925	<	info->setBox( boxVector );
926	<	}
927	<	else{
928	<	if( !the_globals->haveBoxX() ){
929	<	sprintf( painCave.errMsg,
930	<	"SimSetup error, no periodic BoxX size given.\n" );
931	<	painCave.isFatal = 1;
932	<	simError();
784	>	if (globals->haveStatusTime()){
785	>	info[i].statusTime = globals->getStatusTime();
786		}
934	–	boxVector[0] = the_globals->getBoxX();
787
788	<	if( !the_globals->haveBoxY() ){
789	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
788	>	if (globals->haveThermalTime()){
789	>	info[i].thermalTime = globals->getThermalTime();
790		}
942	–	boxVector[1] = the_globals->getBoxY();
791
792	<	if( !the_globals->haveBoxZ() ){
793	<	sprintf( painCave.errMsg,
794	<	"SimSetup error, no periodic BoxZ size given.\n" );
795	<	painCave.isFatal = 1;
948	<	simError();
792	>	info[i].resetIntegrator = 0;
793	>	if( globals->haveResetTime() ){
794	>	info[i].resetTime = globals->getResetTime();
795	>	info[i].resetIntegrator = 1;
796		}
950	–	boxVector[2] = the_globals->getBoxZ();
797
798	<	info->setBox( boxVector );
798	>	// check for the temperature set flag
799	>
800	>	if (globals->haveTempSet())
801	>	info[i].setTemp = globals->getTempSet();
802	>
803	>	// check for the extended State init
804	>
805	>	info[i].useInitXSstate = globals->getUseInitXSstate();
806	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
807	>
808		}
809	+
810	+	//setup seed for random number generator
811	+	int seedValue;
812
813	+	if (globals->haveSeed()){
814	+	seedValue = globals->getSeed();
815
816	+	if(seedValue / 1E9 == 0){
817	+	sprintf(painCave.errMsg,
818	+	"Seed for sprng library should contain at least 9 digits\n"
819	+	"OOPSE will generate a seed for user\n");
820	+	painCave.isFatal = 0;
821	+	simError();
822	+
823	+	//using seed generated by system instead of invalid seed set by user
824	+	#ifndef IS_MPI
825	+	seedValue = make_sprng_seed();
826	+	#else
827	+	if (worldRank == 0){
828	+	seedValue = make_sprng_seed();
829	+	}
830	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
831	+	#endif
832	+	}
833	+	}//end of if branch of globals->haveSeed()
834	+	else{
835
836	+	#ifndef IS_MPI
837	+	seedValue = make_sprng_seed();
838	+	#else
839	+	if (worldRank == 0){
840	+	seedValue = make_sprng_seed();
841	+	}
842	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
843	+	#endif
844	+	}//end of globals->haveSeed()
845	+
846	+	for (int i = 0; i < nInfo; i++){
847	+	info[i].setSeed(seedValue);
848	+	}
849	+
850		#ifdef IS_MPI
851	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
851	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
852		MPIcheckPoint();
853		#endif // is_mpi
961	–
854		}
855
856
857	<	void SimSetup::finalInfoCheck( void ){
857	>	void SimSetup::finalInfoCheck(void){
858		int index;
859		int usesDipoles;
860	<
860	>	int i;
861
862	<	// check electrostatic parameters
863	<
864	<	index = 0;
865	<	usesDipoles = 0;
866	<	while( (index < info->n_atoms) && !usesDipoles ){
867	<	usesDipoles = ((info->atoms)[index])->hasDipole();
868	<	index++;
869	<	}
870	<
862	>	for (i = 0; i < nInfo; i++){
863	>	// check electrostatic parameters
864	>
865	>	index = 0;
866	>	usesDipoles = 0;
867	>	while ((index < info[i].n_atoms) && !usesDipoles){
868	>	usesDipoles = (info[i].atoms[index])->hasDipole();
869	>	index++;
870	>	}
871	>
872		#ifdef IS_MPI
873	<	int myUse = usesDipoles
874	<	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
873	>	int myUse = usesDipoles;
874	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875		#endif //is_mpi
876
877	+	double theEcr, theEst;
878
879	<	if (the_globals->getUseRF() ) {
880	<	info->useReactionField = 1;
987	<
988	<	if( !the_globals->haveECR() ){
989	<	sprintf( painCave.errMsg,
990	<	"SimSetup Warning: using default value of 1/2 the smallest "
991	<	"box length for the electrostaticCutoffRadius.\n"
992	<	"I hope you have a very fast processor!\n");
993	<	painCave.isFatal = 0;
994	<	simError();
995	<	double smallest;
996	<	smallest = info->boxLx;
997	<	if (info->boxLy <= smallest) smallest = info->boxLy;
998	<	if (info->boxLz <= smallest) smallest = info->boxLz;
999	<	info->ecr = 0.5 * smallest;
1000	<	} else {
1001	<	info->ecr        = the_globals->getECR();
1002	<	}
879	>	if (globals->getUseRF()){
880	>	info[i].useReactionField = 1;
881
882	<	if( !the_globals->haveEST() ){
883	<	sprintf( painCave.errMsg,
884	<	"SimSetup Warning: using default value of 0.05 * the "
885	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
886	<	);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	info->est = 0.05 * info->ecr;
1012	<	} else {
1013	<	info->est        = the_globals->getEST();
1014	<	}
1015	<
1016	<	if(!the_globals->haveDielectric() ){
1017	<	sprintf( painCave.errMsg,
1018	<	"SimSetup Error: You are trying to use Reaction Field without"
1019	<	"setting a dielectric constant!\n"
1020	<	);
1021	<	painCave.isFatal = 1;
1022	<	simError();
1023	<	}
1024	<	info->dielectric = the_globals->getDielectric();
1025	<	}
1026	<	else {
1027	<	if (usesDipoles) {
1028	<
1029	<	if( !the_globals->haveECR() ){
1030	<	sprintf( painCave.errMsg,
1031	<	"SimSetup Warning: using default value of 1/2 the smallest "
1032	<	"box length for the electrostaticCutoffRadius.\n"
1033	<	"I hope you have a very fast processor!\n");
882	>	if (!globals->haveECR()){
883	>	sprintf(painCave.errMsg,
884	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
885	>	"\tOOPSE will use a default value of 15.0 angstroms"
886	>	"\tfor the electrostaticCutoffRadius.\n");
887		painCave.isFatal = 0;
888		simError();
889	<	double smallest;
1037	<	smallest = info->boxLx;
1038	<	if (info->boxLy <= smallest) smallest = info->boxLy;
1039	<	if (info->boxLz <= smallest) smallest = info->boxLz;
1040	<	info->ecr = 0.5 * smallest;
1041	<	} else {
1042	<	info->ecr        = the_globals->getECR();
889	>	theEcr = 15.0;
890		}
891	<
892	<	if( !the_globals->haveEST() ){
893	<	sprintf( painCave.errMsg,
894	<	"SimSetup Warning: using default value of 5%% of the "
895	<	"electrostaticCutoffRadius for the "
896	<	"electrostaticSkinThickness\n"
897	<	);
891	>	else{
892	>	theEcr = globals->getECR();
893	>	}
894	>
895	>	if (!globals->haveEST()){
896	>	sprintf(painCave.errMsg,
897	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
898	>	"\tOOPSE will use a default value of\n"
899	>	"\t0.05 * electrostaticCutoffRadius\n"
900	>	"\tfor the electrostaticSkinThickness\n");
901		painCave.isFatal = 0;
902		simError();
903	<	info->est = 0.05 * info->ecr;
1054	<	} else {
1055	<	info->est        = the_globals->getEST();
903	>	theEst = 0.05 * theEcr;
904		}
905	+	else{
906	+	theEst = globals->getEST();
907	+	}
908	+
909	+	info[i].setDefaultEcr(theEcr, theEst);
910	+
911	+	if (!globals->haveDielectric()){
912	+	sprintf(painCave.errMsg,
913	+	"SimSetup Error: No Dielectric constant was set.\n"
914	+	"\tYou are trying to use Reaction Field without"
915	+	"\tsetting a dielectric constant!\n");
916	+	painCave.isFatal = 1;
917	+	simError();
918	+	}
919	+	info[i].dielectric = globals->getDielectric();
920		}
921	<	}
922	<
921	>	else{
922	>	if (usesDipoles){
923	>	if (!globals->haveECR()){
924	>	sprintf(painCave.errMsg,
925	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
926	>	"\tOOPSE will use a default value of 15.0 angstroms"
927	>	"\tfor the electrostaticCutoffRadius.\n");
928	>	painCave.isFatal = 0;
929	>	simError();
930	>	theEcr = 15.0;
931	>	}
932	>	else{
933	>	theEcr = globals->getECR();
934	>	}
935	>
936	>	if (!globals->haveEST()){
937	>	sprintf(painCave.errMsg,
938	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
939	>	"\tOOPSE will use a default value of\n"
940	>	"\t0.05 * electrostaticCutoffRadius\n"
941	>	"\tfor the electrostaticSkinThickness\n");
942	>	painCave.isFatal = 0;
943	>	simError();
944	>	theEst = 0.05 * theEcr;
945	>	}
946	>	else{
947	>	theEst = globals->getEST();
948	>	}
949	>
950	>	info[i].setDefaultEcr(theEcr, theEst);
951	>	}
952	>	}
953	>	}
954		#ifdef IS_MPI
955	<	strcpy( checkPointMsg, "post processing checks out" );
955	>	strcpy(checkPointMsg, "post processing checks out");
956		MPIcheckPoint();
957		#endif // is_mpi
1064	–
958		}
959	+
960	+	void SimSetup::initSystemCoords(void){
961	+	int i;
962
963	<	void SimSetup::initSystemCoords( void ){
963	>	char* inName;
964
965	<	if( the_globals->haveInitialConfig() ){
966	<
967	<	InitializeFromFile* fileInit;
965	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
966	>
967	>	for (i = 0; i < info[0].n_atoms; i++)
968	>	info[0].atoms[i]->setCoords();
969	>
970	>	if (globals->haveInitialConfig()){
971	>	InitializeFromFile* fileInit;
972		#ifdef IS_MPI // is_mpi
973	<	if( worldRank == 0 ){
973	>	if (worldRank == 0){
974		#endif //is_mpi
975	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
975	>	inName = globals->getInitialConfig();
976	>	fileInit = new InitializeFromFile(inName);
977		#ifdef IS_MPI
978	<	}else fileInit = new InitializeFromFile( NULL );
978	>	}
979	>	else
980	>	fileInit = new InitializeFromFile(NULL);
981		#endif
982	<	fileInit->read_xyz( info ); // default velocities on
982	>	fileInit->readInit(info); // default velocities on
983
984	<	delete fileInit;
985	<	}
986	<	else{
984	>	delete fileInit;
985	>	}
986	>	else{
987	>
988	>	// no init from bass
989	>
990	>	sprintf(painCave.errMsg,
991	>	"Cannot intialize a simulation without an initial configuration file.\n");
992	>	painCave.isFatal = 1;;
993	>	simError();
994	>
995	>	}
996
1085	–	#ifdef IS_MPI
1086	–
1087	–	// no init from bass
1088	–
1089	–	sprintf( painCave.errMsg,
1090	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1091	–	painCave.isFatal;
1092	–	simError();
1093	–
1094	–	#else
1095	–
1096	–	initFromBass();
1097	–
1098	–
1099	–	#endif
1100	–	}
1101	–
997		#ifdef IS_MPI
998	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
998	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
999		MPIcheckPoint();
1000		#endif // is_mpi
1106	–
1001		}
1002
1003
1004	<	void SimSetup::makeOutNames( void ){
1004	>	void SimSetup::makeOutNames(void){
1005	>	int k;
1006
1007	+
1008	+	for (k = 0; k < nInfo; k++){
1009		#ifdef IS_MPI
1010	<	if( worldRank == 0 ){
1010	>	if (worldRank == 0){
1011		#endif // is_mpi
1012	<
1013	<	if( the_globals->haveFinalConfig() ){
1014	<	strcpy( info->finalName, the_globals->getFinalConfig() );
1118	<	}
1119	<	else{
1120	<	strcpy( info->finalName, inFileName );
1121	<	char* endTest;
1122	<	int nameLength = strlen( info->finalName );
1123	<	endTest = &(info->finalName[nameLength - 5]);
1124	<	if( !strcmp( endTest, ".bass" ) ){
1125	<	strcpy( endTest, ".eor" );
1012	>
1013	>	if (globals->haveFinalConfig()){
1014	>	strcpy(info[k].finalName, globals->getFinalConfig());
1015		}
1127	–	else if( !strcmp( endTest, ".BASS" ) ){
1128	–	strcpy( endTest, ".eor" );
1129	–	}
1016		else{
1017	<	endTest = &(info->finalName[nameLength - 4]);
1018	<	if( !strcmp( endTest, ".bss" ) ){
1019	<	strcpy( endTest, ".eor" );
1020	<	}
1021	<	else if( !strcmp( endTest, ".mdl" ) ){
1022	<	strcpy( endTest, ".eor" );
1023	<	}
1024	<	else{
1025	<	strcat( info->finalName, ".eor" );
1026	<	}
1017	>	strcpy(info[k].finalName, inFileName);
1018	>	char* endTest;
1019	>	int nameLength = strlen(info[k].finalName);
1020	>	endTest = &(info[k].finalName[nameLength - 5]);
1021	>	if (!strcmp(endTest, ".bass")){
1022	>	strcpy(endTest, ".eor");
1023	>	}
1024	>	else if (!strcmp(endTest, ".BASS")){
1025	>	strcpy(endTest, ".eor");
1026	>	}
1027	>	else{
1028	>	endTest = &(info[k].finalName[nameLength - 4]);
1029	>	if (!strcmp(endTest, ".bss")){
1030	>	strcpy(endTest, ".eor");
1031	>	}
1032	>	else if (!strcmp(endTest, ".mdl")){
1033	>	strcpy(endTest, ".eor");
1034	>	}
1035	>	else{
1036	>	strcat(info[k].finalName, ".eor");
1037	>	}
1038	>	}
1039		}
1040	<	}
1041	<
1042	<	// make the sample and status out names
1043	<
1044	<	strcpy( info->sampleName, inFileName );
1045	<	char* endTest;
1046	<	int nameLength = strlen( info->sampleName );
1047	<	endTest = &(info->sampleName[nameLength - 5]);
1048	<	if( !strcmp( endTest, ".bass" ) ){
1151	<	strcpy( endTest, ".dump" );
1152	<	}
1153	<	else if( !strcmp( endTest, ".BASS" ) ){
1154	<	strcpy( endTest, ".dump" );
1155	<	}
1156	<	else{
1157	<	endTest = &(info->sampleName[nameLength - 4]);
1158	<	if( !strcmp( endTest, ".bss" ) ){
1159	<	strcpy( endTest, ".dump" );
1040	>
1041	>	// make the sample and status out names
1042	>
1043	>	strcpy(info[k].sampleName, inFileName);
1044	>	char* endTest;
1045	>	int nameLength = strlen(info[k].sampleName);
1046	>	endTest = &(info[k].sampleName[nameLength - 5]);
1047	>	if (!strcmp(endTest, ".bass")){
1048	>	strcpy(endTest, ".dump");
1049		}
1050	<	else if( !strcmp( endTest, ".mdl" ) ){
1051	<	strcpy( endTest, ".dump" );
1050	>	else if (!strcmp(endTest, ".BASS")){
1051	>	strcpy(endTest, ".dump");
1052		}
1053		else{
1054	<	strcat( info->sampleName, ".dump" );
1054	>	endTest = &(info[k].sampleName[nameLength - 4]);
1055	>	if (!strcmp(endTest, ".bss")){
1056	>	strcpy(endTest, ".dump");
1057	>	}
1058	>	else if (!strcmp(endTest, ".mdl")){
1059	>	strcpy(endTest, ".dump");
1060	>	}
1061	>	else{
1062	>	strcat(info[k].sampleName, ".dump");
1063	>	}
1064		}
1065	<	}
1066	<
1067	<	strcpy( info->statusName, inFileName );
1068	<	nameLength = strlen( info->statusName );
1069	<	endTest = &(info->statusName[nameLength - 5]);
1070	<	if( !strcmp( endTest, ".bass" ) ){
1173	<	strcpy( endTest, ".stat" );
1174	<	}
1175	<	else if( !strcmp( endTest, ".BASS" ) ){
1176	<	strcpy( endTest, ".stat" );
1177	<	}
1178	<	else{
1179	<	endTest = &(info->statusName[nameLength - 4]);
1180	<	if( !strcmp( endTest, ".bss" ) ){
1181	<	strcpy( endTest, ".stat" );
1065	>
1066	>	strcpy(info[k].statusName, inFileName);
1067	>	nameLength = strlen(info[k].statusName);
1068	>	endTest = &(info[k].statusName[nameLength - 5]);
1069	>	if (!strcmp(endTest, ".bass")){
1070	>	strcpy(endTest, ".stat");
1071		}
1072	<	else if( !strcmp( endTest, ".mdl" ) ){
1073	<	strcpy( endTest, ".stat" );
1072	>	else if (!strcmp(endTest, ".BASS")){
1073	>	strcpy(endTest, ".stat");
1074		}
1075		else{
1076	<	strcat( info->statusName, ".stat" );
1076	>	endTest = &(info[k].statusName[nameLength - 4]);
1077	>	if (!strcmp(endTest, ".bss")){
1078	>	strcpy(endTest, ".stat");
1079	>	}
1080	>	else if (!strcmp(endTest, ".mdl")){
1081	>	strcpy(endTest, ".stat");
1082	>	}
1083	>	else{
1084	>	strcat(info[k].statusName, ".stat");
1085	>	}
1086		}
1087	<	}
1190	<
1087	>
1088		#ifdef IS_MPI
1192	–	}
1193	–	#endif // is_mpi
1089
1090	+	}
1091	+	#endif // is_mpi
1092	+	}
1093		}
1094
1095
1096	<	void SimSetup::sysObjectsCreation( void ){
1096	>	void SimSetup::sysObjectsCreation(void){
1097	>	int i, k;
1098
1099		// create the forceField
1100
#	Line 1211 | Line 1110 | void SimSetup::sysObjectsCreation( void ){
1110
1111		#ifdef IS_MPI
1112		// divide the molecules among the processors
1113	<
1113	>
1114		mpiMolDivide();
1115		#endif //is_mpi
1116	<
1116	>
1117		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1118	<
1118	>
1119		makeSysArrays();
1120
1121	<
1121	>	// make and initialize the molecules (all but atomic coordinates)
1122
1123	+	makeMolecules();
1124
1125	+	for (k = 0; k < nInfo; k++){
1126	+	info[k].identArray = new int[info[k].n_atoms];
1127	+	for (i = 0; i < info[k].n_atoms; i++){
1128	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1129	+	}
1130	+	}
1131		}
1132
1133
1134	<	void SimSetup::createFF( void ){
1134	>	void SimSetup::createFF(void){
1135	>	switch (ffCase){
1136	>	case FF_DUFF:
1137	>	the_ff = new DUFF();
1138	>	break;
1139
1140	<	switch( ffCase ){
1140	>	case FF_LJ:
1141	>	the_ff = new LJFF();
1142	>	break;
1143
1144	<	case FF_DUFF:
1145	<	the_ff = new DUFF();
1146	<	break;
1144	>	case FF_EAM:
1145	>	the_ff = new EAM_FF();
1146	>	break;
1147
1148	<	case FF_LJ:
1149	<	the_ff = new LJFF();
1150	<	break;
1148	>	case FF_H2O:
1149	>	the_ff = new WATER();
1150	>	break;
1151
1152	<	default:
1153	<	sprintf( painCave.errMsg,
1154	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1155	<	painCave.isFatal = 1;
1156	<	simError();
1152	>	default:
1153	>	sprintf(painCave.errMsg,
1154	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1155	>	painCave.isFatal = 1;
1156	>	simError();
1157		}
1158
1159		#ifdef IS_MPI
1160	<	strcpy( checkPointMsg, "ForceField creation successful" );
1160	>	strcpy(checkPointMsg, "ForceField creation successful");
1161		MPIcheckPoint();
1162		#endif // is_mpi
1251	–
1163		}
1164
1165
1166	<	void SimSetup::compList( void ){
1166	>	void SimSetup::compList(void){
1167	>	int i;
1168	>	char* id;
1169	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1170	>	LinkedMolStamp* currentStamp = NULL;
1171	>	comp_stamps = new MoleculeStamp * [n_components];
1172
1257	–	comp_stamps = new MoleculeStamp*[n_components];
1258	–
1173		// make an array of molecule stamps that match the components used.
1174		// also extract the used stamps out into a separate linked list
1175
1176	<	info->nComponents = n_components;
1177	<	info->componentsNmol = components_nmol;
1178	<	info->compStamps = comp_stamps;
1179	<	info->headStamp = new LinkedMolStamp();
1180	<
1181	<	char* id;
1268	<	LinkedMolStamp* headStamp = info->headStamp;
1269	<	LinkedMolStamp* currentStamp = NULL;
1270	<	for( i=0; i<n_components; i++ ){
1176	>	for (i = 0; i < nInfo; i++){
1177	>	info[i].nComponents = n_components;
1178	>	info[i].componentsNmol = components_nmol;
1179	>	info[i].compStamps = comp_stamps;
1180	>	info[i].headStamp = headStamp;
1181	>	}
1182
1183	+
1184	+	for (i = 0; i < n_components; i++){
1185		id = the_components[i]->getType();
1186		comp_stamps[i] = NULL;
1187	<
1187	>
1188		// check to make sure the component isn't already in the list
1189
1190	<	comp_stamps[i] = headStamp->match( id );
1191	<	if( comp_stamps[i] == NULL ){
1279	<
1190	>	comp_stamps[i] = headStamp->match(id);
1191	>	if (comp_stamps[i] == NULL){
1192		// extract the component from the list;
1193	<
1194	<	currentStamp = the_stamps->extractMolStamp( id );
1195	<	if( currentStamp == NULL ){
1196	<	sprintf( painCave.errMsg,
1197	<	"SimSetup error: Component \"%s\" was not found in the "
1198	<	"list of declared molecules\n",
1199	<	id );
1200	<	painCave.isFatal = 1;
1201	<	simError();
1193	>
1194	>	currentStamp = stamps->extractMolStamp(id);
1195	>	if (currentStamp == NULL){
1196	>	sprintf(painCave.errMsg,
1197	>	"SimSetup error: Component \"%s\" was not found in the "
1198	>	"list of declared molecules\n",
1199	>	id);
1200	>	painCave.isFatal = 1;
1201	>	simError();
1202		}
1203	<
1204	<	headStamp->add( currentStamp );
1205	<	comp_stamps[i] = headStamp->match( id );
1203	>
1204	>	headStamp->add(currentStamp);
1205	>	comp_stamps[i] = headStamp->match(id);
1206		}
1207		}
1208
1209		#ifdef IS_MPI
1210	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1210	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1211		MPIcheckPoint();
1212		#endif // is_mpi
1301	–
1302	–
1213		}
1214
1215	<	void SimSetup::calcSysValues( void ){
1215	>	void SimSetup::calcSysValues(void){
1216	>	int i;
1217
1218	+	int* molMembershipArray;
1219	+
1220		tot_atoms = 0;
1221		tot_bonds = 0;
1222		tot_bends = 0;
1223		tot_torsions = 0;
1224	<	for( i=0; i<n_components; i++ ){
1225	<
1226	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1227	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1315	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1224	>	for (i = 0; i < n_components; i++){
1225	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1226	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1227	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1228		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1229		}
1230
1231		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1232	+	molMembershipArray = new int[tot_atoms];
1233
1234	<	info->n_atoms = tot_atoms;
1235	<	info->n_bonds = tot_bonds;
1236	<	info->n_bends = tot_bends;
1237	<	info->n_torsions = tot_torsions;
1238	<	info->n_SRI = tot_SRI;
1239	<	info->n_mol = tot_nmol;
1240	<
1241	<	info->molMembershipArray = new int[tot_atoms];
1234	>	for (i = 0; i < nInfo; i++){
1235	>	info[i].n_atoms = tot_atoms;
1236	>	info[i].n_bonds = tot_bonds;
1237	>	info[i].n_bends = tot_bends;
1238	>	info[i].n_torsions = tot_torsions;
1239	>	info[i].n_SRI = tot_SRI;
1240	>	info[i].n_mol = tot_nmol;
1241	>
1242	>	info[i].molMembershipArray = molMembershipArray;
1243	>	}
1244		}
1245
1331	–
1246		#ifdef IS_MPI
1247
1248	<	void SimSetup::mpiMolDivide( void ){
1249	<
1248	>	void SimSetup::mpiMolDivide(void){
1249	>	int i, j, k;
1250		int localMol, allMol;
1251		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1252
1253	<	mpiSim = new mpiSimulation( info );
1254	<
1253	>	mpiSim = new mpiSimulation(info);
1254	>
1255		globalIndex = mpiSim->divideLabor();
1256
1257		// set up the local variables
1258	<
1258	>
1259		mol2proc = mpiSim->getMolToProcMap();
1260		molCompType = mpiSim->getMolComponentType();
1261	<
1261	>
1262		allMol = 0;
1263		localMol = 0;
1264		local_atoms = 0;
#	Line 1354 | Line 1268 | void SimSetup::mpiMolDivide( void ){
1268		globalAtomIndex = 0;
1269
1270
1271	<	for( i=0; i<n_components; i++ ){
1272	<
1273	<	for( j=0; j<components_nmol[i]; j++ ){
1274	<
1275	<	if( mol2proc[allMol] == worldRank ){
1276	<
1277	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1278	<	local_bonds +=    comp_stamps[i]->getNBonds();
1365	<	local_bends +=    comp_stamps[i]->getNBends();
1366	<	local_torsions += comp_stamps[i]->getNTorsions();
1367	<	localMol++;
1271	>	for (i = 0; i < n_components; i++){
1272	>	for (j = 0; j < components_nmol[i]; j++){
1273	>	if (mol2proc[allMol] == worldRank){
1274	>	local_atoms += comp_stamps[i]->getNAtoms();
1275	>	local_bonds += comp_stamps[i]->getNBonds();
1276	>	local_bends += comp_stamps[i]->getNBends();
1277	>	local_torsions += comp_stamps[i]->getNTorsions();
1278	>	localMol++;
1279		}
1280	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1281	<	info->molMembershipArray[globalAtomIndex] = allMol;
1280	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1281	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1282		globalAtomIndex++;
1283		}
1284
1285	<	allMol++;
1285	>	allMol++;
1286		}
1287		}
1288		local_SRI = local_bonds + local_bends + local_torsions;
1289	<
1290	<	info->n_atoms = mpiSim->getMyNlocal();
1291	<
1292	<	if( local_atoms != info->n_atoms ){
1293	<	sprintf( painCave.errMsg,
1294	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1295	<	" localAtom (%d) are not equal.\n",
1296	<	info->n_atoms,
1386	<	local_atoms );
1289	>
1290	>	info[0].n_atoms = mpiSim->getMyNlocal();
1291	>
1292	>	if (local_atoms != info[0].n_atoms){
1293	>	sprintf(painCave.errMsg,
1294	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1295	>	"\tlocalAtom (%d) are not equal.\n",
1296	>	info[0].n_atoms, local_atoms);
1297		painCave.isFatal = 1;
1298		simError();
1299		}
1300
1301	<	info->n_bonds = local_bonds;
1302	<	info->n_bends = local_bends;
1303	<	info->n_torsions = local_torsions;
1304	<	info->n_SRI = local_SRI;
1305	<	info->n_mol = localMol;
1301	>	info[0].n_bonds = local_bonds;
1302	>	info[0].n_bends = local_bends;
1303	>	info[0].n_torsions = local_torsions;
1304	>	info[0].n_SRI = local_SRI;
1305	>	info[0].n_mol = localMol;
1306
1307	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1307	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1308		MPIcheckPoint();
1309		}
1310	<
1310	>
1311		#endif // is_mpi
1312
1313
1314	<	void SimSetup::makeSysArrays( void ){
1314	>	void SimSetup::makeSysArrays(void){
1315	>
1316	>	#ifndef IS_MPI
1317	>	int k, j;
1318	>	#endif // is_mpi
1319	>	int i, l;
1320
1321	<	// create the atom and short range interaction arrays
1321	>	Atom** the_atoms;
1322	>	Molecule* the_molecules;
1323	>	Exclude** the_excludes;
1324
1408	–	Atom::createArrays(info->n_atoms);
1409	–	the_atoms = new Atom*[info->n_atoms];
1410	–	the_molecules = new Molecule[info->n_mol];
1411	–	int molIndex;
1325
1326	<	// initialize the molecule's stampID's
1326	>	for (l = 0; l < nInfo; l++){
1327	>	// create the atom and short range interaction arrays
1328
1329	+	the_atoms = new Atom * [info[l].n_atoms];
1330	+	the_molecules = new Molecule[info[l].n_mol];
1331	+	int molIndex;
1332	+
1333	+	// initialize the molecule's stampID's
1334	+
1335		#ifdef IS_MPI
1416	–
1336
1337	<	molIndex = 0;
1338	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1339	<
1340	<	if(mol2proc[i] == worldRank ){
1341	<	the_molecules[molIndex].setStampID( molCompType[i] );
1342	<	the_molecules[molIndex].setMyIndex( molIndex );
1343	<	the_molecules[molIndex].setGlobalIndex( i );
1344	<	molIndex++;
1337	>
1338	>	molIndex = 0;
1339	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1340	>	if (mol2proc[i] == worldRank){
1341	>	the_molecules[molIndex].setStampID(molCompType[i]);
1342	>	the_molecules[molIndex].setMyIndex(molIndex);
1343	>	the_molecules[molIndex].setGlobalIndex(i);
1344	>	molIndex++;
1345	>	}
1346		}
1427	–	}
1347
1348		#else // is_mpi
1349	<
1350	<	molIndex = 0;
1351	<	globalAtomIndex = 0;
1352	<	for(i=0; i<n_components; i++){
1353	<	for(j=0; j<components_nmol[i]; j++ ){
1354	<	the_molecules[molIndex].setStampID( i );
1355	<	the_molecules[molIndex].setMyIndex( molIndex );
1356	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1357	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1358	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1359	<	globalAtomIndex++;
1349	>
1350	>	molIndex = 0;
1351	>	globalAtomIndex = 0;
1352	>	for (i = 0; i < n_components; i++){
1353	>	for (j = 0; j < components_nmol[i]; j++){
1354	>	the_molecules[molIndex].setStampID(i);
1355	>	the_molecules[molIndex].setMyIndex(molIndex);
1356	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1357	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1358	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1359	>	globalAtomIndex++;
1360	>	}
1361	>	molIndex++;
1362		}
1442	–	molIndex++;
1363		}
1364	+
1365	+
1366	+	#endif // is_mpi
1367	+
1368	+
1369	+	if (info[l].n_SRI){
1370	+	Exclude::createArray(info[l].n_SRI);
1371	+	the_excludes = new Exclude * [info[l].n_SRI];
1372	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1373	+	the_excludes[ex] = new Exclude(ex);
1374	+	}
1375	+	info[l].globalExcludes = new int;
1376	+	info[l].n_exclude = info[l].n_SRI;
1377	+	}
1378	+	else{
1379	+	Exclude::createArray(1);
1380	+	the_excludes = new Exclude * ;
1381	+	the_excludes[0] = new Exclude(0);
1382	+	the_excludes[0]->setPair(0, 0);
1383	+	info[l].globalExcludes = new int;
1384	+	info[l].globalExcludes[0] = 0;
1385	+	info[l].n_exclude = 0;
1386	+	}
1387	+
1388	+	// set the arrays into the SimInfo object
1389	+
1390	+	info[l].atoms = the_atoms;
1391	+	info[l].molecules = the_molecules;
1392	+	info[l].nGlobalExcludes = 0;
1393	+	info[l].excludes = the_excludes;
1394	+
1395	+	the_ff->setSimInfo(info);
1396		}
1397	<
1397	>	}
1398	>
1399	>	void SimSetup::makeIntegrator(void){
1400	>	int k;
1401	>
1402	>	NVE<RealIntegrator>* myNVE = NULL;
1403	>	NVT<RealIntegrator>* myNVT = NULL;
1404	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1405	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1406	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1407	>
1408	>	for (k = 0; k < nInfo; k++){
1409	>	switch (ensembleCase){
1410	>	case NVE_ENS:
1411	>	if (globals->haveZconstraints()){
1412	>	setupZConstraint(info[k]);
1413	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1414	>	}
1415	>	else{
1416	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1417	>	}
1418	>
1419	>	info->the_integrator = myNVE;
1420	>	break;
1421	>
1422	>	case NVT_ENS:
1423	>	if (globals->haveZconstraints()){
1424	>	setupZConstraint(info[k]);
1425	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1426	>	}
1427	>	else
1428	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1429	>
1430	>	myNVT->setTargetTemp(globals->getTargetTemp());
1431	>
1432	>	if (globals->haveTauThermostat())
1433	>	myNVT->setTauThermostat(globals->getTauThermostat());
1434	>	else{
1435	>	sprintf(painCave.errMsg,
1436	>	"SimSetup error: If you use the NVT\n"
1437	>	"\tensemble, you must set tauThermostat.\n");
1438	>	painCave.isFatal = 1;
1439	>	simError();
1440	>	}
1441	>
1442	>	info->the_integrator = myNVT;
1443	>	break;
1444	>
1445	>	case NPTi_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1449	>	}
1450	>	else
1451	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1452	>
1453	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1454	>
1455	>	if (globals->haveTargetPressure())
1456	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1457	>	else{
1458	>	sprintf(painCave.errMsg,
1459	>	"SimSetup error: If you use a constant pressure\n"
1460	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1461	>	painCave.isFatal = 1;
1462	>	simError();
1463	>	}
1464	>
1465	>	if (globals->haveTauThermostat())
1466	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1467	>	else{
1468	>	sprintf(painCave.errMsg,
1469	>	"SimSetup error: If you use an NPT\n"
1470	>	"\tensemble, you must set tauThermostat.\n");
1471	>	painCave.isFatal = 1;
1472	>	simError();
1473	>	}
1474
1475	+	if (globals->haveTauBarostat())
1476	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1477	+	else{
1478	+	sprintf(painCave.errMsg,
1479	+	"SimSetup error: If you use an NPT\n"
1480	+	"\tensemble, you must set tauBarostat.\n");
1481	+	painCave.isFatal = 1;
1482	+	simError();
1483	+	}
1484	+
1485	+	info->the_integrator = myNPTi;
1486	+	break;
1487	+
1488	+	case NPTf_ENS:
1489	+	if (globals->haveZconstraints()){
1490	+	setupZConstraint(info[k]);
1491	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1492	+	}
1493	+	else
1494	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1495	+
1496	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1497	+
1498	+	if (globals->haveTargetPressure())
1499	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1500	+	else{
1501	+	sprintf(painCave.errMsg,
1502	+	"SimSetup error: If you use a constant pressure\n"
1503	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+	if (globals->haveTauThermostat())
1509	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1510	+
1511	+	else{
1512	+	sprintf(painCave.errMsg,
1513	+	"SimSetup error: If you use an NPT\n"
1514	+	"\tensemble, you must set tauThermostat.\n");
1515	+	painCave.isFatal = 1;
1516	+	simError();
1517	+	}
1518	+
1519	+	if (globals->haveTauBarostat())
1520	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1521	+
1522	+	else{
1523	+	sprintf(painCave.errMsg,
1524	+	"SimSetup error: If you use an NPT\n"
1525	+	"\tensemble, you must set tauBarostat.\n");
1526	+	painCave.isFatal = 1;
1527	+	simError();
1528	+	}
1529	+
1530	+	info->the_integrator = myNPTf;
1531	+	break;
1532	+
1533	+	case NPTxyz_ENS:
1534	+	if (globals->haveZconstraints()){
1535	+	setupZConstraint(info[k]);
1536	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1537	+	}
1538	+	else
1539	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1540	+
1541	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1542	+
1543	+	if (globals->haveTargetPressure())
1544	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1545	+	else{
1546	+	sprintf(painCave.errMsg,
1547	+	"SimSetup error: If you use a constant pressure\n"
1548	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1549	+	painCave.isFatal = 1;
1550	+	simError();
1551	+	}
1552	+
1553	+	if (globals->haveTauThermostat())
1554	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1555	+	else{
1556	+	sprintf(painCave.errMsg,
1557	+	"SimSetup error: If you use an NPT\n"
1558	+	"\tensemble, you must set tauThermostat.\n");
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561	+	}
1562	+
1563	+	if (globals->haveTauBarostat())
1564	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1565	+	else{
1566	+	sprintf(painCave.errMsg,
1567	+	"SimSetup error: If you use an NPT\n"
1568	+	"\tensemble, you must set tauBarostat.\n");
1569	+	painCave.isFatal = 1;
1570	+	simError();
1571	+	}
1572	+
1573	+	info->the_integrator = myNPTxyz;
1574	+	break;
1575	+
1576	+	default:
1577	+	sprintf(painCave.errMsg,
1578	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1579	+	painCave.isFatal = 1;
1580	+	simError();
1581	+	}
1582	+	}
1583	+	}
1584	+
1585	+	void SimSetup::initFortran(void){
1586	+	info[0].refreshSim();
1587	+
1588	+	if (!strcmp(info[0].mixingRule, "standard")){
1589	+	the_ff->initForceField(LB_MIXING_RULE);
1590	+	}
1591	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1592	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1593	+	}
1594	+	else{
1595	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1596	+	info[0].mixingRule);
1597	+	painCave.isFatal = 1;
1598	+	simError();
1599	+	}
1600	+
1601	+
1602	+	#ifdef IS_MPI
1603	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1604	+	MPIcheckPoint();
1605		#endif // is_mpi
1606	+	}
1607
1608	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1609	+	int nZConstraints;
1610	+	ZconStamp** zconStamp;
1611
1612	<	if( info->n_SRI ){
1613	<
1614	<	Exclude::createArray(info->n_SRI);
1615	<	the_excludes = new Exclude*[info->n_SRI];
1616	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1617	<	info->globalExcludes = new int;
1456	<	info->n_exclude = info->n_SRI;
1612	>	if (globals->haveZconstraintTime()){
1613	>	//add sample time of z-constraint  into SimInfo's property list
1614	>	DoubleData* zconsTimeProp = new DoubleData();
1615	>	zconsTimeProp->setID(ZCONSTIME_ID);
1616	>	zconsTimeProp->setData(globals->getZconsTime());
1617	>	theInfo.addProperty(zconsTimeProp);
1618		}
1619		else{
1620	<
1621	<	Exclude::createArray( 1 );
1622	<	the_excludes = new Exclude*;
1623	<	the_excludes[0] = new Exclude(0);
1624	<	the_excludes[0]->setPair( 0,0 );
1464	<	info->globalExcludes = new int;
1465	<	info->globalExcludes[0] = 0;
1466	<	info->n_exclude = 0;
1620	>	sprintf(painCave.errMsg,
1621	>	"ZConstraint error: If you use a ZConstraint,\n"
1622	>	"\tyou must set zconsTime.\n");
1623	>	painCave.isFatal = 1;
1624	>	simError();
1625		}
1626
1627	<	// set the arrays into the SimInfo object
1627	>	//push zconsTol into siminfo, if user does not specify
1628	>	//value for zconsTol, a default value will be used
1629	>	DoubleData* zconsTol = new DoubleData();
1630	>	zconsTol->setID(ZCONSTOL_ID);
1631	>	if (globals->haveZconsTol()){
1632	>	zconsTol->setData(globals->getZconsTol());
1633	>	}
1634	>	else{
1635	>	double defaultZConsTol = 0.01;
1636	>	sprintf(painCave.errMsg,
1637	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1638	>	"\tOOPSE will use a default value of %f.\n"
1639	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1640	>	defaultZConsTol);
1641	>	painCave.isFatal = 0;
1642	>	simError();
1643
1644	<	info->atoms = the_atoms;
1645	<	info->molecules = the_molecules;
1646	<	info->nGlobalExcludes = 0;
1474	<	info->excludes = the_excludes;
1644	>	zconsTol->setData(defaultZConsTol);
1645	>	}
1646	>	theInfo.addProperty(zconsTol);
1647
1648	<	the_ff->setSimInfo( info );
1648	>	//set Force Subtraction Policy
1649	>	StringData* zconsForcePolicy = new StringData();
1650	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1651
1652	+	if (globals->haveZconsForcePolicy()){
1653	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1654	+	}
1655	+	else{
1656	+	sprintf(painCave.errMsg,
1657	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1658	+	"\tOOPSE will use PolicyByMass.\n"
1659	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662	+	zconsForcePolicy->setData("BYMASS");
1663	+	}
1664	+
1665	+	theInfo.addProperty(zconsForcePolicy);
1666	+
1667	+	//Determine the name of ouput file and add it into SimInfo's property list
1668	+	//Be careful, do not use inFileName, since it is a pointer which
1669	+	//point to a string at master node, and slave nodes do not contain that string
1670	+
1671	+	string zconsOutput(theInfo.finalName);
1672	+
1673	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	+
1675	+	StringData* zconsFilename = new StringData();
1676	+	zconsFilename->setID(ZCONSFILENAME_ID);
1677	+	zconsFilename->setData(zconsOutput);
1678	+
1679	+	theInfo.addProperty(zconsFilename);
1680	+
1681	+	//setup index, pos and other parameters of z-constraint molecules
1682	+	nZConstraints = globals->getNzConstraints();
1683	+	theInfo.nZconstraints = nZConstraints;
1684	+
1685	+	zconStamp = globals->getZconStamp();
1686	+	ZConsParaItem tempParaItem;
1687	+
1688	+	ZConsParaData* zconsParaData = new ZConsParaData();
1689	+	zconsParaData->setID(ZCONSPARADATA_ID);
1690	+
1691	+	for (int i = 0; i < nZConstraints; i++){
1692	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1693	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1694	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1695	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1696	+
1697	+	zconsParaData->addItem(tempParaItem);
1698	+	}
1699	+
1700	+	//check the uniqueness of index
1701	+	if(!zconsParaData->isIndexUnique()){
1702	+	sprintf(painCave.errMsg,
1703	+	"ZConstraint Error: molIndex is not unique!\n");
1704	+	painCave.isFatal = 1;
1705	+	simError();
1706	+	}
1707	+
1708	+	//sort the parameters by index of molecules
1709	+	zconsParaData->sortByIndex();
1710	+
1711	+	//push data into siminfo, therefore, we can retrieve later
1712	+	theInfo.addProperty(zconsParaData);
1713		}
1714	+
1715	+	void SimSetup::makeMinimizer(){
1716	+
1717	+	OOPSEMinimizer* myOOPSEMinimizer;
1718	+	MinimizerParameterSet* param;
1719	+	char minimizerName[100];
1720	+
1721	+	for (int i = 0; i < nInfo; i++){
1722	+
1723	+	//prepare parameter set for minimizer
1724	+	param = new MinimizerParameterSet();
1725	+	param->setDefaultParameter();
1726	+
1727	+	if (globals->haveMinimizer()){
1728	+	param->setFTol(globals->getMinFTol());
1729	+	}
1730	+
1731	+	if (globals->haveMinGTol()){
1732	+	param->setGTol(globals->getMinGTol());
1733	+	}
1734	+
1735	+	if (globals->haveMinMaxIter()){
1736	+	param->setMaxIteration(globals->getMinMaxIter());
1737	+	}
1738	+
1739	+	if (globals->haveMinWriteFrq()){
1740	+	param->setMaxIteration(globals->getMinMaxIter());
1741	+	}
1742	+
1743	+	if (globals->haveMinWriteFrq()){
1744	+	param->setWriteFrq(globals->getMinWriteFrq());
1745	+	}
1746	+
1747	+	if (globals->haveMinStepSize()){
1748	+	param->setStepSize(globals->getMinStepSize());
1749	+	}
1750	+
1751	+	if (globals->haveMinLSMaxIter()){
1752	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1753	+	}
1754	+
1755	+	if (globals->haveMinLSTol()){
1756	+	param->setLineSearchTol(globals->getMinLSTol());
1757	+	}
1758	+
1759	+	strcpy(ensemble, globals->getMinimizer());
1760	+
1761	+	if (!strcasecmp(minimizerName, "CG")){
1762	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1763	+	}
1764	+	else if (!strcasecmp(minimizerName, "SD")){
1765	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1766	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1767	+	}
1768	+	else{
1769	+	info[i].the_integrator = myOOPSEMinimizer;
1770	+	}
1771	+
1772	+	//store the minimizer into simInfo
1773	+	info[i].the_minimizer = myOOPSEMinimizer;
1774	+	info[i].has_minimizer = true;
1775	+	}
1776	+
1777	+	}

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