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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 965 by gezelter, Mon Jan 19 21:17:39 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"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTxyz_ENS     4
25
26
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 41 | Line 75 | void SimSetup::parseFile( char* fileName ){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
83	–	int i, j, k, globalAtomIndex;
84	–
122		// gather all of the information from the Bass file
123	<
123	>
124		gatherInfo();
125
126		// creation of complex system objects
127
128		sysObjectsCreation();
129
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	–
130		// check on the post processing info
131	<
131	>
132		finalInfoCheck();
133
110	–
111	–
112	–
134		// initialize the system coordinates
135
136	<	initSystemCoords();
137	<
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	+	if( !(globals->getUseInitTime()) )
140	+	info[0].currentTime = 0.0;
141	+	}
142	+
143		// make the output filenames
144
145		makeOutNames();
121	–
122	–
123	–
146
125	–
126	–
127	–
128	–
129	–
147		// 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;
148
149	<	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	<	}
149	>	makeIntegrator();
150
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	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
154
155		// initialize the Fortran
156
157	<
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
157	>	initFortran();
158		}
159
160
161	<	void SimSetup::makeMolecules( void ){
162	<
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164	<	molInit info;
164	>	molInit molInfo;
165		DirectionalAtom* dAtom;
166		LinkedAssign* extras;
167		LinkedAssign* current_extra;
#	Line 354 | Line 174 | void SimSetup::makeMolecules( void ){
174		bend_set* theBends;
175		torsion_set* theTorsions;
176
177	<
177	>
178		//init the forceField paramters
179
180		the_ff->readParams();
181
182	<
182	>
183		// init the atoms
184
185		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();
186
187	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
188	<	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;
187	>	for (k = 0; k < nInfo; k++){
188	>	the_ff->setSimInfo(&(info[k]));
189
190	<	info.myAtoms = &the_atoms[atomOffset];
191	<	info.myExcludes = &the_excludes[excludeOffset];
192	<	info.myBonds = new Bond*[info.nBonds];
193	<	info.myBends = new Bend*[info.nBends];
383	<	info.myTorsions = new Torsion*[info.nTorsions];
190	>	atomOffset = 0;
191	>	excludeOffset = 0;
192	>	for (i = 0; i < info[k].n_mol; i++){
193	>	stampID = info[k].molecules[i].getStampID();
194
195	<	theBonds = new bond_pair[info.nBonds];
196	<	theBends = new bend_set[info.nBends];
197	<	theTorsions = new torsion_set[info.nTorsions];
198	<
199	<	// make the Atoms
200	<
201	<	for(j=0; j<info.nAtoms; j++){
202	<
203	<	currentAtom = comp_stamps[stampID]->getAtom( j );
204	<	if( currentAtom->haveOrientation() ){
205	<
206	<	dAtom = new DirectionalAtom(j + atomOffset);
207	<	info->n_oriented++;
208	<	info.myAtoms[j] = dAtom;
209	<
210	<	ux = currentAtom->getOrntX();
211	<	uy = currentAtom->getOrntY();
212	<	uz = currentAtom->getOrntZ();
213	<
214	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
215	<
216	<	u = sqrt( uSqr );
217	<	ux = ux / u;
218	<	uy = uy / u;
219	<	uz = uz / u;
220	<
221	<	dAtom->setSUx( ux );
222	<	dAtom->setSUy( uy );
223	<	dAtom->setSUz( uz );
224	<	}
225	<	else{
226	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
227	<	}
228	<	info.myAtoms[j]->setType( currentAtom->getType() );
229	<
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200	>
201	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	>	molInfo.myBends = new Bend * [molInfo.nBends];
205	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206	>
207	>	theBonds = new bond_pair[molInfo.nBonds];
208	>	theBends = new bend_set[molInfo.nBends];
209	>	theTorsions = new torsion_set[molInfo.nTorsions];
210	>
211	>	// make the Atoms
212	>
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220	>
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224	>
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226	>
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231	>
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241	>
242		#ifdef IS_MPI
243	<
244	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
245	<
243	>
244	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245	>
246		#endif // is_mpi
247	<	}
426	<
427	<	// make the bonds
428	<	for(j=0; j<info.nBonds; j++){
429	<
430	<	currentBond = comp_stamps[stampID]->getBond( j );
431	<	theBonds[j].a = currentBond->getA() + atomOffset;
432	<	theBonds[j].b = currentBond->getB() + atomOffset;
247	>	}
248
249	<	exI = theBonds[j].a;
250	<	exJ = theBonds[j].b;
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
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	<	}
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257	>
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264	>	#ifdef IS_MPI
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269	>
270	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271	>	#else  // isn't MPI
272	>
273	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274	>	#endif  //is_mpi
275	>	}
276	>	excludeOffset += molInfo.nBonds;
277	>
278	>	//make the bends
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284	>
285	>	if (currentBend->haveExtras()){
286	>	extras = currentBend->getExtras();
287	>	current_extra = extras;
288	>
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302	>
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321	>
322	>	current_extra = current_extra->getNext();
323	>	}
324	>	}
325	>
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334	>
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341		#ifdef IS_MPI
342	<	tempEx = exI;
343	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
344	<	tempEx = exJ;
345	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
448	<
449	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
450	<	#else  // isn't MPI
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346
347	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
453	<	#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	<	}
511	<	}
512	<
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 );
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348		#else  // isn't MPI
349	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350		#endif  //is_mpi
351	<	}
352	<	excludeOffset += info.nBends;
351	>	}
352	>	excludeOffset += molInfo.nBends;
353
354	<	for(j=0; j<info.nTorsions; j++){
355	<
356	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
357	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
358	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
359	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
549	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
550	<
551	<	exI = theTorsions[j].a;
552	<	exJ = theTorsions[j].d;
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360
361	<	// exclude_I must always be the smaller of the pair
362	<	if( exI > exJ ){
363	<	tempEx = exI;
364	<	exI = exJ;
365	<	exJ = tempEx;
366	<	}
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if (exI > exJ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370		#ifdef IS_MPI
371	<	tempEx = exI;
372	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
373	<	tempEx = exJ;
374	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
375	<
376	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377		#else  // isn't MPI
378	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379		#endif  //is_mpi
380	<	}
381	<	excludeOffset += info.nTorsions;
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382
573	–
574	–	// send the arrays off to the forceField for init.
383
384	<	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 );
384	>	// send the arrays off to the forceField for init.
385
386	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
387	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
388	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
389	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
390	+	theTorsions);
391
582	–	the_molecules[i].initialize( info );
392
393	+	info[k].molecules[i].initialize(molInfo);
394
395	<	atomOffset += info.nAtoms;
396	<	delete[] theBonds;
397	<	delete[] theBends;
398	<	delete[] theTorsions;
395	>
396	>	atomOffset += molInfo.nAtoms;
397	>	delete[] theBonds;
398	>	delete[] theBends;
399	>	delete[] theTorsions;
400	>	}
401		}
402
403		#ifdef IS_MPI
404	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405		MPIcheckPoint();
406		#endif // is_mpi
407
408		// clean up the forcefield
409	+
410		the_ff->calcRcut();
411		the_ff->cleanMe();
599	–
412		}
413
414	<	void SimSetup::initFromBass( void ){
603	<
414	>	void SimSetup::initFromBass(void){
415		int i, j, k;
416		int n_cells;
417		double cellx, celly, cellz;
#	Line 609 | Line 420 | void SimSetup::initFromBass( void ){
420		int n_extra;
421		int have_extra, done;
422
423	<	temp1 = (double)tot_nmol / 4.0;
424	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
425	<	temp3 = ceil( temp2 );
423	>	double vel[3];
424	>	vel[0] = 0.0;
425	>	vel[1] = 0.0;
426	>	vel[2] = 0.0;
427
428	<	have_extra =0;
429	<	if( temp2 < temp3 ){ // we have a non-complete lattice
430	<	have_extra =1;
428	>	temp1 = (double) tot_nmol / 4.0;
429	>	temp2 = pow(temp1, (1.0 / 3.0));
430	>	temp3 = ceil(temp2);
431
432	<	n_cells = (int)temp3 - 1;
433	<	cellx = info->boxLx / temp3;
434	<	celly = info->boxLy / temp3;
435	<	cellz = info->boxLz / temp3;
624	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
625	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
626	<	n_per_extra = (int)ceil( temp1 );
432	>	have_extra = 0;
433	>	if (temp2 < temp3){
434	>	// we have a non-complete lattice
435	>	have_extra = 1;
436
437	<	if( n_per_extra > 4){
438	<	sprintf( painCave.errMsg,
439	<	"SimSetup error. There has been an error in constructing"
440	<	" the non-complete lattice.\n" );
437	>	n_cells = (int) temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444	>
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449		painCave.isFatal = 1;
450		simError();
451		}
452		}
453		else{
454	<	n_cells = (int)temp3;
455	<	cellx = info->boxLx / temp3;
456	<	celly = info->boxLy / temp3;
457	<	cellz = info->boxLz / temp3;
454	>	n_cells = (int) temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460		current_mol = 0;
#	Line 645 | Line 462 | void SimSetup::initFromBass( void ){
462		current_comp = 0;
463		current_atom_ndx = 0;
464
465	<	for( i=0; i < n_cells ; i++ ){
466	<	for( j=0; j < n_cells; j++ ){
467	<	for( k=0; k < n_cells; k++ ){
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<	makeElement( i * cellx,
653	<	j * celly,
654	<	k * cellz );
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471
472	<	makeElement( i * cellx + 0.5 * cellx,
657	<	j * celly + 0.5 * celly,
658	<	k * cellz );
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473
474	<	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 );
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475		}
476		}
477		}
478
479	<	if( have_extra ){
479	>	if (have_extra){
480		done = 0;
481
482		int start_ndx;
483	<	for( i=0; i < (n_cells+1) && !done; i++ ){
484	<	for( j=0; j < (n_cells+1) && !done; j++ ){
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494
495	<	if( i < n_cells ){
495	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	>	makeElement(i * cellx, j * celly, k * cellz);
497	>	done = (current_mol >= tot_nmol);
498
499	<	if( j < n_cells ){
500	<	start_ndx = n_cells;
501	<	}
502	<	else start_ndx = 0;
503	<	}
685	<	else start_ndx = 0;
499	>	if (!done && n_per_extra > 1){
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	>	k * cellz);
502	>	done = (current_mol >= tot_nmol);
503	>	}
504
505	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510
511	<	makeElement( i * cellx,
512	<	j * celly,
513	<	k * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<
516	<	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	<	}
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517		}
518		}
519		}
520
521	<
522	<	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 );
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523		}
524		}
525
526	<	void SimSetup::makeElement( double x, double y, double z ){
728	<
526	>	void SimSetup::makeElement(double x, double y, double z){
527		int k;
528		AtomStamp* current_atom;
529		DirectionalAtom* dAtom;
530		double rotMat[3][3];
531	+	double pos[3];
532
533	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
534	<
535	<	current_atom = comp_stamps[current_comp]->getAtom( k );
536	<	if( !current_atom->havePosition() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup:initFromBass error.\n"
539	<	"\tComponent %s, atom %s does not have a position specified.\n"
540	<	"\tThe initialization routine is unable to give a start"
541	<	" position.\n",
743	<	comp_stamps[current_comp]->getID(),
744	<	current_atom->getType() );
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542		painCave.isFatal = 1;
543		simError();
544		}
545
546	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
547	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
548	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
546	>	pos[0] = x + current_atom->getPosX();
547	>	pos[1] = y + current_atom->getPosY();
548	>	pos[2] = z + current_atom->getPosZ();
549
550	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
550	>	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555		rotMat[0][0] = 1.0;
556		rotMat[0][1] = 0.0;
#	Line 766 | Line 564 | void SimSetup::makeElement( double x, double y, double
564		rotMat[2][1] = 0.0;
565		rotMat[2][2] = 1.0;
566
567	<	dAtom->setA( rotMat );
567	>	dAtom->setA(rotMat);
568		}
569
570		current_atom_ndx++;
#	Line 775 | Line 573 | void SimSetup::makeElement( double x, double y, double
573		current_mol++;
574		current_comp_mol++;
575
576	<	if( current_comp_mol >= components_nmol[current_comp] ){
779	<
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577		current_comp_mol = 0;
578		current_comp++;
579		}
580		}
581
582
583	<	void SimSetup::gatherInfo( void ){
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586		ensembleCase = -1;
587		ffCase = -1;
588
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
589		// 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();
590
591	+	for (i = 0; i < nInfo; i++){
592	+	info[i].target_temp = globals->getTargetTemp();
593	+	info[i].dt = globals->getDt();
594	+	info[i].run_time = globals->getRunTime();
595	+	}
596	+	n_components = globals->getNComponents();
597
598	+
599		// get the forceField
600
601	<	strcpy( force_field, the_globals->getForceField() );
601	>	strcpy(force_field, globals->getForceField());
602
603	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
604	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605	>	}
606	>	else if (!strcasecmp(force_field, "LJ")){
607	>	ffCase = FF_LJ;
608	>	}
609	>	else if (!strcasecmp(force_field, "EAM")){
610	>	ffCase = FF_EAM;
611	>	}
612		else{
613	<	sprintf( painCave.errMsg,
614	<	"SimSetup Error. Unrecognized force field -> %s\n",
615	<	force_field );
616	<	painCave.isFatal = 1;
813	<	simError();
613	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field);
615	>	painCave.isFatal = 1;
616	>	simError();
617		}
618
619	<	// get the ensemble
619	>	// get the ensemble
620
621	<	strcpy( ensemble, the_globals->getEnsemble() );
621	>	strcpy(ensemble, globals->getEnsemble());
622
623	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625	>	}
626	>	else if (!strcasecmp(ensemble, "NVT")){
627	>	ensembleCase = NVT_ENS;
628	>	}
629	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630		ensembleCase = NPTi_ENS;
631	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
632	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
631	>	}
632	>	else if (!strcasecmp(ensemble, "NPTf")){
633	>	ensembleCase = NPTf_ENS;
634	>	}
635	>	else if (!strcasecmp(ensemble, "NPTxyz")){
636	>	ensembleCase = NPTxyz_ENS;
637	>	}
638		else{
639	<	sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	<	"reverting to NVE for this simulation.\n",
642	<	ensemble );
643	<	painCave.isFatal = 0;
644	<	simError();
645	<	strcpy( ensemble, "NVE" );
646	<	ensembleCase = NVE_ENS;
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
641	>	"\treverting to NVE for this simulation.\n",
642	>	ensemble);
643	>	painCave.isFatal = 0;
644	>	simError();
645	>	strcpy(ensemble, "NVE");
646	>	ensembleCase = NVE_ENS;
647		}
837	–	strcpy( info->ensemble, ensemble );
648
649	<	// get the mixing rule
649	>	for (i = 0; i < nInfo; i++){
650	>	strcpy(info[i].ensemble, ensemble);
651
652	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
653	<	info->usePBC = the_globals->getPBC();
654	<
655	<
652	>	// get the mixing rule
653	>
654	>	strcpy(info[i].mixingRule, globals->getMixingRule());
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657	>
658		// get the components and calculate the tot_nMol and indvidual n_mol
659	<
660	<	the_components = the_globals->getComponents();
659	>
660	>	the_components = globals->getComponents();
661		components_nmol = new int[n_components];
662
663
664	<	if( !the_globals->haveNMol() ){
664	>	if (!globals->haveNMol()){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
668		tot_nmol = 0;
669	<	for( i=0; i<n_components; i++ ){
670	<
671	<	if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
864	<	simError();
669	>	for (i = 0; i < n_components; i++){
670	>	if (!the_components[i]->haveNMol()){
671	>	// we have a problem
672	>	sprintf(painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol given.\n"
674	>	"\tCannot calculate the number of atoms.\n");
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
678
679		tot_nmol += the_components[i]->getNMol();
#	Line 869 | Line 681 | void SimSetup::gatherInfo( void ){
681		}
682		}
683		else{
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error.\n"
686	<	"\tSorry, the ability to specify total"
687	<	" nMols and then give molfractions in the components\n"
688	<	"\tis not currently supported."
689	<	" Please give nMol in the components.\n" );
684	>	sprintf(painCave.errMsg,
685	>	"SimSetup error.\n"
686	>	"\tSorry, the ability to specify total"
687	>	" nMols and then give molfractions in the components\n"
688	>	"\tis not currently supported."
689	>	" Please give nMol in the components.\n");
690		painCave.isFatal = 1;
691		simError();
692		}
693
694	<	// set the status, sample, and thermal kick times
695	<
696	<	if( the_globals->haveSampleTime() ){
697	<	info->sampleTime = the_globals->getSampleTime();
698	<	info->statusTime = info->sampleTime;
699	<	info->thermalTime = info->sampleTime;
694	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	>	sprintf(painCave.errMsg,
697	>	"Sample time is not divisible by dt.\n"
698	>	"\tThis will result in samples that are not uniformly\n"
699	>	"\tdistributed in time.  If this is a problem, change\n"
700	>	"\tyour sampleTime variable.\n");
701	>	painCave.isFatal = 0;
702	>	simError();
703		}
889	–	else{
890	–	info->sampleTime = the_globals->getRunTime();
891	–	info->statusTime = info->sampleTime;
892	–	info->thermalTime = info->sampleTime;
893	–	}
704
705	<	if( the_globals->haveStatusTime() ){
706	<	info->statusTime = the_globals->getStatusTime();
705	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
706	>	sprintf(painCave.errMsg,
707	>	"Status time is not divisible by dt.\n"
708	>	"\tThis will result in status reports that are not uniformly\n"
709	>	"\tdistributed in time.  If this is a problem, change \n"
710	>	"\tyour statusTime variable.\n");
711	>	painCave.isFatal = 0;
712	>	simError();
713		}
714
715	<	if( the_globals->haveThermalTime() ){
716	<	info->thermalTime = the_globals->getThermalTime();
717	<	}
715	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
716	>	sprintf(painCave.errMsg,
717	>	"Thermal time is not divisible by dt.\n"
718	>	"\tThis will result in thermalizations that are not uniformly\n"
719	>	"\tdistributed in time.  If this is a problem, change \n"
720	>	"\tyour thermalTime variable.\n");
721	>	painCave.isFatal = 0;
722	>	simError();
723	>	}
724
725	<	// check for the temperature set flag
725	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
726	>	sprintf(painCave.errMsg,
727	>	"Reset time is not divisible by dt.\n"
728	>	"\tThis will result in integrator resets that are not uniformly\n"
729	>	"\tdistributed in time.  If this is a problem, change\n"
730	>	"\tyour resetTime variable.\n");
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734
735	<	if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();
735	>	// set the status, sample, and thermal kick times
736
737	<	// get some of the tricky things that may still be in the globals
737	>	for (i = 0; i < nInfo; i++){
738	>	if (globals->haveSampleTime()){
739	>	info[i].sampleTime = globals->getSampleTime();
740	>	info[i].statusTime = info[i].sampleTime;
741	>	info[i].thermalTime = info[i].sampleTime;
742	>	}
743	>	else{
744	>	info[i].sampleTime = globals->getRunTime();
745	>	info[i].statusTime = info[i].sampleTime;
746	>	info[i].thermalTime = info[i].sampleTime;
747	>	}
748
749	<	double boxVector[3];
750	<	if( the_globals->haveBox() ){
751	<	boxVector[0] = the_globals->getBox();
752	<	boxVector[1] = the_globals->getBox();
753	<	boxVector[2] = the_globals->getBox();
749	>	if (globals->haveStatusTime()){
750	>	info[i].statusTime = globals->getStatusTime();
751	>	}
752	>
753	>	if (globals->haveThermalTime()){
754	>	info[i].thermalTime = globals->getThermalTime();
755	>	}
756	>
757	>	info[i].resetIntegrator = 0;
758	>	if( globals->haveResetTime() ){
759	>	info[i].resetTime = globals->getResetTime();
760	>	info[i].resetIntegrator = 1;
761	>	}
762	>
763	>	// check for the temperature set flag
764
765	<	info->setBox( boxVector );
766	<	}
917	<	else if( the_globals->haveDensity() ){
765	>	if (globals->haveTempSet())
766	>	info[i].setTemp = globals->getTempSet();
767
768	<	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];
768	>	// check for the extended State init
769
770	<	info->setBox( boxVector );
770	>	info[i].useInitXSstate = globals->getUseInitXSstate();
771	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
772	>
773		}
774	<	else{
775	<	if( !the_globals->haveBoxX() ){
776	<	sprintf( painCave.errMsg,
930	<	"SimSetup error, no periodic BoxX size given.\n" );
931	<	painCave.isFatal = 1;
932	<	simError();
933	<	}
934	<	boxVector[0] = the_globals->getBoxX();
774	>
775	>	//setup seed for random number generator
776	>	int seedValue;
777
778	<	if( !the_globals->haveBoxY() ){
779	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
941	<	}
942	<	boxVector[1] = the_globals->getBoxY();
778	>	if (globals->haveSeed()){
779	>	seedValue = globals->getSeed();
780
781	<	if( !the_globals->haveBoxZ() ){
782	<	sprintf( painCave.errMsg,
783	<	"SimSetup error, no periodic BoxZ size given.\n" );
784	<	painCave.isFatal = 1;
781	>	if(seedValue / 1E9 == 0){
782	>	sprintf(painCave.errMsg,
783	>	"Seed for sprng library should contain at least 9 digits\n"
784	>	"OOPSE will generate a seed for user\n");
785	>	painCave.isFatal = 0;
786		simError();
787	+
788	+	//using seed generated by system instead of invalid seed set by user
789	+	#ifndef IS_MPI
790	+	seedValue = make_sprng_seed();
791	+	#else
792	+	if (worldRank == 0){
793	+	seedValue = make_sprng_seed();
794	+	}
795	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	+	#endif
797		}
798	<	boxVector[2] = the_globals->getBoxZ();
798	>	}//end of if branch of globals->haveSeed()
799	>	else{
800	>
801	>	#ifndef IS_MPI
802	>	seedValue = make_sprng_seed();
803	>	#else
804	>	if (worldRank == 0){
805	>	seedValue = make_sprng_seed();
806	>	}
807	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
808	>	#endif
809	>	}//end of globals->haveSeed()
810
811	<	info->setBox( boxVector );
811	>	for (int i = 0; i < nInfo; i++){
812	>	info[i].setSeed(seedValue);
813		}
814
955	–
956	–
815		#ifdef IS_MPI
816	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
816	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
817		MPIcheckPoint();
818		#endif // is_mpi
961	–
819		}
820
821
822	<	void SimSetup::finalInfoCheck( void ){
822	>	void SimSetup::finalInfoCheck(void){
823		int index;
824		int usesDipoles;
825	<
825	>	int i;
826
827	<	// check electrostatic parameters
828	<
829	<	index = 0;
830	<	usesDipoles = 0;
831	<	while( (index < info->n_atoms) && !usesDipoles ){
832	<	usesDipoles = ((info->atoms)[index])->hasDipole();
833	<	index++;
834	<	}
835	<
827	>	for (i = 0; i < nInfo; i++){
828	>	// check electrostatic parameters
829	>
830	>	index = 0;
831	>	usesDipoles = 0;
832	>	while ((index < info[i].n_atoms) && !usesDipoles){
833	>	usesDipoles = (info[i].atoms[index])->hasDipole();
834	>	index++;
835	>	}
836	>
837		#ifdef IS_MPI
838	<	int myUse = usesDipoles
839	<	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
838	>	int myUse = usesDipoles;
839	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840		#endif //is_mpi
841
842	+	double theEcr, theEst;
843
844	<	if (the_globals->getUseRF() ) {
845	<	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	<	}
844	>	if (globals->getUseRF()){
845	>	info[i].useReactionField = 1;
846
847	<	if( !the_globals->haveEST() ){
848	<	sprintf( painCave.errMsg,
849	<	"SimSetup Warning: using default value of 0.05 * the "
850	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
851	<	);
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");
847	>	if (!globals->haveECR()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
850	>	"\tOOPSE will use a default value of 15.0 angstroms"
851	>	"\tfor the electrostaticCutoffRadius.\n");
852		painCave.isFatal = 0;
853		simError();
854	<	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();
854	>	theEcr = 15.0;
855		}
856	<
857	<	if( !the_globals->haveEST() ){
858	<	sprintf( painCave.errMsg,
859	<	"SimSetup Warning: using default value of 5%% of the "
860	<	"electrostaticCutoffRadius for the "
861	<	"electrostaticSkinThickness\n"
862	<	);
856	>	else{
857	>	theEcr = globals->getECR();
858	>	}
859	>
860	>	if (!globals->haveEST()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
863	>	"\tOOPSE will use a default value of\n"
864	>	"\t0.05 * electrostaticCutoffRadius\n"
865	>	"\tfor the electrostaticSkinThickness\n");
866		painCave.isFatal = 0;
867		simError();
868	<	info->est = 0.05 * info->ecr;
1054	<	} else {
1055	<	info->est        = the_globals->getEST();
868	>	theEst = 0.05 * theEcr;
869		}
870	+	else{
871	+	theEst = globals->getEST();
872	+	}
873	+
874	+	info[i].setDefaultEcr(theEcr, theEst);
875	+
876	+	if (!globals->haveDielectric()){
877	+	sprintf(painCave.errMsg,
878	+	"SimSetup Error: No Dielectric constant was set.\n"
879	+	"\tYou are trying to use Reaction Field without"
880	+	"\tsetting a dielectric constant!\n");
881	+	painCave.isFatal = 1;
882	+	simError();
883	+	}
884	+	info[i].dielectric = globals->getDielectric();
885		}
886	<	}
887	<
886	>	else{
887	>	if (usesDipoles){
888	>	if (!globals->haveECR()){
889	>	sprintf(painCave.errMsg,
890	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
891	>	"\tOOPSE will use a default value of 15.0 angstroms"
892	>	"\tfor the electrostaticCutoffRadius.\n");
893	>	painCave.isFatal = 0;
894	>	simError();
895	>	theEcr = 15.0;
896	>	}
897	>	else{
898	>	theEcr = globals->getECR();
899	>	}
900	>
901	>	if (!globals->haveEST()){
902	>	sprintf(painCave.errMsg,
903	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
904	>	"\tOOPSE will use a default value of\n"
905	>	"\t0.05 * electrostaticCutoffRadius\n"
906	>	"\tfor the electrostaticSkinThickness\n");
907	>	painCave.isFatal = 0;
908	>	simError();
909	>	theEst = 0.05 * theEcr;
910	>	}
911	>	else{
912	>	theEst = globals->getEST();
913	>	}
914	>
915	>	info[i].setDefaultEcr(theEcr, theEst);
916	>	}
917	>	}
918	>	}
919		#ifdef IS_MPI
920	<	strcpy( checkPointMsg, "post processing checks out" );
920	>	strcpy(checkPointMsg, "post processing checks out");
921		MPIcheckPoint();
922		#endif // is_mpi
1064	–
923		}
924	+
925	+	void SimSetup::initSystemCoords(void){
926	+	int i;
927
928	<	void SimSetup::initSystemCoords( void ){
928	>	char* inName;
929
930	<	if( the_globals->haveInitialConfig() ){
931	<
932	<	InitializeFromFile* fileInit;
930	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
931	>
932	>	for (i = 0; i < info[0].n_atoms; i++)
933	>	info[0].atoms[i]->setCoords();
934	>
935	>	if (globals->haveInitialConfig()){
936	>	InitializeFromFile* fileInit;
937		#ifdef IS_MPI // is_mpi
938	<	if( worldRank == 0 ){
938	>	if (worldRank == 0){
939		#endif //is_mpi
940	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
940	>	inName = globals->getInitialConfig();
941	>	fileInit = new InitializeFromFile(inName);
942		#ifdef IS_MPI
943	<	}else fileInit = new InitializeFromFile( NULL );
943	>	}
944	>	else
945	>	fileInit = new InitializeFromFile(NULL);
946		#endif
947	<	fileInit->read_xyz( info ); // default velocities on
947	>	fileInit->readInit(info); // default velocities on
948
949	<	delete fileInit;
950	<	}
951	<	else{
949	>	delete fileInit;
950	>	}
951	>	else{
952	>
953	>	// no init from bass
954	>
955	>	sprintf(painCave.errMsg,
956	>	"Cannot intialize a simulation without an initial configuration file.\n");
957	>	painCave.isFatal = 1;;
958	>	simError();
959	>
960	>	}
961
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	–
962		#ifdef IS_MPI
963	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
963	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
964		MPIcheckPoint();
965		#endif // is_mpi
1106	–
966		}
967
968
969	<	void SimSetup::makeOutNames( void ){
969	>	void SimSetup::makeOutNames(void){
970	>	int k;
971
972	+
973	+	for (k = 0; k < nInfo; k++){
974		#ifdef IS_MPI
975	<	if( worldRank == 0 ){
975	>	if (worldRank == 0){
976		#endif // is_mpi
977	<
978	<	if( the_globals->haveFinalConfig() ){
979	<	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" );
977	>
978	>	if (globals->haveFinalConfig()){
979	>	strcpy(info[k].finalName, globals->getFinalConfig());
980		}
1127	–	else if( !strcmp( endTest, ".BASS" ) ){
1128	–	strcpy( endTest, ".eor" );
1129	–	}
981		else{
982	<	endTest = &(info->finalName[nameLength - 4]);
983	<	if( !strcmp( endTest, ".bss" ) ){
984	<	strcpy( endTest, ".eor" );
985	<	}
986	<	else if( !strcmp( endTest, ".mdl" ) ){
987	<	strcpy( endTest, ".eor" );
988	<	}
989	<	else{
990	<	strcat( info->finalName, ".eor" );
991	<	}
982	>	strcpy(info[k].finalName, inFileName);
983	>	char* endTest;
984	>	int nameLength = strlen(info[k].finalName);
985	>	endTest = &(info[k].finalName[nameLength - 5]);
986	>	if (!strcmp(endTest, ".bass")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".BASS")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	endTest = &(info[k].finalName[nameLength - 4]);
994	>	if (!strcmp(endTest, ".bss")){
995	>	strcpy(endTest, ".eor");
996	>	}
997	>	else if (!strcmp(endTest, ".mdl")){
998	>	strcpy(endTest, ".eor");
999	>	}
1000	>	else{
1001	>	strcat(info[k].finalName, ".eor");
1002	>	}
1003	>	}
1004		}
1005	<	}
1006	<
1007	<	// make the sample and status out names
1008	<
1009	<	strcpy( info->sampleName, inFileName );
1010	<	char* endTest;
1011	<	int nameLength = strlen( info->sampleName );
1012	<	endTest = &(info->sampleName[nameLength - 5]);
1013	<	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" );
1005	>
1006	>	// make the sample and status out names
1007	>
1008	>	strcpy(info[k].sampleName, inFileName);
1009	>	char* endTest;
1010	>	int nameLength = strlen(info[k].sampleName);
1011	>	endTest = &(info[k].sampleName[nameLength - 5]);
1012	>	if (!strcmp(endTest, ".bass")){
1013	>	strcpy(endTest, ".dump");
1014		}
1015	<	else if( !strcmp( endTest, ".mdl" ) ){
1016	<	strcpy( endTest, ".dump" );
1015	>	else if (!strcmp(endTest, ".BASS")){
1016	>	strcpy(endTest, ".dump");
1017		}
1018		else{
1019	<	strcat( info->sampleName, ".dump" );
1019	>	endTest = &(info[k].sampleName[nameLength - 4]);
1020	>	if (!strcmp(endTest, ".bss")){
1021	>	strcpy(endTest, ".dump");
1022	>	}
1023	>	else if (!strcmp(endTest, ".mdl")){
1024	>	strcpy(endTest, ".dump");
1025	>	}
1026	>	else{
1027	>	strcat(info[k].sampleName, ".dump");
1028	>	}
1029		}
1030	<	}
1031	<
1032	<	strcpy( info->statusName, inFileName );
1033	<	nameLength = strlen( info->statusName );
1034	<	endTest = &(info->statusName[nameLength - 5]);
1035	<	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" );
1030	>
1031	>	strcpy(info[k].statusName, inFileName);
1032	>	nameLength = strlen(info[k].statusName);
1033	>	endTest = &(info[k].statusName[nameLength - 5]);
1034	>	if (!strcmp(endTest, ".bass")){
1035	>	strcpy(endTest, ".stat");
1036		}
1037	<	else if( !strcmp( endTest, ".mdl" ) ){
1038	<	strcpy( endTest, ".stat" );
1037	>	else if (!strcmp(endTest, ".BASS")){
1038	>	strcpy(endTest, ".stat");
1039		}
1040		else{
1041	<	strcat( info->statusName, ".stat" );
1041	>	endTest = &(info[k].statusName[nameLength - 4]);
1042	>	if (!strcmp(endTest, ".bss")){
1043	>	strcpy(endTest, ".stat");
1044	>	}
1045	>	else if (!strcmp(endTest, ".mdl")){
1046	>	strcpy(endTest, ".stat");
1047	>	}
1048	>	else{
1049	>	strcat(info[k].statusName, ".stat");
1050	>	}
1051		}
1052	<	}
1190	<
1052	>
1053		#ifdef IS_MPI
1192	–	}
1193	–	#endif // is_mpi
1054
1055	+	}
1056	+	#endif // is_mpi
1057	+	}
1058		}
1059
1060
1061	<	void SimSetup::sysObjectsCreation( void ){
1061	>	void SimSetup::sysObjectsCreation(void){
1062	>	int i, k;
1063
1064		// create the forceField
1065
#	Line 1211 | Line 1075 | void SimSetup::sysObjectsCreation( void ){
1075
1076		#ifdef IS_MPI
1077		// divide the molecules among the processors
1078	<
1078	>
1079		mpiMolDivide();
1080		#endif //is_mpi
1081	<
1081	>
1082		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1083	<
1083	>
1084		makeSysArrays();
1085
1086	<
1086	>	// make and initialize the molecules (all but atomic coordinates)
1087
1088	+	makeMolecules();
1089
1090	+	for (k = 0; k < nInfo; k++){
1091	+	info[k].identArray = new int[info[k].n_atoms];
1092	+	for (i = 0; i < info[k].n_atoms; i++){
1093	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1094	+	}
1095	+	}
1096		}
1097
1098
1099	<	void SimSetup::createFF( void ){
1099	>	void SimSetup::createFF(void){
1100	>	switch (ffCase){
1101	>	case FF_DUFF:
1102	>	the_ff = new DUFF();
1103	>	break;
1104
1105	<	switch( ffCase ){
1105	>	case FF_LJ:
1106	>	the_ff = new LJFF();
1107	>	break;
1108
1109	<	case FF_DUFF:
1110	<	the_ff = new DUFF();
1111	<	break;
1109	>	case FF_EAM:
1110	>	the_ff = new EAM_FF();
1111	>	break;
1112
1113	<	case FF_LJ:
1114	<	the_ff = new LJFF();
1115	<	break;
1116	<
1117	<	default:
1241	<	sprintf( painCave.errMsg,
1242	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1243	<	painCave.isFatal = 1;
1244	<	simError();
1113	>	default:
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	>	painCave.isFatal = 1;
1117	>	simError();
1118		}
1119
1120		#ifdef IS_MPI
1121	<	strcpy( checkPointMsg, "ForceField creation successful" );
1121	>	strcpy(checkPointMsg, "ForceField creation successful");
1122		MPIcheckPoint();
1123		#endif // is_mpi
1251	–
1124		}
1125
1126
1127	<	void SimSetup::compList( void ){
1127	>	void SimSetup::compList(void){
1128	>	int i;
1129	>	char* id;
1130	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1131	>	LinkedMolStamp* currentStamp = NULL;
1132	>	comp_stamps = new MoleculeStamp * [n_components];
1133
1257	–	comp_stamps = new MoleculeStamp*[n_components];
1258	–
1134		// make an array of molecule stamps that match the components used.
1135		// also extract the used stamps out into a separate linked list
1136
1137	<	info->nComponents = n_components;
1138	<	info->componentsNmol = components_nmol;
1139	<	info->compStamps = comp_stamps;
1140	<	info->headStamp = new LinkedMolStamp();
1141	<
1142	<	char* id;
1268	<	LinkedMolStamp* headStamp = info->headStamp;
1269	<	LinkedMolStamp* currentStamp = NULL;
1270	<	for( i=0; i<n_components; i++ ){
1137	>	for (i = 0; i < nInfo; i++){
1138	>	info[i].nComponents = n_components;
1139	>	info[i].componentsNmol = components_nmol;
1140	>	info[i].compStamps = comp_stamps;
1141	>	info[i].headStamp = headStamp;
1142	>	}
1143
1144	+
1145	+	for (i = 0; i < n_components; i++){
1146		id = the_components[i]->getType();
1147		comp_stamps[i] = NULL;
1148	<
1148	>
1149		// check to make sure the component isn't already in the list
1150
1151	<	comp_stamps[i] = headStamp->match( id );
1152	<	if( comp_stamps[i] == NULL ){
1279	<
1151	>	comp_stamps[i] = headStamp->match(id);
1152	>	if (comp_stamps[i] == NULL){
1153		// extract the component from the list;
1154	<
1155	<	currentStamp = the_stamps->extractMolStamp( id );
1156	<	if( currentStamp == NULL ){
1157	<	sprintf( painCave.errMsg,
1158	<	"SimSetup error: Component \"%s\" was not found in the "
1159	<	"list of declared molecules\n",
1160	<	id );
1161	<	painCave.isFatal = 1;
1162	<	simError();
1154	>
1155	>	currentStamp = stamps->extractMolStamp(id);
1156	>	if (currentStamp == NULL){
1157	>	sprintf(painCave.errMsg,
1158	>	"SimSetup error: Component \"%s\" was not found in the "
1159	>	"list of declared molecules\n",
1160	>	id);
1161	>	painCave.isFatal = 1;
1162	>	simError();
1163		}
1164	<
1165	<	headStamp->add( currentStamp );
1166	<	comp_stamps[i] = headStamp->match( id );
1164	>
1165	>	headStamp->add(currentStamp);
1166	>	comp_stamps[i] = headStamp->match(id);
1167		}
1168		}
1169
1170		#ifdef IS_MPI
1171	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1171	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1172		MPIcheckPoint();
1173		#endif // is_mpi
1301	–
1302	–
1174		}
1175
1176	<	void SimSetup::calcSysValues( void ){
1176	>	void SimSetup::calcSysValues(void){
1177	>	int i;
1178
1179	+	int* molMembershipArray;
1180	+
1181		tot_atoms = 0;
1182		tot_bonds = 0;
1183		tot_bends = 0;
1184		tot_torsions = 0;
1185	<	for( i=0; i<n_components; i++ ){
1186	<
1187	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1188	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1315	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1185	>	for (i = 0; i < n_components; i++){
1186	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1187	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1188	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1189		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1190		}
1191
1192		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1193	+	molMembershipArray = new int[tot_atoms];
1194
1195	<	info->n_atoms = tot_atoms;
1196	<	info->n_bonds = tot_bonds;
1197	<	info->n_bends = tot_bends;
1198	<	info->n_torsions = tot_torsions;
1199	<	info->n_SRI = tot_SRI;
1200	<	info->n_mol = tot_nmol;
1201	<
1202	<	info->molMembershipArray = new int[tot_atoms];
1195	>	for (i = 0; i < nInfo; i++){
1196	>	info[i].n_atoms = tot_atoms;
1197	>	info[i].n_bonds = tot_bonds;
1198	>	info[i].n_bends = tot_bends;
1199	>	info[i].n_torsions = tot_torsions;
1200	>	info[i].n_SRI = tot_SRI;
1201	>	info[i].n_mol = tot_nmol;
1202	>
1203	>	info[i].molMembershipArray = molMembershipArray;
1204	>	}
1205		}
1206
1331	–
1207		#ifdef IS_MPI
1208
1209	<	void SimSetup::mpiMolDivide( void ){
1210	<
1209	>	void SimSetup::mpiMolDivide(void){
1210	>	int i, j, k;
1211		int localMol, allMol;
1212		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1213
1214	<	mpiSim = new mpiSimulation( info );
1215	<
1214	>	mpiSim = new mpiSimulation(info);
1215	>
1216		globalIndex = mpiSim->divideLabor();
1217
1218		// set up the local variables
1219	<
1219	>
1220		mol2proc = mpiSim->getMolToProcMap();
1221		molCompType = mpiSim->getMolComponentType();
1222	<
1222	>
1223		allMol = 0;
1224		localMol = 0;
1225		local_atoms = 0;
#	Line 1354 | Line 1229 | void SimSetup::mpiMolDivide( void ){
1229		globalAtomIndex = 0;
1230
1231
1232	<	for( i=0; i<n_components; i++ ){
1233	<
1234	<	for( j=0; j<components_nmol[i]; j++ ){
1235	<
1236	<	if( mol2proc[allMol] == worldRank ){
1237	<
1238	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1239	<	local_bonds +=    comp_stamps[i]->getNBonds();
1365	<	local_bends +=    comp_stamps[i]->getNBends();
1366	<	local_torsions += comp_stamps[i]->getNTorsions();
1367	<	localMol++;
1232	>	for (i = 0; i < n_components; i++){
1233	>	for (j = 0; j < components_nmol[i]; j++){
1234	>	if (mol2proc[allMol] == worldRank){
1235	>	local_atoms += comp_stamps[i]->getNAtoms();
1236	>	local_bonds += comp_stamps[i]->getNBonds();
1237	>	local_bends += comp_stamps[i]->getNBends();
1238	>	local_torsions += comp_stamps[i]->getNTorsions();
1239	>	localMol++;
1240		}
1241	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1242	<	info->molMembershipArray[globalAtomIndex] = allMol;
1241	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1242	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1243		globalAtomIndex++;
1244		}
1245
1246	<	allMol++;
1246	>	allMol++;
1247		}
1248		}
1249		local_SRI = local_bonds + local_bends + local_torsions;
1250	<
1251	<	info->n_atoms = mpiSim->getMyNlocal();
1252	<
1253	<	if( local_atoms != info->n_atoms ){
1254	<	sprintf( painCave.errMsg,
1255	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1256	<	" localAtom (%d) are not equal.\n",
1257	<	info->n_atoms,
1386	<	local_atoms );
1250	>
1251	>	info[0].n_atoms = mpiSim->getMyNlocal();
1252	>
1253	>	if (local_atoms != info[0].n_atoms){
1254	>	sprintf(painCave.errMsg,
1255	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1256	>	"\tlocalAtom (%d) are not equal.\n",
1257	>	info[0].n_atoms, local_atoms);
1258		painCave.isFatal = 1;
1259		simError();
1260		}
1261
1262	<	info->n_bonds = local_bonds;
1263	<	info->n_bends = local_bends;
1264	<	info->n_torsions = local_torsions;
1265	<	info->n_SRI = local_SRI;
1266	<	info->n_mol = localMol;
1262	>	info[0].n_bonds = local_bonds;
1263	>	info[0].n_bends = local_bends;
1264	>	info[0].n_torsions = local_torsions;
1265	>	info[0].n_SRI = local_SRI;
1266	>	info[0].n_mol = localMol;
1267
1268	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1268	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1269		MPIcheckPoint();
1270		}
1271	<
1271	>
1272		#endif // is_mpi
1273
1274
1275	<	void SimSetup::makeSysArrays( void ){
1275	>	void SimSetup::makeSysArrays(void){
1276	>
1277	>	#ifndef IS_MPI
1278	>	int k, j;
1279	>	#endif // is_mpi
1280	>	int i, l;
1281
1282	<	// create the atom and short range interaction arrays
1282	>	Atom** the_atoms;
1283	>	Molecule* the_molecules;
1284	>	Exclude** the_excludes;
1285
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;
1286
1287	<	// initialize the molecule's stampID's
1287	>	for (l = 0; l < nInfo; l++){
1288	>	// create the atom and short range interaction arrays
1289
1290	+	the_atoms = new Atom * [info[l].n_atoms];
1291	+	the_molecules = new Molecule[info[l].n_mol];
1292	+	int molIndex;
1293	+
1294	+	// initialize the molecule's stampID's
1295	+
1296		#ifdef IS_MPI
1416	–
1297
1298	<	molIndex = 0;
1299	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1300	<
1301	<	if(mol2proc[i] == worldRank ){
1302	<	the_molecules[molIndex].setStampID( molCompType[i] );
1303	<	the_molecules[molIndex].setMyIndex( molIndex );
1304	<	the_molecules[molIndex].setGlobalIndex( i );
1305	<	molIndex++;
1298	>
1299	>	molIndex = 0;
1300	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1301	>	if (mol2proc[i] == worldRank){
1302	>	the_molecules[molIndex].setStampID(molCompType[i]);
1303	>	the_molecules[molIndex].setMyIndex(molIndex);
1304	>	the_molecules[molIndex].setGlobalIndex(i);
1305	>	molIndex++;
1306	>	}
1307		}
1427	–	}
1308
1309		#else // is_mpi
1310	<
1311	<	molIndex = 0;
1312	<	globalAtomIndex = 0;
1313	<	for(i=0; i<n_components; i++){
1314	<	for(j=0; j<components_nmol[i]; j++ ){
1315	<	the_molecules[molIndex].setStampID( i );
1316	<	the_molecules[molIndex].setMyIndex( molIndex );
1317	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1318	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1319	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1320	<	globalAtomIndex++;
1310	>
1311	>	molIndex = 0;
1312	>	globalAtomIndex = 0;
1313	>	for (i = 0; i < n_components; i++){
1314	>	for (j = 0; j < components_nmol[i]; j++){
1315	>	the_molecules[molIndex].setStampID(i);
1316	>	the_molecules[molIndex].setMyIndex(molIndex);
1317	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1318	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1319	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1320	>	globalAtomIndex++;
1321	>	}
1322	>	molIndex++;
1323		}
1442	–	molIndex++;
1324		}
1444	–	}
1445	–
1325
1326	+
1327		#endif // is_mpi
1328
1329
1330	<	if( info->n_SRI ){
1331	<
1332	<	Exclude::createArray(info->n_SRI);
1333	<	the_excludes = new Exclude*[info->n_SRI];
1334	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1335	<	info->globalExcludes = new int;
1336	<	info->n_exclude = info->n_SRI;
1337	<	}
1338	<	else{
1339	<
1340	<	Exclude::createArray( 1 );
1341	<	the_excludes = new Exclude*;
1342	<	the_excludes[0] = new Exclude(0);
1343	<	the_excludes[0]->setPair( 0,0 );
1344	<	info->globalExcludes = new int;
1345	<	info->globalExcludes[0] = 0;
1346	<	info->n_exclude = 0;
1347	<	}
1330	>	if (info[l].n_SRI){
1331	>	Exclude::createArray(info[l].n_SRI);
1332	>	the_excludes = new Exclude * [info[l].n_SRI];
1333	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1334	>	the_excludes[ex] = new Exclude(ex);
1335	>	}
1336	>	info[l].globalExcludes = new int;
1337	>	info[l].n_exclude = info[l].n_SRI;
1338	>	}
1339	>	else{
1340	>	Exclude::createArray(1);
1341	>	the_excludes = new Exclude * ;
1342	>	the_excludes[0] = new Exclude(0);
1343	>	the_excludes[0]->setPair(0, 0);
1344	>	info[l].globalExcludes = new int;
1345	>	info[l].globalExcludes[0] = 0;
1346	>	info[l].n_exclude = 0;
1347	>	}
1348
1349	<	// set the arrays into the SimInfo object
1349	>	// set the arrays into the SimInfo object
1350
1351	<	info->atoms = the_atoms;
1352	<	info->molecules = the_molecules;
1353	<	info->nGlobalExcludes = 0;
1354	<	info->excludes = the_excludes;
1351	>	info[l].atoms = the_atoms;
1352	>	info[l].molecules = the_molecules;
1353	>	info[l].nGlobalExcludes = 0;
1354	>	info[l].excludes = the_excludes;
1355
1356	<	the_ff->setSimInfo( info );
1356	>	the_ff->setSimInfo(info);
1357	>	}
1358	>	}
1359	>
1360	>	void SimSetup::makeIntegrator(void){
1361	>	int k;
1362	>
1363	>	NVE<RealIntegrator>* myNVE = NULL;
1364	>	NVT<RealIntegrator>* myNVT = NULL;
1365	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1366	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1367	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1368	>
1369	>	for (k = 0; k < nInfo; k++){
1370	>	switch (ensembleCase){
1371	>	case NVE_ENS:
1372	>	if (globals->haveZconstraints()){
1373	>	setupZConstraint(info[k]);
1374	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1375	>	}
1376	>	else{
1377	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1378	>	}
1379	>
1380	>	info->the_integrator = myNVE;
1381	>	break;
1382
1383	+	case NVT_ENS:
1384	+	if (globals->haveZconstraints()){
1385	+	setupZConstraint(info[k]);
1386	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1387	+	}
1388	+	else
1389	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1390	+
1391	+	myNVT->setTargetTemp(globals->getTargetTemp());
1392	+
1393	+	if (globals->haveTauThermostat())
1394	+	myNVT->setTauThermostat(globals->getTauThermostat());
1395	+	else{
1396	+	sprintf(painCave.errMsg,
1397	+	"SimSetup error: If you use the NVT\n"
1398	+	"\tensemble, you must set tauThermostat.\n");
1399	+	painCave.isFatal = 1;
1400	+	simError();
1401	+	}
1402	+
1403	+	info->the_integrator = myNVT;
1404	+	break;
1405	+
1406	+	case NPTi_ENS:
1407	+	if (globals->haveZconstraints()){
1408	+	setupZConstraint(info[k]);
1409	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1410	+	}
1411	+	else
1412	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1413	+
1414	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1415	+
1416	+	if (globals->haveTargetPressure())
1417	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1418	+	else{
1419	+	sprintf(painCave.errMsg,
1420	+	"SimSetup error: If you use a constant pressure\n"
1421	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if (globals->haveTauThermostat())
1427	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1428	+	else{
1429	+	sprintf(painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"\tensemble, you must set tauThermostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	if (globals->haveTauBarostat())
1437	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1438	+	else{
1439	+	sprintf(painCave.errMsg,
1440	+	"SimSetup error: If you use an NPT\n"
1441	+	"\tensemble, you must set tauBarostat.\n");
1442	+	painCave.isFatal = 1;
1443	+	simError();
1444	+	}
1445	+
1446	+	info->the_integrator = myNPTi;
1447	+	break;
1448	+
1449	+	case NPTf_ENS:
1450	+	if (globals->haveZconstraints()){
1451	+	setupZConstraint(info[k]);
1452	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1453	+	}
1454	+	else
1455	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1456	+
1457	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1458	+
1459	+	if (globals->haveTargetPressure())
1460	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1461	+	else{
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup error: If you use a constant pressure\n"
1464	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1465	+	painCave.isFatal = 1;
1466	+	simError();
1467	+	}
1468	+
1469	+	if (globals->haveTauThermostat())
1470	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1471	+
1472	+	else{
1473	+	sprintf(painCave.errMsg,
1474	+	"SimSetup error: If you use an NPT\n"
1475	+	"\tensemble, you must set tauThermostat.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+
1480	+	if (globals->haveTauBarostat())
1481	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1482	+
1483	+	else{
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup error: If you use an NPT\n"
1486	+	"\tensemble, you must set tauBarostat.\n");
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+	info->the_integrator = myNPTf;
1492	+	break;
1493	+
1494	+	case NPTxyz_ENS:
1495	+	if (globals->haveZconstraints()){
1496	+	setupZConstraint(info[k]);
1497	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1498	+	}
1499	+	else
1500	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1501	+
1502	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1503	+
1504	+	if (globals->haveTargetPressure())
1505	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1506	+	else{
1507	+	sprintf(painCave.errMsg,
1508	+	"SimSetup error: If you use a constant pressure\n"
1509	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+
1514	+	if (globals->haveTauThermostat())
1515	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"SimSetup error: If you use an NPT\n"
1519	+	"\tensemble, you must set tauThermostat.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	if (globals->haveTauBarostat())
1525	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1526	+	else{
1527	+	sprintf(painCave.errMsg,
1528	+	"SimSetup error: If you use an NPT\n"
1529	+	"\tensemble, you must set tauBarostat.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+
1534	+	info->the_integrator = myNPTxyz;
1535	+	break;
1536	+
1537	+	default:
1538	+	sprintf(painCave.errMsg,
1539	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+	}
1544		}
1545	+
1546	+	void SimSetup::initFortran(void){
1547	+	info[0].refreshSim();
1548	+
1549	+	if (!strcmp(info[0].mixingRule, "standard")){
1550	+	the_ff->initForceField(LB_MIXING_RULE);
1551	+	}
1552	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1553	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1554	+	}
1555	+	else{
1556	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1557	+	info[0].mixingRule);
1558	+	painCave.isFatal = 1;
1559	+	simError();
1560	+	}
1561	+
1562	+
1563	+	#ifdef IS_MPI
1564	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1565	+	MPIcheckPoint();
1566	+	#endif // is_mpi
1567	+	}
1568	+
1569	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1570	+	int nZConstraints;
1571	+	ZconStamp** zconStamp;
1572	+
1573	+	if (globals->haveZconstraintTime()){
1574	+	//add sample time of z-constraint  into SimInfo's property list
1575	+	DoubleData* zconsTimeProp = new DoubleData();
1576	+	zconsTimeProp->setID(ZCONSTIME_ID);
1577	+	zconsTimeProp->setData(globals->getZconsTime());
1578	+	theInfo.addProperty(zconsTimeProp);
1579	+	}
1580	+	else{
1581	+	sprintf(painCave.errMsg,
1582	+	"ZConstraint error: If you use a ZConstraint,\n"
1583	+	"\tyou must set zconsTime.\n");
1584	+	painCave.isFatal = 1;
1585	+	simError();
1586	+	}
1587	+
1588	+	//push zconsTol into siminfo, if user does not specify
1589	+	//value for zconsTol, a default value will be used
1590	+	DoubleData* zconsTol = new DoubleData();
1591	+	zconsTol->setID(ZCONSTOL_ID);
1592	+	if (globals->haveZconsTol()){
1593	+	zconsTol->setData(globals->getZconsTol());
1594	+	}
1595	+	else{
1596	+	double defaultZConsTol = 0.01;
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1599	+	"\tOOPSE will use a default value of %f.\n"
1600	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1601	+	defaultZConsTol);
1602	+	painCave.isFatal = 0;
1603	+	simError();
1604	+
1605	+	zconsTol->setData(defaultZConsTol);
1606	+	}
1607	+	theInfo.addProperty(zconsTol);
1608	+
1609	+	//set Force Subtraction Policy
1610	+	StringData* zconsForcePolicy = new StringData();
1611	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1612	+
1613	+	if (globals->haveZconsForcePolicy()){
1614	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1615	+	}
1616	+	else{
1617	+	sprintf(painCave.errMsg,
1618	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1619	+	"\tOOPSE will use PolicyByMass.\n"
1620	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1621	+	painCave.isFatal = 0;
1622	+	simError();
1623	+	zconsForcePolicy->setData("BYMASS");
1624	+	}
1625	+
1626	+	theInfo.addProperty(zconsForcePolicy);
1627	+
1628	+	//Determine the name of ouput file and add it into SimInfo's property list
1629	+	//Be careful, do not use inFileName, since it is a pointer which
1630	+	//point to a string at master node, and slave nodes do not contain that string
1631	+
1632	+	string zconsOutput(theInfo.finalName);
1633	+
1634	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1635	+
1636	+	StringData* zconsFilename = new StringData();
1637	+	zconsFilename->setID(ZCONSFILENAME_ID);
1638	+	zconsFilename->setData(zconsOutput);
1639	+
1640	+	theInfo.addProperty(zconsFilename);
1641	+
1642	+	//setup index, pos and other parameters of z-constraint molecules
1643	+	nZConstraints = globals->getNzConstraints();
1644	+	theInfo.nZconstraints = nZConstraints;
1645	+
1646	+	zconStamp = globals->getZconStamp();
1647	+	ZConsParaItem tempParaItem;
1648	+
1649	+	ZConsParaData* zconsParaData = new ZConsParaData();
1650	+	zconsParaData->setID(ZCONSPARADATA_ID);
1651	+
1652	+	for (int i = 0; i < nZConstraints; i++){
1653	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1654	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1655	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1656	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1657	+
1658	+	zconsParaData->addItem(tempParaItem);
1659	+	}
1660	+
1661	+	//check the uniqueness of index
1662	+	if(!zconsParaData->isIndexUnique()){
1663	+	sprintf(painCave.errMsg,
1664	+	"ZConstraint Error: molIndex is not unique!\n");
1665	+	painCave.isFatal = 1;
1666	+	simError();
1667	+	}
1668	+
1669	+	//sort the parameters by index of molecules
1670	+	zconsParaData->sortByIndex();
1671	+
1672	+	//push data into siminfo, therefore, we can retrieve later
1673	+	theInfo.addProperty(zconsParaData);
1674	+	}

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