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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 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 "RigidBody.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 14 | Line 21
21
22		// some defines for ensemble and Forcefield  cases
23
24	<	#define NVE_ENS   0
25	<	#define NVT_ENS   1
26	<	#define NPTi_ENS  2
27	<	#define NPTf_ENS  3
28	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
24	>	#define NVE_ENS        0
25	>	#define NVT_ENS        1
26	>	#define NPTi_ENS       2
27	>	#define NPTf_ENS       3
28	>	#define NPTxyz_ENS     4
29
30
31	<	#define FF_DUFF 0
32	<	#define FF_LJ   1
31	>	#define FF_DUFF  0
32	>	#define FF_LJ    1
33	>	#define FF_EAM   2
34	>	#define FF_H2O   3
35
36	+	using namespace std;
37
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 41 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
81	–	int i, j, k, globalAtomIndex;
82	–
127		// gather all of the information from the Bass file
128	<
128	>
129		gatherInfo();
130
131		// creation of complex system objects
#	Line 89 | Line 133 | void SimSetup::createSim( void ){
133		sysObjectsCreation();
134
135		// check on the post processing info
136	<
136	>
137		finalInfoCheck();
138
139		// initialize the system coordinates
140
141	<	initSystemCoords();
142	<
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	+	if( !(globals->getUseInitTime()) )
145	+	info[0].currentTime = 0.0;
146	+	}
147	+
148		// make the output filenames
149
150		makeOutNames();
103	–
104	–	// make the integrator
151
106	–	makeIntegrator();
107	–
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 113 | Line 157 | void SimSetup::createSim( void ){
157
158		initFortran();
159
160	+	if (globals->haveMinimizer())
161	+	// make minimizer
162	+	makeMinimizer();
163	+	else
164	+	// make the integrator
165	+	makeIntegrator();
166
117	–
167		}
168
169
170	<	void SimSetup::makeMolecules( void ){
171	<
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI;
175	>	int stampID, atomOffset, rbOffset;
176		molInit molInfo;
177		DirectionalAtom* dAtom;
178	+	RigidBody* myRB;
179	+	StuntDouble* mySD;
180		LinkedAssign* extras;
181		LinkedAssign* current_extra;
182		AtomStamp* currentAtom;
183		BondStamp* currentBond;
184		BendStamp* currentBend;
185		TorsionStamp* currentTorsion;
186	+	RigidBodyStamp* currentRigidBody;
187	+	CutoffGroupStamp* currentCutoffGroup;
188	+	CutoffGroup* myCutoffGroup;
189	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192		bond_pair* theBonds;
193		bend_set* theBends;
194		torsion_set* theTorsions;
195
196	<
196	>	set<int> skipList;
197	>
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201	>
202	>	//ConstraintPair* consPair; //constraint pair
203	>	//ConstraintElement* consElement1;  //first element of constraint pair
204	>	//ConstraintElement* consElement2;  //second element of constraint pair
205	>	//int whichRigidBody;
206	>	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	>	//vector<pair<int, int> > jointAtoms;
208		//init the forceField paramters
209
210		the_ff->readParams();
211
142	–
212		// init the atoms
213
214	<	double ux, uy, uz, u, uSqr;
146	<
147	<	atomOffset = 0;
148	<	excludeOffset = 0;
149	<	for(i=0; i<info->n_mol; i++){
150	<
151	<	stampID = the_molecules[i].getStampID();
214	>	int nMembers, nNew, rb1, rb2;
215
216	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
217	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
155	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
156	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
157	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
219	<	molInfo.myAtoms = &the_atoms[atomOffset];
220	<	molInfo.myExcludes = &the_excludes[excludeOffset];
161	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
162	<	molInfo.myBends = new Bend*[molInfo.nBends];
163	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
219	>	atomOffset = 0;
220	>	groupOffset = 0;
221
222	<	theBonds = new bond_pair[molInfo.nBonds];
223	<	theBends = new bend_set[molInfo.nBends];
224	<	theTorsions = new torsion_set[molInfo.nTorsions];
168	<
169	<	// make the Atoms
170	<
171	<	for(j=0; j<molInfo.nAtoms; j++){
172	<
173	<	currentAtom = comp_stamps[stampID]->getAtom( j );
174	<	if( currentAtom->haveOrientation() ){
175	<
176	<	dAtom = new DirectionalAtom(j + atomOffset);
177	<	info->n_oriented++;
178	<	molInfo.myAtoms[j] = dAtom;
179	<
180	<	ux = currentAtom->getOrntX();
181	<	uy = currentAtom->getOrntY();
182	<	uz = currentAtom->getOrntZ();
183	<
184	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
185	<
186	<	u = sqrt( uSqr );
187	<	ux = ux / u;
188	<	uy = uy / u;
189	<	uz = uz / u;
190	<
191	<	dAtom->setSUx( ux );
192	<	dAtom->setSUy( uy );
193	<	dAtom->setSUz( uz );
194	<	}
195	<	else{
196	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197	<	}
198	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
199	<
200	<	#ifdef IS_MPI
201	<
202	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
203	<
204	<	#endif // is_mpi
205	<	}
206	<
207	<	// make the bonds
208	<	for(j=0; j<molInfo.nBonds; j++){
209	<
210	<	currentBond = comp_stamps[stampID]->getBond( j );
211	<	theBonds[j].a = currentBond->getA() + atomOffset;
212	<	theBonds[j].b = currentBond->getB() + atomOffset;
222	>	for (i = 0; i < info[k].n_mol; i++){
223	>	stampID = info[k].molecules[i].getStampID();
224	>	molName = comp_stamps[stampID]->getID();
225
226	<	exI = theBonds[j].a;
227	<	exJ = theBonds[j].b;
226	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
229	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231
232	<	// exclude_I must always be the smaller of the pair
218	<	if( exI > exJ ){
219	<	tempEx = exI;
220	<	exI = exJ;
221	<	exJ = tempEx;
222	<	}
223	<	#ifdef IS_MPI
224	<	tempEx = exI;
225	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
226	<	tempEx = exJ;
227	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
232	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233
234	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
230	<	#else  // isn't MPI
234	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
235
236	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
237	<	#endif  //is_mpi
238	<	}
239	<	excludeOffset += molInfo.nBonds;
236	>	if (molInfo.nBonds > 0)
237	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	>	else
239	>	molInfo.myBonds = NULL;
240
241	<	//make the bends
242	<	for(j=0; j<molInfo.nBends; j++){
241	>	if (molInfo.nBends > 0)
242	>	molInfo.myBends = new Bend*[molInfo.nBends];
243	>	else
244	>	molInfo.myBends = NULL;
245	>
246	>	if (molInfo.nTorsions > 0)
247	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	>	else
249	>	molInfo.myTorsions = NULL;
250	>
251	>	theBonds = new bond_pair[molInfo.nBonds];
252	>	theBends = new bend_set[molInfo.nBends];
253	>	theTorsions = new torsion_set[molInfo.nTorsions];
254
255	<	currentBend = comp_stamps[stampID]->getBend( j );
256	<	theBends[j].a = currentBend->getA() + atomOffset;
257	<	theBends[j].b = currentBend->getB() + atomOffset;
258	<	theBends[j].c = currentBend->getC() + atomOffset;
259	<
260	<	if( currentBend->haveExtras() ){
261	<
262	<	extras = currentBend->getExtras();
263	<	current_extra = extras;
264	<
265	<	while( current_extra != NULL ){
266	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
267	<
268	<	switch( current_extra->getType() ){
269	<
270	<	case 0:
271	<	theBends[j].ghost =
272	<	current_extra->getInt() + atomOffset;
273	<	theBends[j].isGhost = 1;
274	<	break;
275	<
276	<	case 1:
277	<	theBends[j].ghost =
278	<	(int)current_extra->getDouble() + atomOffset;
279	<	theBends[j].isGhost = 1;
280	<	break;
281	<
282	<	default:
283	<	sprintf( painCave.errMsg,
284	<	"SimSetup Error: ghostVectorSource was neither a "
285	<	"double nor an int.\n"
286	<	"-->Bend[%d] in %s\n",
287	<	j, comp_stamps[stampID]->getID() );
288	<	painCave.isFatal = 1;
289	<	simError();
290	<	}
291	<	}
292	<
293	<	else{
294	<
295	<	sprintf( painCave.errMsg,
296	<	"SimSetup Error: unhandled bend assignment:\n"
297	<	"    -->%s in Bend[%d] in %s\n",
298	<	current_extra->getlhs(),
299	<	j, comp_stamps[stampID]->getID() );
300	<	painCave.isFatal = 1;
301	<	simError();
302	<	}
303	<
304	<	current_extra = current_extra->getNext();
305	<	}
255	>	// make the Atoms
256	>
257	>	for (j = 0; j < molInfo.nAtoms; j++){
258	>	currentAtom = comp_stamps[stampID]->getAtom(j);
259	>
260	>	if (currentAtom->haveOrientation()){
261	>	dAtom = new DirectionalAtom((j + atomOffset),
262	>	info[k].getConfiguration());
263	>	info[k].n_oriented++;
264	>	molInfo.myAtoms[j] = dAtom;
265	>
266	>	// Directional Atoms have standard unit vectors which are oriented
267	>	// in space using the three Euler angles.  We assume the standard
268	>	// unit vector was originally along the z axis below.
269	>
270	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
271	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
272	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
273	>
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275	>
276	>	}
277	>	else{
278	>
279	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280	>
281	>	}
282	>
283	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
284	>	#ifdef IS_MPI
285	>
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287	>
288	>	#endif // is_mpi
289	>	}
290	>
291	>	// make the bonds
292	>	for (j = 0; j < molInfo.nBonds; j++){
293	>	currentBond = comp_stamps[stampID]->getBond(j);
294	>	theBonds[j].a = currentBond->getA() + atomOffset;
295	>	theBonds[j].b = currentBond->getB() + atomOffset;
296	>
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299	>
300	>	#ifdef IS_MPI
301	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
302	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
303	>	#else
304	>	exI = tempI + 1;
305	>	exJ = tempJ + 1;
306	>	#endif
307	>
308	>	info[k].excludes->addPair(exI, exJ);
309		}
310	<
311	<	if( !theBends[j].isGhost ){
312	<
313	<	exI = theBends[j].a;
314	<	exJ = theBends[j].c;
310	>
311	>	//make the bends
312	>	for (j = 0; j < molInfo.nBends; j++){
313	>	currentBend = comp_stamps[stampID]->getBend(j);
314	>	theBends[j].a = currentBend->getA() + atomOffset;
315	>	theBends[j].b = currentBend->getB() + atomOffset;
316	>	theBends[j].c = currentBend->getC() + atomOffset;
317	>
318	>	if (currentBend->haveExtras()){
319	>	extras = currentBend->getExtras();
320	>	current_extra = extras;
321	>
322	>	while (current_extra != NULL){
323	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
324	>	switch (current_extra->getType()){
325	>	case 0:
326	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
327	>	theBends[j].isGhost = 1;
328	>	break;
329	>
330	>	case 1:
331	>	theBends[j].ghost = (int) current_extra->getDouble() +
332	>	atomOffset;
333	>	theBends[j].isGhost = 1;
334	>	break;
335	>
336	>	default:
337	>	sprintf(painCave.errMsg,
338	>	"SimSetup Error: ghostVectorSource was neither a "
339	>	"double nor an int.\n"
340	>	"-->Bend[%d] in %s\n",
341	>	j, comp_stamps[stampID]->getID());
342	>	painCave.isFatal = 1;
343	>	simError();
344	>	}
345	>	}
346	>	else{
347	>	sprintf(painCave.errMsg,
348	>	"SimSetup Error: unhandled bend assignment:\n"
349	>	"    -->%s in Bend[%d] in %s\n",
350	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354	>
355	>	current_extra = current_extra->getNext();
356	>	}
357	>	}
358	>
359	>	if (theBends[j].isGhost) {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>
364	>	#ifdef IS_MPI
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	#else
368	>	exI = tempI + 1;
369	>	exJ = tempJ + 1;
370	>	#endif
371	>	info[k].excludes->addPair(exI, exJ);
372	>
373	>	} else {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>	tempK = theBends[j].c;
378	>
379	>	#ifdef IS_MPI
380	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
381	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
382	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
383	>	#else
384	>	exI = tempI + 1;
385	>	exJ = tempJ + 1;
386	>	exK = tempK + 1;
387	>	#endif
388	>
389	>	info[k].excludes->addPair(exI, exK);
390	>	info[k].excludes->addPair(exI, exJ);
391	>	info[k].excludes->addPair(exJ, exK);
392	>	}
393		}
394	<	else{
395	<
396	<	exI = theBends[j].a;
397	<	exJ = theBends[j].b;
398	<	}
399	<
400	<	// exclude_I must always be the smaller of the pair
401	<	if( exI > exJ ){
402	<	tempEx = exI;
403	<	exI = exJ;
404	<	exJ = tempEx;
405	<	}
394	>
395	>	for (j = 0; j < molInfo.nTorsions; j++){
396	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
397	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
398	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
399	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
400	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
401	>
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406	>
407		#ifdef IS_MPI
408	<	tempEx = exI;
409	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
410	<	tempEx = exJ;
411	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
412	<
413	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
414	<	#else  // isn't MPI
415	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
416	<	#endif  //is_mpi
417	<	}
321	<	excludeOffset += molInfo.nBends;
408	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
409	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
410	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
411	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
412	>	#else
413	>	exI = tempI + 1;
414	>	exJ = tempJ + 1;
415	>	exK = tempK + 1;
416	>	exL = tempL + 1;
417	>	#endif
418
419	<	for(j=0; j<molInfo.nTorsions; j++){
419	>	info[k].excludes->addPair(exI, exJ);
420	>	info[k].excludes->addPair(exI, exK);
421	>	info[k].excludes->addPair(exI, exL);
422	>	info[k].excludes->addPair(exJ, exK);
423	>	info[k].excludes->addPair(exJ, exL);
424	>	info[k].excludes->addPair(exK, exL);
425	>	}
426	>
427
428	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
326	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
428	>	molInfo.myRigidBodies.clear();
429
430	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
430	>	for (j = 0; j < molInfo.nRigidBodies; j++){
431
432	<	// exclude_I must always be the smaller of the pair
433	<	if( exI > exJ ){
434	<	tempEx = exI;
435	<	exI = exJ;
436	<	exJ = tempEx;
432	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
433	>	nMembers = currentRigidBody->getNMembers();
434	>
435	>	// Create the Rigid Body:
436	>
437	>	myRB = new RigidBody();
438	>
439	>	sprintf(rbName,"%s_RB_%d", molName, j);
440	>	myRB->setType(rbName);
441	>
442	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
443	>
444	>	// molI is atom numbering inside this molecule
445	>	molI = currentRigidBody->getMember(rb1);
446	>
447	>	// tempI is atom numbering on local processor
448	>	tempI = molI + atomOffset;
449	>
450	>	// currentAtom is the AtomStamp (which we need for
451	>	// rigid body reference positions)
452	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
453	>
454	>	// When we add to the rigid body, add the atom itself and
455	>	// the stamp info:
456	>
457	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
458	>
459	>	// Add this atom to the Skip List for the integrators
460	>	#ifdef IS_MPI
461	>	slI = info[k].atoms[tempI]->getGlobalIndex();
462	>	#else
463	>	slI = tempI;
464	>	#endif
465	>	skipList.insert(slI);
466	>
467	>	}
468	>
469	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
470	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
471	>
472	>	tempI = currentRigidBody->getMember(rb1);
473	>	tempJ = currentRigidBody->getMember(rb2);
474	>
475	>	// Some explanation is required here.
476	>	// Fortran indexing starts at 1, while c indexing starts at 0
477	>	// Also, in parallel computations, the GlobalIndex is
478	>	// used for the exclude list:
479	>
480	>	#ifdef IS_MPI
481	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483	>	#else
484	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486	>	#endif
487	>
488	>	info[k].excludes->addPair(exI, exJ);
489	>
490	>	}
491	>	}
492	>
493	>	molInfo.myRigidBodies.push_back(myRB);
494	>	info[k].rigidBodies.push_back(myRB);
495		}
496	+
497	+
498	+	//create cutoff group for molecule
499	+
500	+	cutoffAtomSet.clear();
501	+	molInfo.myCutoffGroups.clear();
502	+
503	+	for (j = 0; j < nCutoffGroups; j++){
504	+
505	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	+	nMembers = currentCutoffGroup->getNMembers();
507	+
508	+	myCutoffGroup = new CutoffGroup();
509	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	+
511	+	for (int cg = 0; cg < nMembers; cg++) {
512	+
513	+	// molI is atom numbering inside this molecule
514	+	molI = currentCutoffGroup->getMember(cg);
515	+
516	+	// tempI is atom numbering on local processor
517	+	tempI = molI + atomOffset;
518	+
519		#ifdef IS_MPI
520	<	tempEx = exI;
521	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
522	<	tempEx = exJ;
523	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
520	>	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	>	#else
522	>	globalID = info[k].atoms[tempI]->getIndex();
523	>	#endif
524	>
525	>	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526	>
527	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528	>
529	>	cutoffAtomSet.insert(tempI);
530	>	}
531	>
532	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	>	groupOffset++;
534	>
535	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536	>
537	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
538	>
539	>	for(j = 0; j < molInfo.nAtoms; j++){
540	>
541	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	>	myCutoffGroup = new CutoffGroup();
543	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545	>	#ifdef IS_MPI
546	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	>	#else
548	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	>	#endif
550	>	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	>	groupOffset++;
553	>	}
554	>
555	>	}
556	>
557	>	// After this is all set up, scan through the atoms to
558	>	// see if they can be added to the integrableObjects:
559	>
560	>	molInfo.myIntegrableObjects.clear();
561
346	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
347	–	#else  // isn't MPI
348	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	–	#endif  //is_mpi
350	–	}
351	–	excludeOffset += molInfo.nTorsions;
562
563	<
354	<	// send the arrays off to the forceField for init.
563	>	for (j = 0; j < molInfo.nAtoms; j++){
564
565	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
566	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
567	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
568	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
565	>	#ifdef IS_MPI
566	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	>	#else
568	>	slJ = j+atomOffset;
569	>	#endif
570
571	+	// if they aren't on the skip list, then they can be integrated
572
573	<	the_molecules[i].initialize( molInfo );
573	>	if (skipList.find(slJ) == skipList.end()) {
574	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	>	info[k].integrableObjects.push_back(mySD);
576	>	molInfo.myIntegrableObjects.push_back(mySD);
577	>	}
578	>	}
579
580	+	// all rigid bodies are integrated:
581
582	<	atomOffset += molInfo.nAtoms;
583	<	delete[] theBonds;
584	<	delete[] theBends;
585	<	delete[] theTorsions;
582	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	>	info[k].integrableObjects.push_back(mySD);
585	>	molInfo.myIntegrableObjects.push_back(mySD);
586	>	}
587	>
588	>
589	>	/*
590	>
591	>	//creat ConstraintPair.
592	>	molInfo.myConstraintPair.clear();
593	>
594	>	for (j = 0; j < molInfo.nBonds; j++){
595	>
596	>	//if both atoms are in the same rigid body, just skip it
597	>	currentBond = comp_stamps[stampID]->getBond(j);
598	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	>
600	>	tempI = currentBond->getA() + atomOffset;
601	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	>	else
604	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	>
606	>	tempJ =  currentBond->getB() + atomOffset;
607	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	>	else
610	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611	>
612	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	>	molInfo.myConstraintPairs.push_back(consPair);
614	>	}
615	>	}
616	>
617	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	>
621	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622	>
623	>	for(size_t m = 0; m < jointAtoms.size(); m++){
624	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626	>
627	>	consPair = new JointConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>
631	>	}
632	>	}
633	>
634	>	*/
635	>	// send the arrays off to the forceField for init.
636	>
637	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
638	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
639	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
640	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
641	>	theTorsions);
642	>
643	>	info[k].molecules[i].initialize(molInfo);
644	>
645	>
646	>	atomOffset += molInfo.nAtoms;
647	>	delete[] theBonds;
648	>	delete[] theBends;
649	>	delete[] theTorsions;
650	>	}
651		}
652
653		#ifdef IS_MPI
654	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
654	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
655		MPIcheckPoint();
656		#endif // is_mpi
657
376	–	// clean up the forcefield
377	–	the_ff->calcRcut();
378	–	the_ff->cleanMe();
379	–
658		}
659
660	<	void SimSetup::initFromBass( void ){
383	<
660	>	void SimSetup::initFromBass(void){
661		int i, j, k;
662		int n_cells;
663		double cellx, celly, cellz;
#	Line 389 | Line 666 | void SimSetup::initFromBass( void ){
666		int n_extra;
667		int have_extra, done;
668
669	<	temp1 = (double)tot_nmol / 4.0;
670	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
671	<	temp3 = ceil( temp2 );
669	>	double vel[3];
670	>	vel[0] = 0.0;
671	>	vel[1] = 0.0;
672	>	vel[2] = 0.0;
673
674	<	have_extra =0;
675	<	if( temp2 < temp3 ){ // we have a non-complete lattice
676	<	have_extra =1;
674	>	temp1 = (double) tot_nmol / 4.0;
675	>	temp2 = pow(temp1, (1.0 / 3.0));
676	>	temp3 = ceil(temp2);
677
678	<	n_cells = (int)temp3 - 1;
679	<	cellx = info->boxL[0] / temp3;
680	<	celly = info->boxL[1] / temp3;
681	<	cellz = info->boxL[2] / temp3;
404	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406	<	n_per_extra = (int)ceil( temp1 );
678	>	have_extra = 0;
679	>	if (temp2 < temp3){
680	>	// we have a non-complete lattice
681	>	have_extra = 1;
682
683	<	if( n_per_extra > 4){
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error. There has been an error in constructing"
686	<	" the non-complete lattice.\n" );
683	>	n_cells = (int) temp3 - 1;
684	>	cellx = info[0].boxL[0] / temp3;
685	>	celly = info[0].boxL[1] / temp3;
686	>	cellz = info[0].boxL[2] / temp3;
687	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
688	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
689	>	n_per_extra = (int) ceil(temp1);
690	>
691	>	if (n_per_extra > 4){
692	>	sprintf(painCave.errMsg,
693	>	"SimSetup error. There has been an error in constructing"
694	>	" the non-complete lattice.\n");
695		painCave.isFatal = 1;
696		simError();
697		}
698		}
699		else{
700	<	n_cells = (int)temp3;
701	<	cellx = info->boxL[0] / temp3;
702	<	celly = info->boxL[1] / temp3;
703	<	cellz = info->boxL[2] / temp3;
700	>	n_cells = (int) temp3;
701	>	cellx = info[0].boxL[0] / temp3;
702	>	celly = info[0].boxL[1] / temp3;
703	>	cellz = info[0].boxL[2] / temp3;
704		}
705
706		current_mol = 0;
#	Line 425 | Line 708 | void SimSetup::initFromBass( void ){
708		current_comp = 0;
709		current_atom_ndx = 0;
710
711	<	for( i=0; i < n_cells ; i++ ){
712	<	for( j=0; j < n_cells; j++ ){
713	<	for( k=0; k < n_cells; k++ ){
711	>	for (i = 0; i < n_cells ; i++){
712	>	for (j = 0; j < n_cells; j++){
713	>	for (k = 0; k < n_cells; k++){
714	>	makeElement(i * cellx, j * celly, k * cellz);
715
716	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
716	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
717
718	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
718	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
719
720	<	makeElement( i * cellx,
441	<	j * celly + 0.5 * celly,
442	<	k * cellz + 0.5 * cellz );
443	<
444	<	makeElement( i * cellx + 0.5 * cellx,
445	<	j * celly,
446	<	k * cellz + 0.5 * cellz );
720	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
721		}
722		}
723		}
724
725	<	if( have_extra ){
725	>	if (have_extra){
726		done = 0;
727
728		int start_ndx;
729	<	for( i=0; i < (n_cells+1) && !done; i++ ){
730	<	for( j=0; j < (n_cells+1) && !done; j++ ){
729	>	for (i = 0; i < (n_cells + 1) && !done; i++){
730	>	for (j = 0; j < (n_cells + 1) && !done; j++){
731	>	if (i < n_cells){
732	>	if (j < n_cells){
733	>	start_ndx = n_cells;
734	>	}
735	>	else
736	>	start_ndx = 0;
737	>	}
738	>	else
739	>	start_ndx = 0;
740
741	<	if( i < n_cells ){
741	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
742	>	makeElement(i * cellx, j * celly, k * cellz);
743	>	done = (current_mol >= tot_nmol);
744
745	<	if( j < n_cells ){
746	<	start_ndx = n_cells;
747	<	}
748	<	else start_ndx = 0;
749	<	}
465	<	else start_ndx = 0;
745	>	if (!done && n_per_extra > 1){
746	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
747	>	k * cellz);
748	>	done = (current_mol >= tot_nmol);
749	>	}
750
751	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
751	>	if (!done && n_per_extra > 2){
752	>	makeElement(i * cellx, j * celly + 0.5 * celly,
753	>	k * cellz + 0.5 * cellz);
754	>	done = (current_mol >= tot_nmol);
755	>	}
756
757	<	makeElement( i * cellx,
758	<	j * celly,
759	<	k * cellz );
760	<	done = ( current_mol >= tot_nmol );
761	<
762	<	if( !done && n_per_extra > 1 ){
475	<	makeElement( i * cellx + 0.5 * cellx,
476	<	j * celly + 0.5 * celly,
477	<	k * cellz );
478	<	done = ( current_mol >= tot_nmol );
479	<	}
480	<
481	<	if( !done && n_per_extra > 2){
482	<	makeElement( i * cellx,
483	<	j * celly + 0.5 * celly,
484	<	k * cellz + 0.5 * cellz );
485	<	done = ( current_mol >= tot_nmol );
486	<	}
487	<
488	<	if( !done && n_per_extra > 3){
489	<	makeElement( i * cellx + 0.5 * cellx,
490	<	j * celly,
491	<	k * cellz + 0.5 * cellz );
492	<	done = ( current_mol >= tot_nmol );
493	<	}
494	<	}
757	>	if (!done && n_per_extra > 3){
758	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
759	>	k * cellz + 0.5 * cellz);
760	>	done = (current_mol >= tot_nmol);
761	>	}
762	>	}
763		}
764		}
765		}
766
767	<
768	<	for( i=0; i<info->n_atoms; i++ ){
501	<	info->atoms[i]->set_vx( 0.0 );
502	<	info->atoms[i]->set_vy( 0.0 );
503	<	info->atoms[i]->set_vz( 0.0 );
767	>	for (i = 0; i < info[0].n_atoms; i++){
768	>	info[0].atoms[i]->setVel(vel);
769		}
770		}
771
772	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
772	>	void SimSetup::makeElement(double x, double y, double z){
773		int k;
774		AtomStamp* current_atom;
775		DirectionalAtom* dAtom;
776		double rotMat[3][3];
777	+	double pos[3];
778
779	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
780	<
781	<	current_atom = comp_stamps[current_comp]->getAtom( k );
782	<	if( !current_atom->havePosition() ){
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup:initFromBass error.\n"
785	<	"\tComponent %s, atom %s does not have a position specified.\n"
786	<	"\tThe initialization routine is unable to give a start"
787	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
779	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
780	>	current_atom = comp_stamps[current_comp]->getAtom(k);
781	>	if (!current_atom->havePosition()){
782	>	sprintf(painCave.errMsg,
783	>	"SimSetup:initFromBass error.\n"
784	>	"\tComponent %s, atom %s does not have a position specified.\n"
785	>	"\tThe initialization routine is unable to give a start"
786	>	" position.\n",
787	>	comp_stamps[current_comp]->getID(), current_atom->getType());
788		painCave.isFatal = 1;
789		simError();
790		}
791
792	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
793	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
794	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
792	>	pos[0] = x + current_atom->getPosX();
793	>	pos[1] = y + current_atom->getPosY();
794	>	pos[2] = z + current_atom->getPosZ();
795
796	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
796	>	info[0].atoms[current_atom_ndx]->setPos(pos);
797
798	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
798	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
799	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
800
801		rotMat[0][0] = 1.0;
802		rotMat[0][1] = 0.0;
#	Line 546 | Line 810 | void SimSetup::makeElement( double x, double y, double
810		rotMat[2][1] = 0.0;
811		rotMat[2][2] = 1.0;
812
813	<	dAtom->setA( rotMat );
813	>	dAtom->setA(rotMat);
814		}
815
816		current_atom_ndx++;
#	Line 555 | Line 819 | void SimSetup::makeElement( double x, double y, double
819		current_mol++;
820		current_comp_mol++;
821
822	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
822	>	if (current_comp_mol >= components_nmol[current_comp]){
823		current_comp_mol = 0;
824		current_comp++;
825		}
826		}
827
828
829	<	void SimSetup::gatherInfo( void ){
830	<	int i,j,k;
829	>	void SimSetup::gatherInfo(void){
830	>	int i;
831
832		ensembleCase = -1;
833		ffCase = -1;
834
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
835		// set the easy ones first
836	<	info->target_temp = globals->getTargetTemp();
837	<	info->dt = globals->getDt();
838	<	info->run_time = globals->getRunTime();
836	>
837	>	for (i = 0; i < nInfo; i++){
838	>	info[i].target_temp = globals->getTargetTemp();
839	>	info[i].dt = globals->getDt();
840	>	info[i].run_time = globals->getRunTime();
841	>	}
842		n_components = globals->getNComponents();
843
844
845		// get the forceField
846
847	<	strcpy( force_field, globals->getForceField() );
847	>	strcpy(force_field, globals->getForceField());
848
849	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
850	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
849	>	if (!strcasecmp(force_field, "DUFF")){
850	>	ffCase = FF_DUFF;
851	>	}
852	>	else if (!strcasecmp(force_field, "LJ")){
853	>	ffCase = FF_LJ;
854	>	}
855	>	else if (!strcasecmp(force_field, "EAM")){
856	>	ffCase = FF_EAM;
857	>	}
858	>	else if (!strcasecmp(force_field, "WATER")){
859	>	ffCase = FF_H2O;
860	>	}
861		else{
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup Error. Unrecognized force field -> %s\n",
864	<	force_field );
865	<	painCave.isFatal = 1;
594	<	simError();
862	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
863	>	force_field);
864	>	painCave.isFatal = 1;
865	>	simError();
866		}
867
868	<	// get the ensemble
868	>	// get the ensemble
869
870	<	strcpy( ensemble, globals->getEnsemble() );
870	>	strcpy(ensemble, globals->getEnsemble());
871
872	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
873	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
874	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
872	>	if (!strcasecmp(ensemble, "NVE")){
873	>	ensembleCase = NVE_ENS;
874	>	}
875	>	else if (!strcasecmp(ensemble, "NVT")){
876	>	ensembleCase = NVT_ENS;
877	>	}
878	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
879		ensembleCase = NPTi_ENS;
880	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
881	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
882	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
880	>	}
881	>	else if (!strcasecmp(ensemble, "NPTf")){
882	>	ensembleCase = NPTf_ENS;
883	>	}
884	>	else if (!strcasecmp(ensemble, "NPTxyz")){
885	>	ensembleCase = NPTxyz_ENS;
886	>	}
887		else{
888	<	sprintf( painCave.errMsg,
889	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
890	<	"reverting to NVE for this simulation.\n",
891	<	ensemble );
892	<	painCave.isFatal = 0;
893	<	simError();
894	<	strcpy( ensemble, "NVE" );
895	<	ensembleCase = NVE_ENS;
888	>	sprintf(painCave.errMsg,
889	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
890	>	"\treverting to NVE for this simulation.\n",
891	>	ensemble);
892	>	painCave.isFatal = 0;
893	>	simError();
894	>	strcpy(ensemble, "NVE");
895	>	ensembleCase = NVE_ENS;
896		}
618	–	strcpy( info->ensemble, ensemble );
897
898	<	// get the mixing rule
898	>	for (i = 0; i < nInfo; i++){
899	>	strcpy(info[i].ensemble, ensemble);
900
901	<	strcpy( info->mixingRule, globals->getMixingRule() );
902	<	info->usePBC = globals->getPBC();
903	<
904	<
901	>	// get the mixing rule
902	>
903	>	strcpy(info[i].mixingRule, globals->getMixingRule());
904	>	info[i].usePBC = globals->getPBC();
905	>	}
906	>
907		// get the components and calculate the tot_nMol and indvidual n_mol
908	<
908	>
909		the_components = globals->getComponents();
910		components_nmol = new int[n_components];
911
912
913	<	if( !globals->haveNMol() ){
913	>	if (!globals->haveNMol()){
914		// we don't have the total number of molecules, so we assume it is
915		// given in each component
916
917		tot_nmol = 0;
918	<	for( i=0; i<n_components; i++ ){
919	<
920	<	if( !the_components[i]->haveNMol() ){
921	<	// we have a problem
922	<	sprintf( painCave.errMsg,
923	<	"SimSetup Error. No global NMol or component NMol"
924	<	" given. Cannot calculate the number of atoms.\n" );
925	<	painCave.isFatal = 1;
645	<	simError();
918	>	for (i = 0; i < n_components; i++){
919	>	if (!the_components[i]->haveNMol()){
920	>	// we have a problem
921	>	sprintf(painCave.errMsg,
922	>	"SimSetup Error. No global NMol or component NMol given.\n"
923	>	"\tCannot calculate the number of atoms.\n");
924	>	painCave.isFatal = 1;
925	>	simError();
926		}
927
928		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 930 | void SimSetup::gatherInfo( void ){
930		}
931		}
932		else{
933	<	sprintf( painCave.errMsg,
934	<	"SimSetup error.\n"
935	<	"\tSorry, the ability to specify total"
936	<	" nMols and then give molfractions in the components\n"
937	<	"\tis not currently supported."
938	<	" Please give nMol in the components.\n" );
933	>	sprintf(painCave.errMsg,
934	>	"SimSetup error.\n"
935	>	"\tSorry, the ability to specify total"
936	>	" nMols and then give molfractions in the components\n"
937	>	"\tis not currently supported."
938	>	" Please give nMol in the components.\n");
939		painCave.isFatal = 1;
940		simError();
941		}
942
943	<	// set the status, sample, and thermal kick times
944	<
945	<	if( globals->haveSampleTime() ){
946	<	info->sampleTime = globals->getSampleTime();
947	<	info->statusTime = info->sampleTime;
948	<	info->thermalTime = info->sampleTime;
943	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
944	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945	>	sprintf(painCave.errMsg,
946	>	"Sample time is not divisible by dt.\n"
947	>	"\tThis will result in samples that are not uniformly\n"
948	>	"\tdistributed in time.  If this is a problem, change\n"
949	>	"\tyour sampleTime variable.\n");
950	>	painCave.isFatal = 0;
951	>	simError();
952		}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
953
954	<	if( globals->haveStatusTime() ){
955	<	info->statusTime = globals->getStatusTime();
954	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955	>	sprintf(painCave.errMsg,
956	>	"Status time is not divisible by dt.\n"
957	>	"\tThis will result in status reports that are not uniformly\n"
958	>	"\tdistributed in time.  If this is a problem, change \n"
959	>	"\tyour statusTime variable.\n");
960	>	painCave.isFatal = 0;
961	>	simError();
962		}
963
964	<	if( globals->haveThermalTime() ){
965	<	info->thermalTime = globals->getThermalTime();
966	<	}
964	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
965	>	sprintf(painCave.errMsg,
966	>	"Thermal time is not divisible by dt.\n"
967	>	"\tThis will result in thermalizations that are not uniformly\n"
968	>	"\tdistributed in time.  If this is a problem, change \n"
969	>	"\tyour thermalTime variable.\n");
970	>	painCave.isFatal = 0;
971	>	simError();
972	>	}
973
974	<	// check for the temperature set flag
974	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
975	>	sprintf(painCave.errMsg,
976	>	"Reset time is not divisible by dt.\n"
977	>	"\tThis will result in integrator resets that are not uniformly\n"
978	>	"\tdistributed in time.  If this is a problem, change\n"
979	>	"\tyour resetTime variable.\n");
980	>	painCave.isFatal = 0;
981	>	simError();
982	>	}
983
984	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
984	>	// set the status, sample, and thermal kick times
985
986	<	// get some of the tricky things that may still be in the globals
986	>	for (i = 0; i < nInfo; i++){
987	>	if (globals->haveSampleTime()){
988	>	info[i].sampleTime = globals->getSampleTime();
989	>	info[i].statusTime = info[i].sampleTime;
990	>	}
991	>	else{
992	>	info[i].sampleTime = globals->getRunTime();
993	>	info[i].statusTime = info[i].sampleTime;
994	>	}
995
996	<	double boxVector[3];
997	<	if( globals->haveBox() ){
692	<	boxVector[0] = globals->getBox();
693	<	boxVector[1] = globals->getBox();
694	<	boxVector[2] = globals->getBox();
695	<
696	<	info->setBox( boxVector );
697	<	}
698	<	else if( globals->haveDensity() ){
699	<
700	<	double vol;
701	<	vol = (double)tot_nmol / globals->getDensity();
702	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	<	boxVector[1] = boxVector[0];
704	<	boxVector[2] = boxVector[0];
705	<
706	<	info->setBox( boxVector );
707	<	}
708	<	else{
709	<	if( !globals->haveBoxX() ){
710	<	sprintf( painCave.errMsg,
711	<	"SimSetup error, no periodic BoxX size given.\n" );
712	<	painCave.isFatal = 1;
713	<	simError();
996	>	if (globals->haveStatusTime()){
997	>	info[i].statusTime = globals->getStatusTime();
998		}
715	–	boxVector[0] = globals->getBoxX();
999
1000	<	if( !globals->haveBoxY() ){
1001	<	sprintf( painCave.errMsg,
1002	<	"SimSetup error, no periodic BoxY size given.\n" );
1003	<	painCave.isFatal = 1;
721	<	simError();
1000	>	if (globals->haveThermalTime()){
1001	>	info[i].thermalTime = globals->getThermalTime();
1002	>	} else {
1003	>	info[i].thermalTime = globals->getRunTime();
1004		}
723	–	boxVector[1] = globals->getBoxY();
1005
1006	<	if( !globals->haveBoxZ() ){
1007	<	sprintf( painCave.errMsg,
1008	<	"SimSetup error, no periodic BoxZ size given.\n" );
1009	<	painCave.isFatal = 1;
729	<	simError();
1006	>	info[i].resetIntegrator = 0;
1007	>	if( globals->haveResetTime() ){
1008	>	info[i].resetTime = globals->getResetTime();
1009	>	info[i].resetIntegrator = 1;
1010		}
731	–	boxVector[2] = globals->getBoxZ();
1011
1012	<	info->setBox( boxVector );
1012	>	// check for the temperature set flag
1013	>
1014	>	if (globals->haveTempSet())
1015	>	info[i].setTemp = globals->getTempSet();
1016	>
1017	>	// check for the extended State init
1018	>
1019	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1020	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021	>
1022	>	// check for thermodynamic integration
1023	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1026	>	info[i].thermIntLambda = globals->getThermIntLambda();
1027	>	info[i].thermIntK = globals->getThermIntK();
1028	>
1029	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	>	info[i].restraint = myRestraint;
1031	>	}
1032	>	else {
1033	>	sprintf(painCave.errMsg,
1034	>	"SimSetup Error:\n"
1035	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1036	>	"\tthermodynamicIntegrationLambda (and/or\n"
1037	>	"\tthermodynamicIntegrationK) was not specified.\n"
1038	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	>	painCave.isFatal = 1;
1040	>	simError();
1041	>	}
1042	>	}
1043	>	else if(globals->getUseLiquidThermInt()) {
1044	>	if (globals->getUseSolidThermInt()) {
1045	>	sprintf( painCave.errMsg,
1046	>	"SimSetup Warning: It appears that you have both solid and\n"
1047	>	"\tliquid thermodynamic integration activated in your .bass\n"
1048	>	"\tfile. To avoid confusion, specify only one technique in\n"
1049	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1050	>	"\twill be assumed for the current simulation. If this is not\n"
1051	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1052	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1053	>	painCave.isFatal = 0;
1054	>	simError();
1055	>	}
1056	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1057	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1058	>	info[i].thermIntLambda = globals->getThermIntLambda();
1059	>	info[i].thermIntK = globals->getThermIntK();
1060	>	}
1061	>	else {
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error:\n"
1064	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1065	>	"\tthermodynamicIntegrationLambda (and/or\n"
1066	>	"\tthermodynamicIntegrationK) was not specified.\n"
1067	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	}
1071	>	}
1072	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1073	>	sprintf(painCave.errMsg,
1074	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1075	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1076	>	"\t'true' in your .bass file.  These keywords are set to\n"
1077	>	"\t'false' by default, so your lambda and/or k values are\n"
1078	>	"\tbeing ignored.\n");
1079	>	painCave.isFatal = 0;
1080	>	simError();
1081	>	}
1082		}
1083	+
1084	+	//setup seed for random number generator
1085	+	int seedValue;
1086	+
1087	+	if (globals->haveSeed()){
1088	+	seedValue = globals->getSeed();
1089
1090	+	if(seedValue / 1E9 == 0){
1091	+	sprintf(painCave.errMsg,
1092	+	"Seed for sprng library should contain at least 9 digits\n"
1093	+	"OOPSE will generate a seed for user\n");
1094	+	painCave.isFatal = 0;
1095	+	simError();
1096
1097	+	//using seed generated by system instead of invalid seed set by user
1098	+	#ifndef IS_MPI
1099	+	seedValue = make_sprng_seed();
1100	+	#else
1101	+	if (worldRank == 0){
1102	+	seedValue = make_sprng_seed();
1103	+	}
1104	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1105	+	#endif
1106	+	}
1107	+	}//end of if branch of globals->haveSeed()
1108	+	else{
1109
1110	+	#ifndef IS_MPI
1111	+	seedValue = make_sprng_seed();
1112	+	#else
1113	+	if (worldRank == 0){
1114	+	seedValue = make_sprng_seed();
1115	+	}
1116	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1117	+	#endif
1118	+	}//end of globals->haveSeed()
1119	+
1120	+	for (int i = 0; i < nInfo; i++){
1121	+	info[i].setSeed(seedValue);
1122	+	}
1123	+
1124		#ifdef IS_MPI
1125	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1125	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1126		MPIcheckPoint();
1127		#endif // is_mpi
742	–
1128		}
1129
1130
1131	<	void SimSetup::finalInfoCheck( void ){
1131	>	void SimSetup::finalInfoCheck(void){
1132		int index;
1133		int usesDipoles;
1134	<
1134	>	int usesCharges;
1135	>	int i;
1136
1137	<	// check electrostatic parameters
1138	<
1139	<	index = 0;
1140	<	usesDipoles = 0;
1141	<	while( (index < info->n_atoms) && !usesDipoles ){
1142	<	usesDipoles = ((info->atoms)[index])->hasDipole();
1143	<	index++;
1144	<	}
1145	<
1137	>	for (i = 0; i < nInfo; i++){
1138	>	// check electrostatic parameters
1139	>
1140	>	index = 0;
1141	>	usesDipoles = 0;
1142	>	while ((index < info[i].n_atoms) && !usesDipoles){
1143	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1144	>	index++;
1145	>	}
1146	>	index = 0;
1147	>	usesCharges = 0;
1148	>	while ((index < info[i].n_atoms) && !usesCharges){
1149	>	usesCharges= (info[i].atoms[index])->hasCharge();
1150	>	index++;
1151	>	}
1152		#ifdef IS_MPI
1153	<	int myUse = usesDipoles;
1154	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1153	>	int myUse = usesDipoles;
1154	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155		#endif //is_mpi
1156
1157	<	double theEcr, theEst;
1157	>	double theRcut, theRsw;
1158
1159	<	if (globals->getUseRF() ) {
1160	<	info->useReactionField = 1;
769	<
770	<	if( !globals->haveECR() ){
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup Warning: using default value of 1/2 the smallest "
773	<	"box length for the electrostaticCutoffRadius.\n"
774	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
784	<	}
1159	>	if (globals->haveRcut()) {
1160	>	theRcut = globals->getRcut();
1161
1162	<	if( !globals->haveEST() ){
1163	<	sprintf( painCave.errMsg,
1164	<	"SimSetup Warning: using default value of 0.05 * the "
1165	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1166	<	);
1167	<	painCave.isFatal = 0;
1168	<	simError();
793	<	theEst = 0.05 * theEcr;
1162	>	if (globals->haveRsw())
1163	>	theRsw = globals->getRsw();
1164	>	else
1165	>	theRsw = theRcut;
1166	>
1167	>	info[i].setDefaultRcut(theRcut, theRsw);
1168	>
1169		} else {
1170	<	theEst= globals->getEST();
1171	<	}
1170	>
1171	>	the_ff->calcRcut();
1172	>	theRcut = info[i].getRcut();
1173
1174	<	info->setEcr( theEcr, theEst );
1175	<
1176	<	if(!globals->haveDielectric() ){
1177	<	sprintf( painCave.errMsg,
1178	<	"SimSetup Error: You are trying to use Reaction Field without"
1179	<	"setting a dielectric constant!\n"
804	<	);
805	<	painCave.isFatal = 1;
806	<	simError();
1174	>	if (globals->haveRsw())
1175	>	theRsw = globals->getRsw();
1176	>	else
1177	>	theRsw = theRcut;
1178	>
1179	>	info[i].setDefaultRcut(theRcut, theRsw);
1180		}
1181	<	info->dielectric = globals->getDielectric();
1182	<	}
1183	<	else {
811	<	if (usesDipoles) {
1181	>
1182	>	if (globals->getUseRF()){
1183	>	info[i].useReactionField = 1;
1184
1185	<	if( !globals->haveECR() ){
1186	<	sprintf( painCave.errMsg,
1187	<	"SimSetup Warning: using default value of 1/2 the smallest "
1188	<	"box length for the electrostaticCutoffRadius.\n"
1189	<	"I hope you have a very fast processor!\n");
1190	<	painCave.isFatal = 0;
1191	<	simError();
1192	<	double smallest;
821	<	smallest = info->boxL[0];
822	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
1185	>	if (!globals->haveRcut()){
1186	>	sprintf(painCave.errMsg,
1187	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1188	>	"\tOOPSE will use a default value of 15.0 angstroms"
1189	>	"\tfor the cutoffRadius.\n");
1190	>	painCave.isFatal = 0;
1191	>	simError();
1192	>	theRcut = 15.0;
1193		}
1194	<
1195	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the "
833	<	"electrostaticSkinThickness\n"
834	<	);
835	<	painCave.isFatal = 0;
836	<	simError();
837	<	theEst = 0.05 * theEcr;
838	<	} else {
839	<	theEst= globals->getEST();
1194	>	else{
1195	>	theRcut = globals->getRcut();
1196		}
1197
1198	<	info->setEcr( theEcr, theEst );
1199	<	}
1200	<	}
1198	>	if (!globals->haveRsw()){
1199	>	sprintf(painCave.errMsg,
1200	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1201	>	"\tOOPSE will use a default value of\n"
1202	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1203	>	painCave.isFatal = 0;
1204	>	simError();
1205	>	theRsw = 0.95 * theRcut;
1206	>	}
1207	>	else{
1208	>	theRsw = globals->getRsw();
1209	>	}
1210
1211	<	#ifdef IS_MPI
847	<	strcpy( checkPointMsg, "post processing checks out" );
848	<	MPIcheckPoint();
849	<	#endif // is_mpi
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212
1213	<	}
1214	<
1215	<	void SimSetup::initSystemCoords( void ){
1216	<
1217	<	if( globals->haveInitialConfig() ){
1218	<
1219	<	InitializeFromFile* fileInit;
1220	<	#ifdef IS_MPI // is_mpi
1221	<	if( worldRank == 0 ){
1222	<	#endif //is_mpi
1223	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1224	<	#ifdef IS_MPI
863	<	}else fileInit = new InitializeFromFile( NULL );
864	<	#endif
865	<	fileInit->readInit( info ); // default velocities on
866	<
867	<	delete fileInit;
868	<	}
869	<	else{
870	<
871	<	#ifdef IS_MPI
872	<
873	<	// no init from bass
874	<
875	<	sprintf( painCave.errMsg,
876	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	<	painCave.isFatal;
878	<	simError();
879	<
880	<	#else
881	<
882	<	initFromBass();
1213	>	if (!globals->haveDielectric()){
1214	>	sprintf(painCave.errMsg,
1215	>	"SimSetup Error: No Dielectric constant was set.\n"
1216	>	"\tYou are trying to use Reaction Field without"
1217	>	"\tsetting a dielectric constant!\n");
1218	>	painCave.isFatal = 1;
1219	>	simError();
1220	>	}
1221	>	info[i].dielectric = globals->getDielectric();
1222	>	}
1223	>	else{
1224	>	if (usesDipoles || usesCharges){
1225
1226	+	if (!globals->haveRcut()){
1227	+	sprintf(painCave.errMsg,
1228	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	+	"\tOOPSE will use a default value of 15.0 angstroms"
1230	+	"\tfor the cutoffRadius.\n");
1231	+	painCave.isFatal = 0;
1232	+	simError();
1233	+	theRcut = 15.0;
1234	+	}
1235	+	else{
1236	+	theRcut = globals->getRcut();
1237	+	}
1238	+
1239	+	if (!globals->haveRsw()){
1240	+	sprintf(painCave.errMsg,
1241	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	+	"\tOOPSE will use a default value of\n"
1243	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	+	painCave.isFatal = 0;
1245	+	simError();
1246	+	theRsw = 0.95 * theRcut;
1247	+	}
1248	+	else{
1249	+	theRsw = globals->getRsw();
1250	+	}
1251	+
1252	+	info[i].setDefaultRcut(theRcut, theRsw);
1253	+
1254	+	}
1255	+	}
1256	+	}
1257	+	#ifdef IS_MPI
1258	+	strcpy(checkPointMsg, "post processing checks out");
1259	+	MPIcheckPoint();
1260	+	#endif // is_mpi
1261
1262	+	// clean up the forcefield
1263	+	the_ff->cleanMe();
1264	+	}
1265	+
1266	+	void SimSetup::initSystemCoords(void){
1267	+	int i;
1268	+
1269	+	char* inName;
1270	+
1271	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1272	+
1273	+	for (i = 0; i < info[0].n_atoms; i++)
1274	+	info[0].atoms[i]->setCoords();
1275	+
1276	+	if (globals->haveInitialConfig()){
1277	+	InitializeFromFile* fileInit;
1278	+	#ifdef IS_MPI // is_mpi
1279	+	if (worldRank == 0){
1280	+	#endif //is_mpi
1281	+	inName = globals->getInitialConfig();
1282	+	fileInit = new InitializeFromFile(inName);
1283	+	#ifdef IS_MPI
1284	+	}
1285	+	else
1286	+	fileInit = new InitializeFromFile(NULL);
1287		#endif
1288	<	}
1288	>	fileInit->readInit(info); // default velocities on
1289
1290	+	delete fileInit;
1291	+	}
1292	+	else{
1293	+
1294	+	// no init from bass
1295	+
1296	+	sprintf(painCave.errMsg,
1297	+	"Cannot intialize a simulation without an initial configuration file.\n");
1298	+	painCave.isFatal = 1;;
1299	+	simError();
1300	+
1301	+	}
1302	+
1303		#ifdef IS_MPI
1304	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1304	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1305		MPIcheckPoint();
1306		#endif // is_mpi
892	–
1307		}
1308
1309
1310	<	void SimSetup::makeOutNames( void ){
1310	>	void SimSetup::makeOutNames(void){
1311	>	int k;
1312
1313	+
1314	+	for (k = 0; k < nInfo; k++){
1315		#ifdef IS_MPI
1316	<	if( worldRank == 0 ){
1316	>	if (worldRank == 0){
1317		#endif // is_mpi
1318	<
1319	<	if( globals->haveFinalConfig() ){
1320	<	strcpy( info->finalName, globals->getFinalConfig() );
1321	<	}
1322	<	else{
1323	<	strcpy( info->finalName, inFileName );
1318	>
1319	>	if (globals->haveFinalConfig()){
1320	>	strcpy(info[k].finalName, globals->getFinalConfig());
1321	>	}
1322	>	else{
1323	>	strcpy(info[k].finalName, inFileName);
1324	>	char* endTest;
1325	>	int nameLength = strlen(info[k].finalName);
1326	>	endTest = &(info[k].finalName[nameLength - 5]);
1327	>	if (!strcmp(endTest, ".bass")){
1328	>	strcpy(endTest, ".eor");
1329	>	}
1330	>	else if (!strcmp(endTest, ".BASS")){
1331	>	strcpy(endTest, ".eor");
1332	>	}
1333	>	else{
1334	>	endTest = &(info[k].finalName[nameLength - 4]);
1335	>	if (!strcmp(endTest, ".bss")){
1336	>	strcpy(endTest, ".eor");
1337	>	}
1338	>	else if (!strcmp(endTest, ".mdl")){
1339	>	strcpy(endTest, ".eor");
1340	>	}
1341	>	else{
1342	>	strcat(info[k].finalName, ".eor");
1343	>	}
1344	>	}
1345	>	}
1346	>
1347	>	// make the sample and status out names
1348	>
1349	>	strcpy(info[k].sampleName, inFileName);
1350		char* endTest;
1351	<	int nameLength = strlen( info->finalName );
1352	<	endTest = &(info->finalName[nameLength - 5]);
1353	<	if( !strcmp( endTest, ".bass" ) ){
1354	<	strcpy( endTest, ".eor" );
1351	>	int nameLength = strlen(info[k].sampleName);
1352	>	endTest = &(info[k].sampleName[nameLength - 5]);
1353	>	if (!strcmp(endTest, ".bass")){
1354	>	strcpy(endTest, ".dump");
1355		}
1356	<	else if( !strcmp( endTest, ".BASS" ) ){
1357	<	strcpy( endTest, ".eor" );
1356	>	else if (!strcmp(endTest, ".BASS")){
1357	>	strcpy(endTest, ".dump");
1358		}
1359		else{
1360	<	endTest = &(info->finalName[nameLength - 4]);
1361	<	if( !strcmp( endTest, ".bss" ) ){
1362	<	strcpy( endTest, ".eor" );
1363	<	}
1364	<	else if( !strcmp( endTest, ".mdl" ) ){
1365	<	strcpy( endTest, ".eor" );
1366	<	}
1367	<	else{
1368	<	strcat( info->finalName, ".eor" );
1369	<	}
1360	>	endTest = &(info[k].sampleName[nameLength - 4]);
1361	>	if (!strcmp(endTest, ".bss")){
1362	>	strcpy(endTest, ".dump");
1363	>	}
1364	>	else if (!strcmp(endTest, ".mdl")){
1365	>	strcpy(endTest, ".dump");
1366	>	}
1367	>	else{
1368	>	strcat(info[k].sampleName, ".dump");
1369	>	}
1370		}
1371	<	}
1372	<
1373	<	// make the sample and status out names
1374	<
1375	<	strcpy( info->sampleName, inFileName );
1376	<	char* endTest;
934	<	int nameLength = strlen( info->sampleName );
935	<	endTest = &(info->sampleName[nameLength - 5]);
936	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
945	<	strcpy( endTest, ".dump" );
1371	>
1372	>	strcpy(info[k].statusName, inFileName);
1373	>	nameLength = strlen(info[k].statusName);
1374	>	endTest = &(info[k].statusName[nameLength - 5]);
1375	>	if (!strcmp(endTest, ".bass")){
1376	>	strcpy(endTest, ".stat");
1377		}
1378	<	else if( !strcmp( endTest, ".mdl" ) ){
1379	<	strcpy( endTest, ".dump" );
1378	>	else if (!strcmp(endTest, ".BASS")){
1379	>	strcpy(endTest, ".stat");
1380		}
1381		else{
1382	<	strcat( info->sampleName, ".dump" );
1382	>	endTest = &(info[k].statusName[nameLength - 4]);
1383	>	if (!strcmp(endTest, ".bss")){
1384	>	strcpy(endTest, ".stat");
1385	>	}
1386	>	else if (!strcmp(endTest, ".mdl")){
1387	>	strcpy(endTest, ".stat");
1388	>	}
1389	>	else{
1390	>	strcat(info[k].statusName, ".stat");
1391	>	}
1392		}
1393	<	}
1394	<
1395	<	strcpy( info->statusName, inFileName );
1396	<	nameLength = strlen( info->statusName );
1397	<	endTest = &(info->statusName[nameLength - 5]);
1398	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".stat" );
1393	>
1394	>	strcpy(info[k].rawPotName, inFileName);
1395	>	nameLength = strlen(info[k].rawPotName);
1396	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1397	>	if (!strcmp(endTest, ".bass")){
1398	>	strcpy(endTest, ".raw");
1399		}
1400	<	else if( !strcmp( endTest, ".mdl" ) ){
1401	<	strcpy( endTest, ".stat" );
1400	>	else if (!strcmp(endTest, ".BASS")){
1401	>	strcpy(endTest, ".raw");
1402		}
1403		else{
1404	<	strcat( info->statusName, ".stat" );
1404	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1405	>	if (!strcmp(endTest, ".bss")){
1406	>	strcpy(endTest, ".raw");
1407	>	}
1408	>	else if (!strcmp(endTest, ".mdl")){
1409	>	strcpy(endTest, ".raw");
1410	>	}
1411	>	else{
1412	>	strcat(info[k].rawPotName, ".raw");
1413	>	}
1414		}
1415	<	}
976	<
1415	>
1416		#ifdef IS_MPI
978	–	}
979	–	#endif // is_mpi
1417
1418	+	}
1419	+	#endif // is_mpi
1420	+	}
1421		}
1422
1423
1424	<	void SimSetup::sysObjectsCreation( void ){
1424	>	void SimSetup::sysObjectsCreation(void){
1425	>	int i, k;
1426
986	–	int i;
987	–
1427		// create the forceField
1428
1429		createFF();
#	Line 999 | Line 1438 | void SimSetup::sysObjectsCreation( void ){
1438
1439		#ifdef IS_MPI
1440		// divide the molecules among the processors
1441	<
1441	>
1442		mpiMolDivide();
1443		#endif //is_mpi
1444	<
1444	>
1445		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1446	<
1446	>
1447		makeSysArrays();
1448
1449		// make and initialize the molecules (all but atomic coordinates)
1450	<
1450	>
1451		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1017	–
1452
1453	<
1453	>	for (k = 0; k < nInfo; k++){
1454	>	info[k].identArray = new int[info[k].n_atoms];
1455	>	for (i = 0; i < info[k].n_atoms; i++){
1456	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1457	>	}
1458	>	}
1459		}
1460
1461
1462	<	void SimSetup::createFF( void ){
1462	>	void SimSetup::createFF(void){
1463	>	switch (ffCase){
1464	>	case FF_DUFF:
1465	>	the_ff = new DUFF();
1466	>	break;
1467
1468	<	switch( ffCase ){
1468	>	case FF_LJ:
1469	>	the_ff = new LJFF();
1470	>	break;
1471
1472	<	case FF_DUFF:
1473	<	the_ff = new DUFF();
1474	<	break;
1472	>	case FF_EAM:
1473	>	the_ff = new EAM_FF();
1474	>	break;
1475
1476	<	case FF_LJ:
1477	<	the_ff = new LJFF();
1478	<	break;
1476	>	case FF_H2O:
1477	>	the_ff = new WATER();
1478	>	break;
1479
1480	<	default:
1481	<	sprintf( painCave.errMsg,
1482	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1483	<	painCave.isFatal = 1;
1484	<	simError();
1480	>	default:
1481	>	sprintf(painCave.errMsg,
1482	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1483	>	painCave.isFatal = 1;
1484	>	simError();
1485		}
1486
1487		#ifdef IS_MPI
1488	<	strcpy( checkPointMsg, "ForceField creation successful" );
1488	>	strcpy(checkPointMsg, "ForceField creation successful");
1489		MPIcheckPoint();
1490		#endif // is_mpi
1046	–
1491		}
1492
1493
1494	<	void SimSetup::compList( void ){
1051	<
1494	>	void SimSetup::compList(void){
1495		int i;
1496	+	char* id;
1497	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1498	+	LinkedMolStamp* currentStamp = NULL;
1499	+	comp_stamps = new MoleculeStamp * [n_components];
1500	+	bool haveCutoffGroups;
1501
1502	<	comp_stamps = new MoleculeStamp*[n_components];
1503	<
1502	>	haveCutoffGroups = false;
1503	>
1504		// make an array of molecule stamps that match the components used.
1505		// also extract the used stamps out into a separate linked list
1506
1507	<	info->nComponents = n_components;
1508	<	info->componentsNmol = components_nmol;
1509	<	info->compStamps = comp_stamps;
1510	<	info->headStamp = new LinkedMolStamp();
1511	<
1512	<	char* id;
1065	<	LinkedMolStamp* headStamp = info->headStamp;
1066	<	LinkedMolStamp* currentStamp = NULL;
1067	<	for( i=0; i<n_components; i++ ){
1507	>	for (i = 0; i < nInfo; i++){
1508	>	info[i].nComponents = n_components;
1509	>	info[i].componentsNmol = components_nmol;
1510	>	info[i].compStamps = comp_stamps;
1511	>	info[i].headStamp = headStamp;
1512	>	}
1513
1514	+
1515	+	for (i = 0; i < n_components; i++){
1516		id = the_components[i]->getType();
1517		comp_stamps[i] = NULL;
1518	<
1518	>
1519		// check to make sure the component isn't already in the list
1520
1521	<	comp_stamps[i] = headStamp->match( id );
1522	<	if( comp_stamps[i] == NULL ){
1076	<
1521	>	comp_stamps[i] = headStamp->match(id);
1522	>	if (comp_stamps[i] == NULL){
1523		// extract the component from the list;
1524	<
1525	<	currentStamp = stamps->extractMolStamp( id );
1526	<	if( currentStamp == NULL ){
1527	<	sprintf( painCave.errMsg,
1528	<	"SimSetup error: Component \"%s\" was not found in the "
1529	<	"list of declared molecules\n",
1530	<	id );
1531	<	painCave.isFatal = 1;
1532	<	simError();
1524	>
1525	>	currentStamp = stamps->extractMolStamp(id);
1526	>	if (currentStamp == NULL){
1527	>	sprintf(painCave.errMsg,
1528	>	"SimSetup error: Component \"%s\" was not found in the "
1529	>	"list of declared molecules\n",
1530	>	id);
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533		}
1534	<
1535	<	headStamp->add( currentStamp );
1536	<	comp_stamps[i] = headStamp->match( id );
1534	>
1535	>	headStamp->add(currentStamp);
1536	>	comp_stamps[i] = headStamp->match(id);
1537		}
1538	+
1539	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1540	+	haveCutoffGroups = true;
1541		}
1542	+
1543	+	for (i = 0; i < nInfo; i++)
1544	+	info[i].haveCutoffGroups = haveCutoffGroups;
1545
1546		#ifdef IS_MPI
1547	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1547	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1548		MPIcheckPoint();
1549		#endif // is_mpi
1098	–
1099	–
1550		}
1551
1552	<	void SimSetup::calcSysValues( void ){
1553	<	int i, j, k;
1552	>	void SimSetup::calcSysValues(void){
1553	>	int i, j;
1554	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1555
1556	+	int* molMembershipArray;
1557	+	CutoffGroupStamp* cg;
1558
1559		tot_atoms = 0;
1560		tot_bonds = 0;
1561		tot_bends = 0;
1562		tot_torsions = 0;
1563	<	for( i=0; i<n_components; i++ ){
1564	<
1565	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1566	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1567	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1563	>	tot_rigid = 0;
1564	>	tot_groups = 0;
1565	>	for (i = 0; i < n_components; i++){
1566	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1567	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1568	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1569		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1570	<	}
1570	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1571
1572	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1573	+	atomsingroups = 0;
1574	+	for (j=0; j < ncutgroups; j++) {
1575	+	cg = comp_stamps[i]->getCutoffGroup(j);
1576	+	atomsingroups += cg->getNMembers();
1577	+	}
1578	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1579	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1580	+	}
1581	+
1582		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1583	+	molMembershipArray = new int[tot_atoms];
1584
1585	<	info->n_atoms = tot_atoms;
1586	<	info->n_bonds = tot_bonds;
1587	<	info->n_bends = tot_bends;
1588	<	info->n_torsions = tot_torsions;
1589	<	info->n_SRI = tot_SRI;
1590	<	info->n_mol = tot_nmol;
1591	<
1592	<	info->molMembershipArray = new int[tot_atoms];
1585	>	for (i = 0; i < nInfo; i++){
1586	>	info[i].n_atoms = tot_atoms;
1587	>	info[i].n_bonds = tot_bonds;
1588	>	info[i].n_bends = tot_bends;
1589	>	info[i].n_torsions = tot_torsions;
1590	>	info[i].n_SRI = tot_SRI;
1591	>	info[i].n_mol = tot_nmol;
1592	>	info[i].ngroup = tot_groups;
1593	>	info[i].molMembershipArray = molMembershipArray;
1594	>	}
1595		}
1596
1130	–
1597		#ifdef IS_MPI
1598
1599	<	void SimSetup::mpiMolDivide( void ){
1134	<
1599	>	void SimSetup::mpiMolDivide(void){
1600		int i, j, k;
1601		int localMol, allMol;
1602		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1603	+	int local_rigid, local_groups;
1604	+	vector<int> globalMolIndex;
1605	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1606	+	CutoffGroupStamp* cg;
1607
1608	<	mpiSim = new mpiSimulation( info );
1140	<
1141	<	globalIndex = mpiSim->divideLabor();
1608	>	mpiSim = new mpiSimulation(info);
1609
1610	+	mpiSim->divideLabor();
1611	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1612	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1613	+
1614		// set up the local variables
1615	<
1615	>
1616		mol2proc = mpiSim->getMolToProcMap();
1617		molCompType = mpiSim->getMolComponentType();
1618	<
1618	>
1619		allMol = 0;
1620		localMol = 0;
1621		local_atoms = 0;
1622		local_bonds = 0;
1623		local_bends = 0;
1624		local_torsions = 0;
1625	<	globalAtomIndex = 0;
1625	>	local_rigid = 0;
1626	>	local_groups = 0;
1627	>	globalAtomCounter = 0;
1628
1629	+	for (i = 0; i < n_components; i++){
1630	+	for (j = 0; j < components_nmol[i]; j++){
1631	+	if (mol2proc[allMol] == worldRank){
1632	+	local_atoms += comp_stamps[i]->getNAtoms();
1633	+	local_bonds += comp_stamps[i]->getNBonds();
1634	+	local_bends += comp_stamps[i]->getNBends();
1635	+	local_torsions += comp_stamps[i]->getNTorsions();
1636	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1637
1638	<	for( i=0; i<n_components; i++ ){
1638	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1639	>	atomsingroups = 0;
1640	>	for (k=0; k < ncutgroups; k++) {
1641	>	cg = comp_stamps[i]->getCutoffGroup(k);
1642	>	atomsingroups += cg->getNMembers();
1643	>	}
1644	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1645	>	ncutgroups;
1646	>	local_groups += ngroupsinstamp;
1647
1648	<	for( j=0; j<components_nmol[i]; j++ ){
1160	<
1161	<	if( mol2proc[allMol] == worldRank ){
1162	<
1163	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1164	<	local_bonds +=    comp_stamps[i]->getNBonds();
1165	<	local_bends +=    comp_stamps[i]->getNBends();
1166	<	local_torsions += comp_stamps[i]->getNTorsions();
1167	<	localMol++;
1648	>	localMol++;
1649		}
1650	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1651	<	info->molMembershipArray[globalAtomIndex] = allMol;
1652	<	globalAtomIndex++;
1650	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1651	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1652	>	globalAtomCounter++;
1653		}
1654
1655	<	allMol++;
1655	>	allMol++;
1656		}
1657		}
1658		local_SRI = local_bonds + local_bends + local_torsions;
1659	+
1660	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1661
1662	<	info->n_atoms = mpiSim->getMyNlocal();
1663	<
1664	<	if( local_atoms != info->n_atoms ){
1665	<	sprintf( painCave.errMsg,
1666	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1184	<	" localAtom (%d) are not equal.\n",
1185	<	info->n_atoms,
1186	<	local_atoms );
1662	>	if (local_atoms != info[0].n_atoms){
1663	>	sprintf(painCave.errMsg,
1664	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1665	>	"\tlocalAtom (%d) are not equal.\n",
1666	>	info[0].n_atoms, local_atoms);
1667		painCave.isFatal = 1;
1668		simError();
1669		}
1670
1671	<	info->n_bonds = local_bonds;
1672	<	info->n_bends = local_bends;
1673	<	info->n_torsions = local_torsions;
1674	<	info->n_SRI = local_SRI;
1675	<	info->n_mol = localMol;
1671	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1672	>	if (local_groups != info[0].ngroup){
1673	>	sprintf(painCave.errMsg,
1674	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1675	>	"\tlocalGroups (%d) are not equal.\n",
1676	>	info[0].ngroup, local_groups);
1677	>	painCave.isFatal = 1;
1678	>	simError();
1679	>	}
1680	>
1681	>	info[0].n_bonds = local_bonds;
1682	>	info[0].n_bends = local_bends;
1683	>	info[0].n_torsions = local_torsions;
1684	>	info[0].n_SRI = local_SRI;
1685	>	info[0].n_mol = localMol;
1686
1687	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1687	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1688		MPIcheckPoint();
1689		}
1690	<
1690	>
1691		#endif // is_mpi
1692
1693
1694	<	void SimSetup::makeSysArrays( void ){
1695	<	int i, j, k;
1694	>	void SimSetup::makeSysArrays(void){
1695	>
1696	>	#ifndef IS_MPI
1697	>	int k, j;
1698	>	#endif // is_mpi
1699	>	int i, l;
1700
1701	+	Atom** the_atoms;
1702	+	Molecule* the_molecules;
1703
1704	<	// create the atom and short range interaction arrays
1704	>	for (l = 0; l < nInfo; l++){
1705	>	// create the atom and short range interaction arrays
1706
1707	<	Atom::createArrays(info->n_atoms);
1708	<	the_atoms = new Atom*[info->n_atoms];
1709	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1707	>	the_atoms = new Atom * [info[l].n_atoms];
1708	>	the_molecules = new Molecule[info[l].n_mol];
1709	>	int molIndex;
1710
1711	<	// initialize the molecule's stampID's
1711	>	// initialize the molecule's stampID's
1712
1713		#ifdef IS_MPI
1218	–
1714
1715	<	molIndex = 0;
1716	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1717	<
1718	<	if(mol2proc[i] == worldRank ){
1719	<	the_molecules[molIndex].setStampID( molCompType[i] );
1720	<	the_molecules[molIndex].setMyIndex( molIndex );
1721	<	the_molecules[molIndex].setGlobalIndex( i );
1722	<	molIndex++;
1715	>
1716	>	molIndex = 0;
1717	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1718	>	if (mol2proc[i] == worldRank){
1719	>	the_molecules[molIndex].setStampID(molCompType[i]);
1720	>	the_molecules[molIndex].setMyIndex(molIndex);
1721	>	the_molecules[molIndex].setGlobalIndex(i);
1722	>	molIndex++;
1723	>	}
1724		}
1229	–	}
1725
1726		#else // is_mpi
1727	<
1728	<	molIndex = 0;
1729	<	globalAtomIndex = 0;
1730	<	for(i=0; i<n_components; i++){
1731	<	for(j=0; j<components_nmol[i]; j++ ){
1732	<	the_molecules[molIndex].setStampID( i );
1733	<	the_molecules[molIndex].setMyIndex( molIndex );
1734	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1735	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1736	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1737	<	globalAtomIndex++;
1727	>
1728	>	molIndex = 0;
1729	>	globalAtomCounter = 0;
1730	>	for (i = 0; i < n_components; i++){
1731	>	for (j = 0; j < components_nmol[i]; j++){
1732	>	the_molecules[molIndex].setStampID(i);
1733	>	the_molecules[molIndex].setMyIndex(molIndex);
1734	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1735	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1736	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1737	>	globalAtomCounter++;
1738	>	}
1739	>	molIndex++;
1740		}
1244	–	molIndex++;
1741		}
1246	–	}
1247	–
1742
1743	+
1744		#endif // is_mpi
1745
1746	+	info[l].globalExcludes = new int;
1747	+	info[l].globalExcludes[0] = 0;
1748	+
1749	+	// set the arrays into the SimInfo object
1750
1751	<	if( info->n_SRI ){
1751	>	info[l].atoms = the_atoms;
1752	>	info[l].molecules = the_molecules;
1753	>	info[l].nGlobalExcludes = 0;
1754
1755	<	Exclude::createArray(info->n_SRI);
1255	<	the_excludes = new Exclude*[info->n_SRI];
1256	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1257	<	info->globalExcludes = new int;
1258	<	info->n_exclude = info->n_SRI;
1259	<	}
1260	<	else{
1261	<
1262	<	Exclude::createArray( 1 );
1263	<	the_excludes = new Exclude*;
1264	<	the_excludes[0] = new Exclude(0);
1265	<	the_excludes[0]->setPair( 0,0 );
1266	<	info->globalExcludes = new int;
1267	<	info->globalExcludes[0] = 0;
1268	<	info->n_exclude = 0;
1755	>	the_ff->setSimInfo(info);
1756		}
1757	+	}
1758
1759	<	// set the arrays into the SimInfo object
1759	>	void SimSetup::makeIntegrator(void){
1760	>	int k;
1761
1762	<	info->atoms = the_atoms;
1763	<	info->molecules = the_molecules;
1764	<	info->nGlobalExcludes = 0;
1765	<	info->excludes = the_excludes;
1762	>	NVE<RealIntegrator>* myNVE = NULL;
1763	>	NVT<RealIntegrator>* myNVT = NULL;
1764	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1765	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1766	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1767	>
1768	>	for (k = 0; k < nInfo; k++){
1769	>	switch (ensembleCase){
1770	>	case NVE_ENS:
1771	>	if (globals->haveZconstraints()){
1772	>	setupZConstraint(info[k]);
1773	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1774	>	}
1775	>	else{
1776	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1777	>	}
1778	>
1779	>	info->the_integrator = myNVE;
1780	>	break;
1781
1782	<	the_ff->setSimInfo( info );
1782	>	case NVT_ENS:
1783	>	if (globals->haveZconstraints()){
1784	>	setupZConstraint(info[k]);
1785	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1786	>	}
1787	>	else
1788	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1789
1790	<	}
1790	>	myNVT->setTargetTemp(globals->getTargetTemp());
1791
1792	<	void SimSetup::makeIntegrator( void ){
1792	>	if (globals->haveTauThermostat())
1793	>	myNVT->setTauThermostat(globals->getTauThermostat());
1794	>	else{
1795	>	sprintf(painCave.errMsg,
1796	>	"SimSetup error: If you use the NVT\n"
1797	>	"\tensemble, you must set tauThermostat.\n");
1798	>	painCave.isFatal = 1;
1799	>	simError();
1800	>	}
1801
1802	<	NVT<RealIntegrator>*  myNVT = NULL;
1803	<	NPTi<RealIntegrator>* myNPTi = NULL;
1286	<	NPTf<RealIntegrator>* myNPTf = NULL;
1287	<	NPTim<RealIntegrator>* myNPTim = NULL;
1288	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1802	>	info->the_integrator = myNVT;
1803	>	break;
1804
1805	<	switch( ensembleCase ){
1805	>	case NPTi_ENS:
1806	>	if (globals->haveZconstraints()){
1807	>	setupZConstraint(info[k]);
1808	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1809	>	}
1810	>	else
1811	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1812
1813	<	case NVE_ENS:
1293	<	new NVE<RealIntegrator>( info, the_ff );
1294	<	break;
1813	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1814
1815	<	case NVT_ENS:
1816	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1817	<	myNVT->setTargetTemp(globals->getTargetTemp());
1815	>	if (globals->haveTargetPressure())
1816	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1817	>	else{
1818	>	sprintf(painCave.errMsg,
1819	>	"SimSetup error: If you use a constant pressure\n"
1820	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1821	>	painCave.isFatal = 1;
1822	>	simError();
1823	>	}
1824
1825	<	if (globals->haveTauThermostat())
1826	<	myNVT->setTauThermostat(globals->getTauThermostat());
1825	>	if (globals->haveTauThermostat())
1826	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1827	>	else{
1828	>	sprintf(painCave.errMsg,
1829	>	"SimSetup error: If you use an NPT\n"
1830	>	"\tensemble, you must set tauThermostat.\n");
1831	>	painCave.isFatal = 1;
1832	>	simError();
1833	>	}
1834
1835	<	else {
1836	<	sprintf( painCave.errMsg,
1837	<	"SimSetup error: If you use the NVT\n"
1838	<	"    ensemble, you must set tauThermostat.\n");
1839	<	painCave.isFatal = 1;
1840	<	simError();
1841	<	}
1842	<	break;
1835	>	if (globals->haveTauBarostat())
1836	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1837	>	else{
1838	>	sprintf(painCave.errMsg,
1839	>	"SimSetup error: If you use an NPT\n"
1840	>	"\tensemble, you must set tauBarostat.\n");
1841	>	painCave.isFatal = 1;
1842	>	simError();
1843	>	}
1844
1845	<	case NPTi_ENS:
1846	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1314	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1845	>	info->the_integrator = myNPTi;
1846	>	break;
1847
1848	<	if (globals->haveTargetPressure())
1849	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1850	<	else {
1851	<	sprintf( painCave.errMsg,
1852	<	"SimSetup error: If you use a constant pressure\n"
1853	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1854	<	painCave.isFatal = 1;
1323	<	simError();
1324	<	}
1325	<
1326	<	if( globals->haveTauThermostat() )
1327	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	<	else{
1329	<	sprintf( painCave.errMsg,
1330	<	"SimSetup error: If you use an NPT\n"
1331	<	"    ensemble, you must set tauThermostat.\n");
1332	<	painCave.isFatal = 1;
1333	<	simError();
1334	<	}
1848	>	case NPTf_ENS:
1849	>	if (globals->haveZconstraints()){
1850	>	setupZConstraint(info[k]);
1851	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1852	>	}
1853	>	else
1854	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1855
1856	<	if( globals->haveTauBarostat() )
1337	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	<	else{
1339	<	sprintf( painCave.errMsg,
1340	<	"SimSetup error: If you use an NPT\n"
1341	<	"    ensemble, you must set tauBarostat.\n");
1342	<	painCave.isFatal = 1;
1343	<	simError();
1344	<	}
1345	<	break;
1856	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1857
1858	<	case NPTf_ENS:
1859	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1860	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1858	>	if (globals->haveTargetPressure())
1859	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1860	>	else{
1861	>	sprintf(painCave.errMsg,
1862	>	"SimSetup error: If you use a constant pressure\n"
1863	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1864	>	painCave.isFatal = 1;
1865	>	simError();
1866	>	}
1867
1868	<	if (globals->haveTargetPressure())
1869	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	<	else {
1354	<	sprintf( painCave.errMsg,
1355	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	<	painCave.isFatal = 1;
1358	<	simError();
1359	<	}
1868	>	if (globals->haveTauThermostat())
1869	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1870
1871	<	if( globals->haveTauThermostat() )
1872	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1873	<	else{
1874	<	sprintf( painCave.errMsg,
1875	<	"SimSetup error: If you use an NPT\n"
1876	<	"    ensemble, you must set tauThermostat.\n");
1877	<	painCave.isFatal = 1;
1368	<	simError();
1369	<	}
1871	>	else{
1872	>	sprintf(painCave.errMsg,
1873	>	"SimSetup error: If you use an NPT\n"
1874	>	"\tensemble, you must set tauThermostat.\n");
1875	>	painCave.isFatal = 1;
1876	>	simError();
1877	>	}
1878
1879	<	if( globals->haveTauBarostat() )
1880	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	<	else{
1374	<	sprintf( painCave.errMsg,
1375	<	"SimSetup error: If you use an NPT\n"
1376	<	"    ensemble, you must set tauBarostat.\n");
1377	<	painCave.isFatal = 1;
1378	<	simError();
1379	<	}
1380	<	break;
1381	<
1382	<	case NPTim_ENS:
1383	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1384	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1879	>	if (globals->haveTauBarostat())
1880	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1881
1882	<	if (globals->haveTargetPressure())
1883	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1884	<	else {
1885	<	sprintf( painCave.errMsg,
1886	<	"SimSetup error: If you use a constant pressure\n"
1887	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1888	<	painCave.isFatal = 1;
1393	<	simError();
1394	<	}
1395	<
1396	<	if( globals->haveTauThermostat() )
1397	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	<	else{
1399	<	sprintf( painCave.errMsg,
1400	<	"SimSetup error: If you use an NPT\n"
1401	<	"    ensemble, you must set tauThermostat.\n");
1402	<	painCave.isFatal = 1;
1403	<	simError();
1404	<	}
1882	>	else{
1883	>	sprintf(painCave.errMsg,
1884	>	"SimSetup error: If you use an NPT\n"
1885	>	"\tensemble, you must set tauBarostat.\n");
1886	>	painCave.isFatal = 1;
1887	>	simError();
1888	>	}
1889
1890	<	if( globals->haveTauBarostat() )
1891	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	<	else{
1409	<	sprintf( painCave.errMsg,
1410	<	"SimSetup error: If you use an NPT\n"
1411	<	"    ensemble, you must set tauBarostat.\n");
1412	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<	break;
1890	>	info->the_integrator = myNPTf;
1891	>	break;
1892
1893	<	case NPTfm_ENS:
1894	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1895	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1893	>	case NPTxyz_ENS:
1894	>	if (globals->haveZconstraints()){
1895	>	setupZConstraint(info[k]);
1896	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	>	}
1898	>	else
1899	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900
1901	<	if (globals->haveTargetPressure())
1422	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	<	else {
1424	<	sprintf( painCave.errMsg,
1425	<	"SimSetup error: If you use a constant pressure\n"
1426	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1430	<
1431	<	if( globals->haveTauThermostat() )
1432	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	<	else{
1434	<	sprintf( painCave.errMsg,
1435	<	"SimSetup error: If you use an NPT\n"
1436	<	"    ensemble, you must set tauThermostat.\n");
1437	<	painCave.isFatal = 1;
1438	<	simError();
1439	<	}
1901	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1902
1903	<	if( globals->haveTauBarostat() )
1904	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1905	<	else{
1906	<	sprintf( painCave.errMsg,
1907	<	"SimSetup error: If you use an NPT\n"
1908	<	"    ensemble, you must set tauBarostat.\n");
1909	<	painCave.isFatal = 1;
1910	<	simError();
1911	<	}
1450	<	break;
1903	>	if (globals->haveTargetPressure())
1904	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1905	>	else{
1906	>	sprintf(painCave.errMsg,
1907	>	"SimSetup error: If you use a constant pressure\n"
1908	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1909	>	painCave.isFatal = 1;
1910	>	simError();
1911	>	}
1912
1913	<	default:
1914	<	sprintf( painCave.errMsg,
1915	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1916	<	painCave.isFatal = 1;
1917	<	simError();
1918	<	}
1913	>	if (globals->haveTauThermostat())
1914	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1915	>	else{
1916	>	sprintf(painCave.errMsg,
1917	>	"SimSetup error: If you use an NPT\n"
1918	>	"\tensemble, you must set tauThermostat.\n");
1919	>	painCave.isFatal = 1;
1920	>	simError();
1921	>	}
1922
1923	+	if (globals->haveTauBarostat())
1924	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1925	+	else{
1926	+	sprintf(painCave.errMsg,
1927	+	"SimSetup error: If you use an NPT\n"
1928	+	"\tensemble, you must set tauBarostat.\n");
1929	+	painCave.isFatal = 1;
1930	+	simError();
1931	+	}
1932	+
1933	+	info->the_integrator = myNPTxyz;
1934	+	break;
1935	+
1936	+	default:
1937	+	sprintf(painCave.errMsg,
1938	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1939	+	painCave.isFatal = 1;
1940	+	simError();
1941	+	}
1942	+	}
1943		}
1944
1945	<	void SimSetup::initFortran( void ){
1945	>	void SimSetup::initFortran(void){
1946	>	info[0].refreshSim();
1947
1948	<	info->refreshSim();
1949	<
1465	<	if( !strcmp( info->mixingRule, "standard") ){
1466	<	the_ff->initForceField( LB_MIXING_RULE );
1948	>	if (!strcmp(info[0].mixingRule, "standard")){
1949	>	the_ff->initForceField(LB_MIXING_RULE);
1950		}
1951	<	else if( !strcmp( info->mixingRule, "explicit") ){
1952	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1951	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1952	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1953		}
1954		else{
1955	<	sprintf( painCave.errMsg,
1956	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	<	info->mixingRule );
1955	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1956	>	info[0].mixingRule);
1957		painCave.isFatal = 1;
1958		simError();
1959		}
1960
1961
1962		#ifdef IS_MPI
1963	<	strcpy( checkPointMsg,
1482	<	"Successfully intialized the mixingRule for Fortran." );
1963	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1964		MPIcheckPoint();
1965		#endif // is_mpi
1966	+	}
1967
1968	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1969	+	int nZConstraints;
1970	+	ZconStamp** zconStamp;
1971	+
1972	+	if (globals->haveZconstraintTime()){
1973	+	//add sample time of z-constraint  into SimInfo's property list
1974	+	DoubleData* zconsTimeProp = new DoubleData();
1975	+	zconsTimeProp->setID(ZCONSTIME_ID);
1976	+	zconsTimeProp->setData(globals->getZconsTime());
1977	+	theInfo.addProperty(zconsTimeProp);
1978	+	}
1979	+	else{
1980	+	sprintf(painCave.errMsg,
1981	+	"ZConstraint error: If you use a ZConstraint,\n"
1982	+	"\tyou must set zconsTime.\n");
1983	+	painCave.isFatal = 1;
1984	+	simError();
1985	+	}
1986	+
1987	+	//push zconsTol into siminfo, if user does not specify
1988	+	//value for zconsTol, a default value will be used
1989	+	DoubleData* zconsTol = new DoubleData();
1990	+	zconsTol->setID(ZCONSTOL_ID);
1991	+	if (globals->haveZconsTol()){
1992	+	zconsTol->setData(globals->getZconsTol());
1993	+	}
1994	+	else{
1995	+	double defaultZConsTol = 0.01;
1996	+	sprintf(painCave.errMsg,
1997	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1998	+	"\tOOPSE will use a default value of %f.\n"
1999	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2000	+	defaultZConsTol);
2001	+	painCave.isFatal = 0;
2002	+	simError();
2003	+
2004	+	zconsTol->setData(defaultZConsTol);
2005	+	}
2006	+	theInfo.addProperty(zconsTol);
2007	+
2008	+	//set Force Subtraction Policy
2009	+	StringData* zconsForcePolicy = new StringData();
2010	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2011	+
2012	+	if (globals->haveZconsForcePolicy()){
2013	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2014	+	}
2015	+	else{
2016	+	sprintf(painCave.errMsg,
2017	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2018	+	"\tOOPSE will use PolicyByMass.\n"
2019	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2020	+	painCave.isFatal = 0;
2021	+	simError();
2022	+	zconsForcePolicy->setData("BYMASS");
2023	+	}
2024	+
2025	+	theInfo.addProperty(zconsForcePolicy);
2026	+
2027	+	//set zcons gap
2028	+	DoubleData* zconsGap = new DoubleData();
2029	+	zconsGap->setID(ZCONSGAP_ID);
2030	+
2031	+	if (globals->haveZConsGap()){
2032	+	zconsGap->setData(globals->getZconsGap());
2033	+	theInfo.addProperty(zconsGap);
2034	+	}
2035	+
2036	+	//set zcons fixtime
2037	+	DoubleData* zconsFixtime = new DoubleData();
2038	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2039	+
2040	+	if (globals->haveZConsFixTime()){
2041	+	zconsFixtime->setData(globals->getZconsFixtime());
2042	+	theInfo.addProperty(zconsFixtime);
2043	+	}
2044	+
2045	+	//set zconsUsingSMD
2046	+	IntData* zconsUsingSMD = new IntData();
2047	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2048	+
2049	+	if (globals->haveZConsUsingSMD()){
2050	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2051	+	theInfo.addProperty(zconsUsingSMD);
2052	+	}
2053	+
2054	+	//Determine the name of ouput file and add it into SimInfo's property list
2055	+	//Be careful, do not use inFileName, since it is a pointer which
2056	+	//point to a string at master node, and slave nodes do not contain that string
2057	+
2058	+	string zconsOutput(theInfo.finalName);
2059	+
2060	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2061	+
2062	+	StringData* zconsFilename = new StringData();
2063	+	zconsFilename->setID(ZCONSFILENAME_ID);
2064	+	zconsFilename->setData(zconsOutput);
2065	+
2066	+	theInfo.addProperty(zconsFilename);
2067	+
2068	+	//setup index, pos and other parameters of z-constraint molecules
2069	+	nZConstraints = globals->getNzConstraints();
2070	+	theInfo.nZconstraints = nZConstraints;
2071	+
2072	+	zconStamp = globals->getZconStamp();
2073	+	ZConsParaItem tempParaItem;
2074	+
2075	+	ZConsParaData* zconsParaData = new ZConsParaData();
2076	+	zconsParaData->setID(ZCONSPARADATA_ID);
2077	+
2078	+	for (int i = 0; i < nZConstraints; i++){
2079	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2080	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2081	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2082	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2083	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2084	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2085	+	zconsParaData->addItem(tempParaItem);
2086	+	}
2087	+
2088	+	//check the uniqueness of index
2089	+	if(!zconsParaData->isIndexUnique()){
2090	+	sprintf(painCave.errMsg,
2091	+	"ZConstraint Error: molIndex is not unique!\n");
2092	+	painCave.isFatal = 1;
2093	+	simError();
2094	+	}
2095	+
2096	+	//sort the parameters by index of molecules
2097	+	zconsParaData->sortByIndex();
2098	+
2099	+	//push data into siminfo, therefore, we can retrieve later
2100	+	theInfo.addProperty(zconsParaData);
2101		}
2102	+
2103	+	void SimSetup::makeMinimizer(){
2104	+
2105	+	OOPSEMinimizer* myOOPSEMinimizer;
2106	+	MinimizerParameterSet* param;
2107	+	char minimizerName[100];
2108	+
2109	+	for (int i = 0; i < nInfo; i++){
2110	+
2111	+	//prepare parameter set for minimizer
2112	+	param = new MinimizerParameterSet();
2113	+	param->setDefaultParameter();
2114	+
2115	+	if (globals->haveMinimizer()){
2116	+	param->setFTol(globals->getMinFTol());
2117	+	}
2118	+
2119	+	if (globals->haveMinGTol()){
2120	+	param->setGTol(globals->getMinGTol());
2121	+	}
2122	+
2123	+	if (globals->haveMinMaxIter()){
2124	+	param->setMaxIteration(globals->getMinMaxIter());
2125	+	}
2126	+
2127	+	if (globals->haveMinWriteFrq()){
2128	+	param->setMaxIteration(globals->getMinMaxIter());
2129	+	}
2130	+
2131	+	if (globals->haveMinWriteFrq()){
2132	+	param->setWriteFrq(globals->getMinWriteFrq());
2133	+	}
2134	+
2135	+	if (globals->haveMinStepSize()){
2136	+	param->setStepSize(globals->getMinStepSize());
2137	+	}
2138	+
2139	+	if (globals->haveMinLSMaxIter()){
2140	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2141	+	}
2142	+
2143	+	if (globals->haveMinLSTol()){
2144	+	param->setLineSearchTol(globals->getMinLSTol());
2145	+	}
2146	+
2147	+	strcpy(minimizerName, globals->getMinimizer());
2148	+
2149	+	if (!strcasecmp(minimizerName, "CG")){
2150	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2151	+	}
2152	+	else if (!strcasecmp(minimizerName, "SD")){
2153	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2154	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2155	+	}
2156	+	else{
2157	+	sprintf(painCave.errMsg,
2158	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2159	+	painCave.isFatal = 0;
2160	+	simError();
2161	+
2162	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2163	+	}
2164	+	info[i].the_integrator = myOOPSEMinimizer;
2165	+
2166	+	//store the minimizer into simInfo
2167	+	info[i].the_minimizer = myOOPSEMinimizer;
2168	+	info[i].has_minimizer = true;
2169	+	}
2170	+
2171	+	}

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