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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
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 21 | Line 25
25		#define NVT_ENS        1
26		#define NPTi_ENS       2
27		#define NPTf_ENS       3
28	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
28	>	#define NPTxyz_ENS     4
29
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#define FF_EAM  2
30
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	<
67	>
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
71	<
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 50 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
84	<	info = the_info;
85	<	nInfo = theNinfo;
86	<	isInfoArray = 1;
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 ){
61	<
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();
89	<	mpiEventLoop();
90	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125		void SimSetup::createSim(void){
126
97	–	int i, j, k, globalAtomIndex;
98	–
127		// gather all of the information from the Bass file
128
129		gatherInfo();
#	Line 110 | Line 138 | void SimSetup::createSim(void){
138
139		// initialize the system coordinates
140
141	<	if( !isInfoArray ) initSystemCoords();
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();
118	–
119	–	// make the integrator
151
121	–	makeIntegrator();
122	–
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 128 | 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
132	–
167		}
168
169
170	<	void SimSetup::makeMolecules( void ){
171	<
172	<	int k,l;
173	<	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
158	–
212		// init the atoms
213
214	<	double ux, uy, uz, u, uSqr;
162	<
163	<	for(k=0; k<nInfo; k++){
164	<
165	<	the_ff->setSimInfo( &(info[k]) );
214	>	int nMembers, nNew, rb1, rb2;
215
216	+	for (k = 0; k < nInfo; k++){
217	+	the_ff->setSimInfo(&(info[k]));
218	+
219		atomOffset = 0;
220	<	excludeOffset = 0;
221	<	for(i=0; i<info[k].n_mol; i++){
222	<
220	>	groupOffset = 0;
221	>
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	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
227	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
228	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
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.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231	>
232	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233
234		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	–	molInfo.myBends = new Bend*[molInfo.nBends];
183	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
235
236	+	if (molInfo.nBonds > 0)
237	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	+	else
239	+	molInfo.myBonds = NULL;
240	+
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	<
254	>
255		// make the Atoms
256	<
257	<	for(j=0; j<molInfo.nAtoms; j++){
258	<
259	<	currentAtom = comp_stamps[stampID]->getAtom( j );
260	<	if( currentAtom->haveOrientation() ){
261	<
262	<	dAtom = new DirectionalAtom( (j + atomOffset),
263	<	info[k].getConfiguration() );
264	<	info[k].n_oriented++;
265	<	molInfo.myAtoms[j] = dAtom;
266	<
267	<	ux = currentAtom->getOrntX();
268	<	uy = currentAtom->getOrntY();
269	<	uz = currentAtom->getOrntZ();
270	<
271	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
272	<
273	<	u = sqrt( uSqr );
274	<	ux = ux / u;
275	<	uy = uy / u;
276	<	uz = uz / u;
277	<
278	<	dAtom->setSUx( ux );
279	<	dAtom->setSUy( uy );
280	<	dAtom->setSUz( uz );
281	<	}
282	<	else{
283	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
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( globalIndex[j+atomOffset] );
287	<
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	<
294	<	currentBond = comp_stamps[stampID]->getBond( j );
295	<	theBonds[j].a = currentBond->getA() + atomOffset;
296	<	theBonds[j].b = currentBond->getB() + atomOffset;
297	<
298	<	exI = theBonds[j].a;
299	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
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	<	tempEx = exI;
302	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
303	<	tempEx = exJ;
304	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
305	<
306	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
307	<	#else  // isn't MPI
308	<
254	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	<	#endif  //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	<	excludeOffset += molInfo.nBonds;
258	<
310	>
311		//make the bends
312	<	for(j=0; j<molInfo.nBends; j++){
313	<
314	<	currentBend = comp_stamps[stampID]->getBend( j );
315	<	theBends[j].a = currentBend->getA() + atomOffset;
316	<	theBends[j].b = currentBend->getB() + atomOffset;
317	<	theBends[j].c = currentBend->getC() + atomOffset;
318	<
319	<	if( currentBend->haveExtras() ){
320	<
321	<	extras = currentBend->getExtras();
322	<	current_extra = extras;
323	<
324	<	while( current_extra != NULL ){
325	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
326	<
327	<	switch( current_extra->getType() ){
328	<
329	<	case 0:
330	<	theBends[j].ghost =
331	<	current_extra->getInt() + atomOffset;
332	<	theBends[j].isGhost = 1;
333	<	break;
334	<
335	<	case 1:
336	<	theBends[j].ghost =
337	<	(int)current_extra->getDouble() + atomOffset;
338	<	theBends[j].isGhost = 1;
339	<	break;
340	<
341	<	default:
342	<	sprintf( painCave.errMsg,
343	<	"SimSetup Error: ghostVectorSource was neither a "
344	<	"double nor an int.\n"
345	<	"-->Bend[%d] in %s\n",
346	<	j, comp_stamps[stampID]->getID() );
347	<	painCave.isFatal = 1;
348	<	simError();
349	<	}
350	<	}
351	<
352	<	else{
353	<
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup Error: unhandled bend assignment:\n"
356	<	"    -->%s in Bend[%d] in %s\n",
357	<	current_extra->getlhs(),
358	<	j, comp_stamps[stampID]->getID() );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
362	<
363	<	current_extra = current_extra->getNext();
312	<	}
313	<	}
314	<
315	<	if( !theBends[j].isGhost ){
316	<
317	<	exI = theBends[j].a;
318	<	exJ = theBends[j].c;
319	<	}
320	<	else{
321	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].b;
324	<	}
325	<
326	<	// exclude_I must always be the smaller of the pair
327	<	if( exI > exJ ){
328	<	tempEx = exI;
329	<	exI = exJ;
330	<	exJ = tempEx;
331	<	}
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	<	tempEx = exI;
366	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	<	tempEx = exJ;
368	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
369	<
370	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
371	<	#else  // isn't MPI
372	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
373	<	#endif  //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	<	excludeOffset += molInfo.nBends;
395	<
396	<	for(j=0; j<molInfo.nTorsions; j++){
397	<
398	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
399	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
400	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
401	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
402	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
403	<
404	<	exI = theTorsions[j].a;
405	<	exJ = theTorsions[j].d;
406	<
356	<	// exclude_I must always be the smaller of the pair
357	<	if( exI > exJ ){
358	<	tempEx = exI;
359	<	exI = exJ;
360	<	exJ = tempEx;
361	<	}
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 = info[k].atoms[tempEx]->getGlobalIndex() + 1;
410	<	tempEx = exJ;
411	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
412	<
413	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
414	<	#else  // isn't MPI
415	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
416	<	#endif  //is_mpi
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	>	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	<	excludeOffset += molInfo.nTorsions;
426	>
427
428	+	molInfo.myRigidBodies.clear();
429
430	<	// send the arrays off to the forceField for init.
431	<
432	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
433	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
434	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
435	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
430	>	for (j = 0; j < molInfo.nRigidBodies; j++){
431	>
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	<	info[k].molecules[i].initialize( molInfo );
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	+	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
562	+
563	+	for (j = 0; j < molInfo.nAtoms; j++){
564	+
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	+	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	+	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	<	}
650	>	}
651		}
652	<
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
398	–
399	–	// clean up the forcefield
657
401	–	the_ff->calcRcut();
402	–	the_ff->cleanMe();
403	–
658		}
659
660	<	void SimSetup::initFromBass( void ){
407	<
660	>	void SimSetup::initFromBass(void){
661		int i, j, k;
662		int n_cells;
663		double cellx, celly, cellz;
#	Line 418 | Line 671 | void SimSetup::initFromBass( void ){
671		vel[1] = 0.0;
672		vel[2] = 0.0;
673
674	<	temp1 = (double)tot_nmol / 4.0;
675	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
676	<	temp3 = ceil( temp2 );
674	>	temp1 = (double) tot_nmol / 4.0;
675	>	temp2 = pow(temp1, (1.0 / 3.0));
676	>	temp3 = ceil(temp2);
677
678	<	have_extra =0;
679	<	if( temp2 < temp3 ){ // we have a non-complete lattice
680	<	have_extra =1;
678	>	have_extra = 0;
679	>	if (temp2 < temp3){
680	>	// we have a non-complete lattice
681	>	have_extra = 1;
682
683	<	n_cells = (int)temp3 - 1;
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 );
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" );
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;
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;
#	Line 454 | 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,
462	<	j * celly,
463	<	k * cellz );
716	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
717
718	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
718	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
719
720	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
472	<
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	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	<	}
494	<	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 ){
504	<	makeElement( i * cellx + 0.5 * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
509	<
510	<	if( !done && n_per_extra > 2){
511	<	makeElement( i * cellx,
512	<	j * celly + 0.5 * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
516	<
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
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	<	for( i=0; i<info[0].n_atoms; i++ ){
768	<	info[0].atoms[i]->setVel( vel );
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 ){
534	<
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",
550	<	comp_stamps[current_comp]->getID(),
551	<	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	<
791	>
792		pos[0] = x + current_atom->getPosX();
793		pos[1] = y + current_atom->getPosY();
794		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
795
796	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
796	>	info[0].atoms[current_atom_ndx]->setPos(pos);
797
798	<	dAtom = (DirectionalAtom *)info[0].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 575 | 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 584 | 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] ){
588	<
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
835		// set the easy ones first
836
837	<	for( i=0; i<nInfo; i++){
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();
#	Line 610 | Line 844 | void SimSetup::gatherInfo( void ){
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;
851	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
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;
623	<	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		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
897
898	+	for (i = 0; i < nInfo; i++){
899	+	strcpy(info[i].ensemble, ensemble);
900	+
901		// get the mixing rule
902
903	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
903	>	strcpy(info[i].mixingRule, globals->getMixingRule());
904		info[i].usePBC = globals->getPBC();
905		}
906	<
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;
677	<	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 682 | 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	+	//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	+	}
953	+
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() && !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	+	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		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
985
986	<	if( globals->haveSampleTime() ){
986	>	for (i = 0; i < nInfo; i++){
987	>	if (globals->haveSampleTime()){
988		info[i].sampleTime = globals->getSampleTime();
989		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
990		}
991		else{
992		info[i].sampleTime = globals->getRunTime();
993		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
994		}
995	<
996	<	if( globals->haveStatusTime() ){
995	>
996	>	if (globals->haveStatusTime()){
997		info[i].statusTime = globals->getStatusTime();
998		}
999	<
1000	<	if( globals->haveThermalTime() ){
999	>
1000	>	if (globals->haveThermalTime()){
1001		info[i].thermalTime = globals->getThermalTime();
1002	+	} else {
1003	+	info[i].thermalTime = globals->getRunTime();
1004		}
1005
1006	<	// check for the temperature set flag
1006	>	info[i].resetIntegrator = 0;
1007	>	if( globals->haveResetTime() ){
1008	>	info[i].resetTime = globals->getResetTime();
1009	>	info[i].resetIntegrator = 1;
1010	>	}
1011
1012	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
1012	>	// check for the temperature set flag
1013
1014	<	// get some of the tricky things that may still be in the globals
1015	<
1016	<	double boxVector[3];
1017	<	if( globals->haveBox() ){
1018	<	boxVector[0] = globals->getBox();
1019	<	boxVector[1] = globals->getBox();
1020	<	boxVector[2] = globals->getBox();
1021	<
1022	<	info[i].setBox( boxVector );
1023	<	}
1024	<	else if( globals->haveDensity() ){
1025	<
1026	<	double vol;
1027	<	vol = (double)tot_nmol / globals->getDensity();
1028	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
1029	<	boxVector[1] = boxVector[0];
1030	<	boxVector[2] = boxVector[0];
1031	<
1032	<	info[i].setBox( boxVector );
1033	<	}
1034	<	else{
1035	<	if( !globals->haveBoxX() ){
1036	<	sprintf( painCave.errMsg,
1037	<	"SimSetup error, no periodic BoxX size given.\n" );
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();
1040	>	simError();
1041		}
1042	<	boxVector[0] = globals->getBoxX();
1043	<
1044	<	if( !globals->haveBoxY() ){
1042	>	}
1043	>	else if(globals->getUseLiquidThermInt()) {
1044	>	if (globals->getUseSolidThermInt()) {
1045		sprintf( painCave.errMsg,
1046	<	"SimSetup error, no periodic BoxY size given.\n" );
1047	<	painCave.isFatal = 1;
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	<	boxVector[1] = globals->getBoxY();
1057	<
1058	<	if( !globals->haveBoxZ() ){
1059	<	sprintf( painCave.errMsg,
1060	<	"SimSetup error, no periodic BoxZ size given.\n" );
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();
1069	>	simError();
1070		}
765	–	boxVector[2] = globals->getBoxZ();
766	–
767	–	info[i].setBox( boxVector );
1071		}
1072	<
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
776	–
1128		}
1129
1130
1131	<	void SimSetup::finalInfoCheck( void ){
1131	>	void SimSetup::finalInfoCheck(void){
1132		int index;
1133		int usesDipoles;
1134	+	int usesCharges;
1135		int i;
1136
1137	<	for(i=0; i<nInfo; i++){
1137	>	for (i = 0; i < nInfo; i++){
1138		// check electrostatic parameters
1139	<
1139	>
1140		index = 0;
1141		usesDipoles = 0;
1142	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1142	>	while ((index < info[i].n_atoms) && !usesDipoles){
1143		usesDipoles = (info[i].atoms[index])->hasDipole();
1144		index++;
1145		}
1146	<
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 );
1154	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155		#endif //is_mpi
1156	<
1157	<	double theEcr, theEst;
1158	<
1159	<	if (globals->getUseRF() ) {
1160	<	info[i].useReactionField = 1;
1156	>
1157	>	double theRcut, theRsw;
1158	>
1159	>	if (globals->haveRcut()) {
1160	>	theRcut = globals->getRcut();
1161	>
1162	>	if (globals->haveRsw())
1163	>	theRsw = globals->getRsw();
1164	>	else
1165	>	theRsw = theRcut;
1166
1167	<	if( !globals->haveECR() ){
1168	<	sprintf( painCave.errMsg,
1169	<	"SimSetup Warning: using default value of 1/2 the smallest "
808	<	"box length for the electrostaticCutoffRadius.\n"
809	<	"I hope you have a very fast processor!\n");
810	<	painCave.isFatal = 0;
811	<	simError();
812	<	double smallest;
813	<	smallest = info[i].boxL[0];
814	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	<	theEcr = 0.5 * smallest;
817	<	} else {
818	<	theEcr = globals->getECR();
819	<	}
1167	>	info[i].setDefaultRcut(theRcut, theRsw);
1168	>
1169	>	} else {
1170
1171	<	if( !globals->haveEST() ){
1172	<	sprintf( painCave.errMsg,
1173	<	"SimSetup Warning: using default value of 0.05 * the "
1174	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1175	<	);
1176	<	painCave.isFatal = 0;
1177	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
831	<	}
1171	>	the_ff->calcRcut();
1172	>	theRcut = info[i].getRcut();
1173	>
1174	>	if (globals->haveRsw())
1175	>	theRsw = globals->getRsw();
1176	>	else
1177	>	theRsw = theRcut;
1178
1179	<	info[i].setEcr( theEcr, theEst );
1179	>	info[i].setDefaultRcut(theRcut, theRsw);
1180	>	}
1181	>
1182	>	if (globals->getUseRF()){
1183	>	info[i].useReactionField = 1;
1184
1185	<	if(!globals->haveDielectric() ){
1186	<	sprintf( painCave.errMsg,
1187	<	"SimSetup Error: You are trying to use Reaction Field without"
1188	<	"setting a dielectric constant!\n"
1189	<	);
1190	<	painCave.isFatal = 1;
1191	<	simError();
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	<	info[i].dielectric = globals->getDielectric();
1195	<	}
1196	<	else {
1197	<	if (usesDipoles) {
1194	>	else{
1195	>	theRcut = globals->getRcut();
1196	>	}
1197	>
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	>	info[i].setDefaultRcut(theRcut, theRsw);
1212	>
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
848	–	if( !globals->haveECR() ){
849	–	sprintf( painCave.errMsg,
850	–	"SimSetup Warning: using default value of 1/2 the smallest "
851	–	"box length for the electrostaticCutoffRadius.\n"
852	–	"I hope you have a very fast processor!\n");
853	–	painCave.isFatal = 0;
854	–	simError();
855	–	double smallest;
856	–	smallest = info[i].boxL[0];
857	–	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	–	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	–	theEcr = 0.5 * smallest;
860	–	} else {
861	–	theEcr = globals->getECR();
862	–	}
863	–
864	–	if( !globals->haveEST() ){
865	–	sprintf( painCave.errMsg,
866	–	"SimSetup Warning: using default value of 0.05 * the "
867	–	"electrostaticCutoffRadius for the "
868	–	"electrostaticSkinThickness\n"
869	–	);
870	–	painCave.isFatal = 0;
871	–	simError();
872	–	theEst = 0.05 * theEcr;
873	–	} else {
874	–	theEst= globals->getEST();
875	–	}
876	–
877	–	info[i].setEcr( theEcr, theEst );
1254		}
1255	<	}
1255	>	}
1256		}
881	–
1257		#ifdef IS_MPI
1258	<	strcpy( checkPointMsg, "post processing checks out" );
1258	>	strcpy(checkPointMsg, "post processing checks out");
1259		MPIcheckPoint();
1260		#endif // is_mpi
1261
1262	+	// clean up the forcefield
1263	+	the_ff->cleanMe();
1264		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
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	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1274	<
1275	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1276	<
899	<	if( globals->haveInitialConfig() ){
900	<
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 ){
1279	>	if (worldRank == 0){
1280		#endif //is_mpi
1281		inName = globals->getInitialConfig();
1282	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
1282	>	fileInit = new InitializeFromFile(inName);
1283		#ifdef IS_MPI
1284	<	}else fileInit = new InitializeFromFile( NULL );
1284	>	}
1285	>	else
1286	>	fileInit = new InitializeFromFile(NULL);
1287		#endif
1288	<	fileInit->readInit( info ); // default velocities on
1289	<
1288	>	fileInit->readInit(info); // default velocities on
1289	>
1290		delete fileInit;
1291		}
1292		else{
1293
917	–	#ifdef IS_MPI
918	–
1294		// no init from bass
1295
1296	<	sprintf( painCave.errMsg,
1297	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1298	<	painCave.isFatal;
1296	>	sprintf(painCave.errMsg,
1297	>	"Cannot intialize a simulation without an initial configuration file.\n");
1298	>	painCave.isFatal = 1;;
1299		simError();
1300
1301	<	#else
1302	<
928	<	initFromBass();
929	<
930	<
931	<	#endif
932	<	}
933	<
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
938	–
1307		}
1308
1309
1310	<	void SimSetup::makeOutNames( void ){
943	<
1310	>	void SimSetup::makeOutNames(void){
1311		int k;
1312
946	–
947	–	for(k=0; k<nInfo; k++){
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[k].finalName, globals->getFinalConfig() );
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	<	}
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	<
1346	>
1347		// make the sample and status out names
1348	<
1349	<	strcpy( info[k].sampleName, inFileName );
1348	>
1349	>	strcpy(info[k].sampleName, inFileName);
1350		char* endTest;
1351	<	int nameLength = strlen( info[k].sampleName );
1351	>	int nameLength = strlen(info[k].sampleName);
1352		endTest = &(info[k].sampleName[nameLength - 5]);
1353	<	if( !strcmp( endTest, ".bass" ) ){
1354	<	strcpy( endTest, ".dump" );
1353	>	if (!strcmp(endTest, ".bass")){
1354	>	strcpy(endTest, ".dump");
1355		}
1356	<	else if( !strcmp( endTest, ".BASS" ) ){
1357	<	strcpy( endTest, ".dump" );
1356	>	else if (!strcmp(endTest, ".BASS")){
1357	>	strcpy(endTest, ".dump");
1358		}
1359		else{
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	<	}
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	<	strcpy( info[k].statusName, inFileName );
1373	<	nameLength = strlen( info[k].statusName );
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" );
1375	>	if (!strcmp(endTest, ".bass")){
1376	>	strcpy(endTest, ".stat");
1377		}
1378	<	else if( !strcmp( endTest, ".BASS" ) ){
1379	<	strcpy( endTest, ".stat" );
1378	>	else if (!strcmp(endTest, ".BASS")){
1379	>	strcpy(endTest, ".stat");
1380		}
1381		else{
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	<	}
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	<
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, ".BASS")){
1401	>	strcpy(endTest, ".raw");
1402	>	}
1403	>	else{
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	>
1416		#ifdef IS_MPI
1417	+
1418		}
1419		#endif // is_mpi
1420		}
1421		}
1422
1423
1424	<	void SimSetup::sysObjectsCreation( void ){
1425	<
1426	<	int i,k;
1038	<
1424	>	void SimSetup::sysObjectsCreation(void){
1425	>	int i, k;
1426	>
1427		// create the forceField
1428
1429		createFF();
#	Line 1050 | 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();
1452	<
1453	<	for(k=0; k<nInfo; k++){
1452	>
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++){
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	<	case FF_EAM:
1481	<	the_ff = new EAM_FF();
1482	<	break;
1483	<
1484	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	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
1101	–
1491		}
1492
1493
1494	<	void SimSetup::compList( void ){
1106	<
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];
1499	>	comp_stamps = new MoleculeStamp * [n_components];
1500	>	bool haveCutoffGroups;
1501	>
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	<	for(i=0; i<nInfo; i++){
1506	>
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		}
1122	–
1513
1124	–	for( i=0; i<n_components; i++ ){
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 ){
1133	<
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
1550	+	}
1551
1552	+	void SimSetup::calcSysValues(void){
1553	+	int i, j;
1554	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1555
1556	<	}
1556	>	int* molMembershipArray;
1557	>	CutoffGroupStamp* cg;
1558
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
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	+	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	<	for(i=0; i<nInfo; i++){
1584	>
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	<
1592	>	info[i].ngroup = tot_groups;
1593		info[i].molMembershipArray = molMembershipArray;
1594	<	}
1594	>	}
1595		}
1596
1597		#ifdef IS_MPI
1598
1599	<	void SimSetup::mpiMolDivide( void ){
1194	<
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 );
1200	<
1201	<	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++ ){
1220	<
1221	<	if( mol2proc[allMol] == worldRank ){
1222	<
1223	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1648	>	localMol++;
1649		}
1650	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1651	<	info[0].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[0].n_atoms = mpiSim->getMyNlocal();
1663	<
1664	<	if( local_atoms != info[0].n_atoms ){
1665	<	sprintf( painCave.errMsg,
1666	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	<	" localAtom (%d) are not equal.\n",
1245	<	info[0].n_atoms,
1246	<	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[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, l;
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;
1269	–	Exclude** the_excludes;
1703
1704	<
1272	<	for(l=0; l<nInfo; l++){
1273	<
1704	>	for (l = 0; l < nInfo; l++){
1705		// create the atom and short range interaction arrays
1706	<
1707	<	the_atoms = new Atom*[info[l].n_atoms];
1706	>
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
1712	<
1712	>
1713		#ifdef IS_MPI
1714	<
1715	<
1714	>
1715	>
1716		molIndex = 0;
1717	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1718	<
1719	<	if(mol2proc[i] == worldRank ){
1720	<	the_molecules[molIndex].setStampID( molCompType[i] );
1721	<	the_molecules[molIndex].setMyIndex( molIndex );
1722	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
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		}
1725	<
1725	>
1726		#else // is_mpi
1727	<
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[l].molMembershipArray[globalAtomIndex] = molIndex;
1737	<	globalAtomIndex++;
1738	<	}
1739	<	molIndex++;
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		}
1741		}
1312	–
1313	–
1314	–	#endif // is_mpi
1742
1743
1744	<	if( info[l].n_SRI ){
1318	<
1319	<	Exclude::createArray(info[l].n_SRI);
1320	<	the_excludes = new Exclude*[info[l].n_SRI];
1321	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	<	the_excludes[ex] = new Exclude(ex);
1323	<	}
1324	<	info[l].globalExcludes = new int;
1325	<	info[l].n_exclude = info[l].n_SRI;
1326	<	}
1327	<	else{
1328	<
1329	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1331	<	the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair( 0,0 );
1333	<	info[l].globalExcludes = new int;
1334	<	info[l].globalExcludes[0] = 0;
1335	<	info[l].n_exclude = 0;
1336	<	}
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		info[l].atoms = the_atoms;
1752		info[l].molecules = the_molecules;
1753		info[l].nGlobalExcludes = 0;
1343	–	info[l].excludes = the_excludes;
1344	–
1345	–	the_ff->setSimInfo( info );
1754
1755	+	the_ff->setSimInfo(info);
1756		}
1757		}
1758
1759	<	void SimSetup::makeIntegrator( void ){
1351	<
1759	>	void SimSetup::makeIntegrator(void){
1760		int k;
1761
1762	<	NVT<RealIntegrator>*  myNVT = NULL;
1763	<	NPTi<RealIntegrator>* myNPTi = NULL;
1764	<	NPTf<RealIntegrator>* myNPTf = NULL;
1765	<	NPTim<RealIntegrator>* myNPTim = NULL;
1766	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1767	<
1768	<	for(k=0; k<nInfo; k++){
1769	<
1770	<	switch( ensembleCase ){
1771	<
1772	<	case NVE_ENS:
1773	<	if (globals->haveZconstraints()){
1774	<	setupZConstraint(info[k]);
1775	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
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	<	else
1783	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1784	<	break;
1785	<
1786	<	case NVT_ENS:
1787	<	if (globals->haveZconstraints()){
1788	<	setupZConstraint(info[k]);
1377	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	<	}
1379	<	else
1380	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
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	<	myNVT->setTargetTemp(globals->getTargetTemp());
1383	<
1384	<	if (globals->haveTauThermostat())
1385	<	myNVT->setTauThermostat(globals->getTauThermostat());
1386	<
1387	<	else {
1388	<	sprintf( painCave.errMsg,
1389	<	"SimSetup error: If you use the NVT\n"
1390	<	"    ensemble, you must set tauThermostat.\n");
1391	<	painCave.isFatal = 1;
1392	<	simError();
1393	<	}
1394	<	break;
1395	<
1396	<	case NPTi_ENS:
1397	<	if (globals->haveZconstraints()){
1398	<	setupZConstraint(info[k]);
1399	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	<	}
1401	<	else
1402	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1790	>	myNVT->setTargetTemp(globals->getTargetTemp());
1791
1792	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1793	<
1794	<	if (globals->haveTargetPressure())
1795	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1796	<	else {
1797	<	sprintf( painCave.errMsg,
1798	<	"SimSetup error: If you use a constant pressure\n"
1799	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1800	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<
1416	<	if( globals->haveTauThermostat() )
1417	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	<	else{
1419	<	sprintf( painCave.errMsg,
1420	<	"SimSetup error: If you use an NPT\n"
1421	<	"    ensemble, you must set tauThermostat.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauBarostat() )
1427	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauBarostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<	break;
1436	<
1437	<	case NPTf_ENS:
1438	<	if (globals->haveZconstraints()){
1439	<	setupZConstraint(info[k]);
1440	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	<	}
1442	<	else
1443	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
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	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1803	<
1447	<	if (globals->haveTargetPressure())
1448	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	<	else {
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use a constant pressure\n"
1452	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1466	<
1467	<	if( globals->haveTauBarostat() )
1468	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NPTim_ENS:
1479	<	if (globals->haveZconstraints()){
1480	<	setupZConstraint(info[k]);
1481	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	<	}
1483	<	else
1484	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1802	>	info->the_integrator = myNVT;
1803	>	break;
1804
1805	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1806	<
1807	<	if (globals->haveTargetPressure())
1808	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1809	<	else {
1810	<	sprintf( painCave.errMsg,
1811	<	"SimSetup error: If you use a constant pressure\n"
1493	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	<	painCave.isFatal = 1;
1495	<	simError();
1496	<	}
1497	<
1498	<	if( globals->haveTauThermostat() )
1499	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	<	else{
1501	<	sprintf( painCave.errMsg,
1502	<	"SimSetup error: If you use an NPT\n"
1503	<	"    ensemble, you must set tauThermostat.\n");
1504	<	painCave.isFatal = 1;
1505	<	simError();
1506	<	}
1507	<
1508	<	if( globals->haveTauBarostat() )
1509	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	<	else{
1511	<	sprintf( painCave.errMsg,
1512	<	"SimSetup error: If you use an NPT\n"
1513	<	"    ensemble, you must set tauBarostat.\n");
1514	<	painCave.isFatal = 1;
1515	<	simError();
1516	<	}
1517	<	break;
1518	<
1519	<	case NPTfm_ENS:
1520	<	if (globals->haveZconstraints()){
1521	<	setupZConstraint(info[k]);
1522	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	<	}
1524	<	else
1525	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
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	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1814	<
1815	<	if (globals->haveTargetPressure())
1816	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1817	<	else {
1818	<	sprintf( painCave.errMsg,
1819	<	"SimSetup error: If you use a constant pressure\n"
1820	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1821	<	painCave.isFatal = 1;
1822	<	simError();
1823	<	}
1824	<
1825	<	if( globals->haveTauThermostat() )
1826	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1827	<	else{
1828	<	sprintf( painCave.errMsg,
1829	<	"SimSetup error: If you use an NPT\n"
1830	<	"    ensemble, you must set tauThermostat.\n");
1831	<	painCave.isFatal = 1;
1832	<	simError();
1833	<	}
1834	<
1835	<	if( globals->haveTauBarostat() )
1836	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1837	<	else{
1838	<	sprintf( painCave.errMsg,
1839	<	"SimSetup error: If you use an NPT\n"
1840	<	"    ensemble, you must set tauBarostat.\n");
1841	<	painCave.isFatal = 1;
1842	<	simError();
1843	<	}
1844	<	break;
1845	<
1846	<	default:
1847	<	sprintf( painCave.errMsg,
1848	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1849	<	painCave.isFatal = 1;
1850	<	simError();
1813	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1814	>
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	>	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	>	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	>	info->the_integrator = myNPTi;
1846	>	break;
1847	>
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	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1857	>
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->haveTauThermostat())
1869	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1870	>
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());
1881	>
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	>	info->the_integrator = myNPTf;
1891	>	break;
1892	>
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	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1902	>
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	>	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 ){
1570	<
1945	>	void SimSetup::initFortran(void){
1946		info[0].refreshSim();
1947	<
1948	<	if( !strcmp( info[0].mixingRule, "standard") ){
1949	<	the_ff->initForceField( LB_MIXING_RULE );
1947	>
1948	>	if (!strcmp(info[0].mixingRule, "standard")){
1949	>	the_ff->initForceField(LB_MIXING_RULE);
1950		}
1951	<	else if( !strcmp( info[0].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",
1582	<	info[0].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,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1963	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1964		MPIcheckPoint();
1965		#endif // is_mpi
1593	–
1966		}
1967
1968	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1969	<	{
1970	<	int nZConstraints;
1599	<	ZconStamp** zconStamp;
1600	<
1601	<	if(globals->haveZconstraintTime()){
1602	<
1603	<	//add sample time of z-constraint  into SimInfo's property list
1604	<	DoubleData* zconsTimeProp = new DoubleData();
1605	<	zconsTimeProp->setID(ZCONSTIME_ID);
1606	<	zconsTimeProp->setData(globals->getZconsTime());
1607	<	theInfo.addProperty(zconsTimeProp);
1608	<	}
1609	<	else{
1610	<	sprintf( painCave.errMsg,
1611	<	"ZConstraint error: If you use an ZConstraint\n"
1612	<	" , you must set sample time.\n");
1613	<	painCave.isFatal = 1;
1614	<	simError();
1615	<	}
1968	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1969	>	int nZConstraints;
1970	>	ZconStamp** zconStamp;
1971
1972	<	//
1973	<	nZConstraints = globals->getNzConstraints();
1974	<	theInfo.nZconstraints = nZConstraints;
1975	<
1976	<	zconStamp = globals->getZconStamp();
1977	<	ZConsParaItem tempParaItem;
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	<	ZConsParaData* zconsParaData = new ZConsParaData();
1988	<	zconsParaData->setID(ZCONSPARADATA_ID);
1989	<
1990	<	for(int i = 0; i < nZConstraints; i++){
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	<
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	<	//sort the parameters by index of molecules
2120	<	zconsParaData->sortByIndex();
2121	<
1639	<	//push data into siminfo, therefore, we can retrieve later
1640	<	theInfo.addProperty(zconsParaData);
2119	>	if (globals->haveMinGTol()){
2120	>	param->setGTol(globals->getMinGTol());
2121	>	}
2122
2123	<	//push zconsTol into siminfo, if user does not specify
2124	<	//value for zconsTol, a default value will be used
1644	<	DoubleData* zconsTol = new DoubleData();
1645	<	zconsTol->setID(ZCONSTOL_ID);
1646	<	if(globals->haveZconsTol()){
1647	<	zconsTol->setData(globals->getZconsTol());
2123	>	if (globals->haveMinMaxIter()){
2124	>	param->setMaxIteration(globals->getMinMaxIter());
2125		}
1649	–	else{
1650	–	double defaultZConsTol = 1E-6;
1651	–	sprintf( painCave.errMsg,
1652	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1653	–	" , default value %f is used.\n", defaultZConsTol);
1654	–	painCave.isFatal = 0;
1655	–	simError();
2126
2127	<	zconsTol->setData(defaultZConsTol);
2128	<	}
2129	<	theInfo.addProperty(zconsTol);
2130	<
2131	<	//Determine the name of ouput file and add it into SimInfo's property list
2132	<	//Be careful, do not use inFileName, since it is a pointer which
2133	<	//point to a string at master node, and slave nodes do not contain that string
2127	>	if (globals->haveMinWriteFrq()){
2128	>	param->setMaxIteration(globals->getMinMaxIter());
2129	>	}
2130	>
2131	>	if (globals->haveMinWriteFrq()){
2132	>	param->setWriteFrq(globals->getMinWriteFrq());
2133	>	}
2134
2135	<	string zconsOutput(theInfo.finalName);
2136	<
2137	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2138	<
2139	<	StringData* zconsFilename = new StringData();
2140	<	zconsFilename->setID(ZCONSFILENAME_ID);
2141	<	zconsFilename->setData(zconsOutput);
2142	<
2143	<	theInfo.addProperty(zconsFilename);
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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