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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 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, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
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	+	#ifdef IS_MPI
220	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	+	info[k].globalGroupMembership[i] = 0;
223	+	#else
224	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	+	for (i = 0; i < info[k].n_atoms; i++)
226	+	info[k].globalGroupMembership[i] = 0;
227	+	#endif
228	+
229		atomOffset = 0;
230	<	excludeOffset = 0;
231	<	for(i=0; i<info[k].n_mol; i++){
232	<
230	>	groupOffset = 0;
231	>
232	>	for (i = 0; i < info[k].n_mol; i++){
233		stampID = info[k].molecules[i].getStampID();
234	+	molName = comp_stamps[stampID]->getID();
235
236	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
237	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
238	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
236	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
239		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241	>
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244		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];
245
246	+	if (molInfo.nBonds > 0)
247	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	+	else
249	+	molInfo.myBonds = NULL;
250	+
251	+	if (molInfo.nBends > 0)
252	+	molInfo.myBends = new Bend*[molInfo.nBends];
253	+	else
254	+	molInfo.myBends = NULL;
255	+
256	+	if (molInfo.nTorsions > 0)
257	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	+	else
259	+	molInfo.myTorsions = NULL;
260	+
261		theBonds = new bond_pair[molInfo.nBonds];
262		theBends = new bend_set[molInfo.nBends];
263		theTorsions = new torsion_set[molInfo.nTorsions];
264	<
264	>
265		// make the Atoms
266	<
267	<	for(j=0; j<molInfo.nAtoms; j++){
268	<
269	<	currentAtom = comp_stamps[stampID]->getAtom( j );
270	<	if( currentAtom->haveOrientation() ){
271	<
272	<	dAtom = new DirectionalAtom( (j + atomOffset),
273	<	info[k].getConfiguration() );
274	<	info[k].n_oriented++;
275	<	molInfo.myAtoms[j] = dAtom;
276	<
277	<	ux = currentAtom->getOrntX();
278	<	uy = currentAtom->getOrntY();
279	<	uz = currentAtom->getOrntZ();
280	<
281	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
282	<
283	<	u = sqrt( uSqr );
284	<	ux = ux / u;
285	<	uy = uy / u;
286	<	uz = uz / u;
287	<
288	<	dAtom->setSUx( ux );
289	<	dAtom->setSUy( uy );
290	<	dAtom->setSUz( uz );
291	<	}
292	<	else{
293	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
266	>
267	>	for (j = 0; j < molInfo.nAtoms; j++){
268	>	currentAtom = comp_stamps[stampID]->getAtom(j);
269	>
270	>	if (currentAtom->haveOrientation()){
271	>	dAtom = new DirectionalAtom((j + atomOffset),
272	>	info[k].getConfiguration());
273	>	info[k].n_oriented++;
274	>	molInfo.myAtoms[j] = dAtom;
275	>
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279	>
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283	>
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288	>
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290	>
291	>	}
292	>
293	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
294		#ifdef IS_MPI
295	<
224	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	<
295	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296		#endif // is_mpi
297		}
298	<
299	<	// make the bonds
300	<	for(j=0; j<molInfo.nBonds; j++){
301	<
302	<	currentBond = comp_stamps[stampID]->getBond( j );
303	<	theBonds[j].a = currentBond->getA() + atomOffset;
304	<	theBonds[j].b = currentBond->getB() + atomOffset;
305	<
306	<	exI = theBonds[j].a;
307	<	exJ = theBonds[j].b;
308	<
309	<	// exclude_I must always be the smaller of the pair
310	<	if( exI > exJ ){
311	<	tempEx = exI;
312	<	exI = exJ;
313	<	exJ = tempEx;
314	<	}
315	<	#ifdef IS_MPI
316	<	tempEx = exI;
247	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	<	tempEx = exJ;
249	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	<	#else  // isn't MPI
253	<
254	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	<	#endif  //is_mpi
298	>
299	>	// make the bonds
300	>	for (j = 0; j < molInfo.nBonds; j++){
301	>	currentBond = comp_stamps[stampID]->getBond(j);
302	>	theBonds[j].a = currentBond->getA() + atomOffset;
303	>	theBonds[j].b = currentBond->getB() + atomOffset;
304	>
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307	>
308	>	#ifdef IS_MPI
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315	>
316	>	info[k].excludes->addPair(exI, exJ);
317		}
318	<	excludeOffset += molInfo.nBonds;
258	<
318	>
319		//make the bends
320	<	for(j=0; j<molInfo.nBends; j++){
321	<
322	<	currentBend = comp_stamps[stampID]->getBend( j );
323	<	theBends[j].a = currentBend->getA() + atomOffset;
324	<	theBends[j].b = currentBend->getB() + atomOffset;
325	<	theBends[j].c = currentBend->getC() + atomOffset;
326	<
327	<	if( currentBend->haveExtras() ){
328	<
329	<	extras = currentBend->getExtras();
330	<	current_extra = extras;
331	<
332	<	while( current_extra != NULL ){
333	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
334	<
335	<	switch( current_extra->getType() ){
336	<
337	<	case 0:
338	<	theBends[j].ghost =
339	<	current_extra->getInt() + atomOffset;
340	<	theBends[j].isGhost = 1;
341	<	break;
342	<
343	<	case 1:
344	<	theBends[j].ghost =
345	<	(int)current_extra->getDouble() + atomOffset;
346	<	theBends[j].isGhost = 1;
347	<	break;
348	<
349	<	default:
350	<	sprintf( painCave.errMsg,
351	<	"SimSetup Error: ghostVectorSource was neither a "
352	<	"double nor an int.\n"
353	<	"-->Bend[%d] in %s\n",
354	<	j, comp_stamps[stampID]->getID() );
355	<	painCave.isFatal = 1;
356	<	simError();
357	<	}
358	<	}
359	<
360	<	else{
361	<
362	<	sprintf( painCave.errMsg,
363	<	"SimSetup Error: unhandled bend assignment:\n"
364	<	"    -->%s in Bend[%d] in %s\n",
365	<	current_extra->getlhs(),
366	<	j, comp_stamps[stampID]->getID() );
367	<	painCave.isFatal = 1;
368	<	simError();
369	<	}
370	<
371	<	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	<	}
320	>	for (j = 0; j < molInfo.nBends; j++){
321	>	currentBend = comp_stamps[stampID]->getBend(j);
322	>	theBends[j].a = currentBend->getA() + atomOffset;
323	>	theBends[j].b = currentBend->getB() + atomOffset;
324	>	theBends[j].c = currentBend->getC() + atomOffset;
325	>
326	>	if (currentBend->haveExtras()){
327	>	extras = currentBend->getExtras();
328	>	current_extra = extras;
329	>
330	>	while (current_extra != NULL){
331	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
332	>	switch (current_extra->getType()){
333	>	case 0:
334	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
335	>	theBends[j].isGhost = 1;
336	>	break;
337	>
338	>	case 1:
339	>	theBends[j].ghost = (int) current_extra->getDouble() +
340	>	atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343	>
344	>	default:
345	>	sprintf(painCave.errMsg,
346	>	"SimSetup Error: ghostVectorSource was neither a "
347	>	"double nor an int.\n"
348	>	"-->Bend[%d] in %s\n",
349	>	j, comp_stamps[stampID]->getID());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353	>	}
354	>	else{
355	>	sprintf(painCave.errMsg,
356	>	"SimSetup Error: unhandled bend assignment:\n"
357	>	"    -->%s in Bend[%d] in %s\n",
358	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	}
362	>
363	>	current_extra = current_extra->getNext();
364	>	}
365	>	}
366	>
367	>	if (theBends[j].isGhost) {
368	>
369	>	tempI = theBends[j].a;
370	>	tempJ = theBends[j].b;
371	>
372		#ifdef IS_MPI
373	<	tempEx = exI;
374	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	<	tempEx = exJ;
376	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
377	<
378	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
379	<	#else  // isn't MPI
380	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
381	<	#endif  //is_mpi
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380	>
381	>	} else {
382	>
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387	>	#ifdef IS_MPI
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395	>	#endif
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401		}
402	<	excludeOffset += molInfo.nBends;
403	<
404	<	for(j=0; j<molInfo.nTorsions; j++){
405	<
406	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
407	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
408	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
409	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
410	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
411	<
412	<	exI = theTorsions[j].a;
413	<	exJ = theTorsions[j].d;
414	<
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	<	}
402	>
403	>	for (j = 0; j < molInfo.nTorsions; j++){
404	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
405	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
406	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
407	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
408	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
409	>
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414	>
415		#ifdef IS_MPI
416	<	tempEx = exI;
417	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
418	<	tempEx = exJ;
419	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
420	<
421	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
422	<	#else  // isn't MPI
423	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
424	<	#endif  //is_mpi
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425	>	#endif
426	>
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433		}
434	<	excludeOffset += molInfo.nTorsions;
434	>
435
436	+	molInfo.myRigidBodies.clear();
437
438	<	// send the arrays off to the forceField for init.
438	>	for (j = 0; j < molInfo.nRigidBodies; j++){
439	>
440	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	>	nMembers = currentRigidBody->getNMembers();
442	>
443	>	// Create the Rigid Body:
444	>
445	>	myRB = new RigidBody();
446	>
447	>	sprintf(rbName,"%s_RB_%d", molName, j);
448	>	myRB->setType(rbName);
449	>
450	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
451	>
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454	>
455	>	// tempI is atom numbering on local processor
456	>	tempI = molI + atomOffset;
457	>
458	>	// currentAtom is the AtomStamp (which we need for
459	>	// rigid body reference positions)
460	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
461	>
462	>	// When we add to the rigid body, add the atom itself and
463	>	// the stamp info:
464	>
465	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	>
467	>	// Add this atom to the Skip List for the integrators
468	>	#ifdef IS_MPI
469	>	slI = info[k].atoms[tempI]->getGlobalIndex();
470	>	#else
471	>	slI = tempI;
472	>	#endif
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488	>	#ifdef IS_MPI
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500	>
501	>	molInfo.myRigidBodies.push_back(myRB);
502	>	info[k].rigidBodies.push_back(myRB);
503	>	}
504
505	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
506	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
507	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
508	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
505	>
506	>	//create cutoff group for molecule
507	>
508	>	cutoffAtomSet.clear();
509	>	molInfo.myCutoffGroups.clear();
510
511	+	for (j = 0; j < nCutoffGroups; j++){
512	+
513	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	+	nMembers = currentCutoffGroup->getNMembers();
515	+
516	+	myCutoffGroup = new CutoffGroup();
517	+
518	+	#ifdef IS_MPI
519	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
520	+	#else
521	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
522	+	#endif
523	+
524	+	for (int cg = 0; cg < nMembers; cg++) {
525	+
526	+	// molI is atom numbering inside this molecule
527	+	molI = currentCutoffGroup->getMember(cg);
528	+
529	+	// tempI is atom numbering on local processor
530	+	tempI = molI + atomOffset;
531	+
532	+	#ifdef IS_MPI
533	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
535	+	#else
536	+	globalID = info[k].atoms[tempI]->getIndex();
537	+	info[k].globalGroupMembership[globalID] = j + groupOffset;
538	+	#endif
539	+
540	+
541	+
542	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
543	+
544	+	cutoffAtomSet.insert(tempI);
545	+	}
546	+
547	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
548	+	groupOffset++;
549	+
550	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551
552	<	info[k].molecules[i].initialize( molInfo );
552	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
553	>
554	>	for(j = 0; j < molInfo.nAtoms; j++){
555	>
556	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557	>	myCutoffGroup = new CutoffGroup();
558	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559
560	+	#ifdef IS_MPI
561	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564	+	#else
565	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
566	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
567	+	info[k].globalGroupMembership[globalID] = j+groupOffset;
568	+	#endif
569	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
570	+	groupOffset++;
571	+	}
572	+
573	+	}
574	+
575	+	// After this is all set up, scan through the atoms to
576	+	// see if they can be added to the integrableObjects:
577	+
578	+	molInfo.myIntegrableObjects.clear();
579
580	+
581	+	for (j = 0; j < molInfo.nAtoms; j++){
582	+
583	+	#ifdef IS_MPI
584	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
585	+	#else
586	+	slJ = j+atomOffset;
587	+	#endif
588	+
589	+	// if they aren't on the skip list, then they can be integrated
590	+
591	+	if (skipList.find(slJ) == skipList.end()) {
592	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
593	+	info[k].integrableObjects.push_back(mySD);
594	+	molInfo.myIntegrableObjects.push_back(mySD);
595	+	}
596	+	}
597	+
598	+	// all rigid bodies are integrated:
599	+
600	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
601	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
602	+	info[k].integrableObjects.push_back(mySD);
603	+	molInfo.myIntegrableObjects.push_back(mySD);
604	+	}
605	+
606	+
607	+	/*
608	+
609	+	//creat ConstraintPair.
610	+	molInfo.myConstraintPair.clear();
611	+
612	+	for (j = 0; j < molInfo.nBonds; j++){
613	+
614	+	//if both atoms are in the same rigid body, just skip it
615	+	currentBond = comp_stamps[stampID]->getBond(j);
616	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617	+
618	+	tempI = currentBond->getA() + atomOffset;
619	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621	+	else
622	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
623	+
624	+	tempJ =  currentBond->getB() + atomOffset;
625	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627	+	else
628	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
629	+
630	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
631	+	molInfo.myConstraintPairs.push_back(consPair);
632	+	}
633	+	}
634	+
635	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638	+
639	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640	+
641	+	for(size_t m = 0; m < jointAtoms.size(); m++){
642	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644	+
645	+	consPair = new JointConstraintPair(consElement1, consElement2);
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648	+
649	+	}
650	+	}
651	+
652	+	*/
653	+	// send the arrays off to the forceField for init.
654	+
655	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
656	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
657	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
658	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
659	+	theTorsions);
660	+
661	+	info[k].molecules[i].initialize(molInfo);
662	+
663	+
664		atomOffset += molInfo.nAtoms;
665		delete[] theBonds;
666		delete[] theBends;
667		delete[] theTorsions;
668		}
669	+
670	+
671	+
672	+	#ifdef IS_MPI
673	+	// Since the globalGroupMembership has been zero filled and we've only
674	+	// poked values into the atoms we know, we can do an Allreduce
675	+	// to get the full globalGroupMembership array (We think).
676	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677	+	// docs said we could.
678	+
679	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
680	+
681	+	MPI_Allreduce(info[k].globalGroupMembership,
682	+	ggMjunk,
683	+	mpiSim->getNAtomsGlobal(),
684	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685	+
686	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687	+	info[k].globalGroupMembership[i] = ggMjunk[i];
688	+
689	+	delete[] ggMjunk;
690	+
691	+	#endif
692	+
693	+
694	+
695		}
696	<
696	>
697		#ifdef IS_MPI
698	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
698	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
699		MPIcheckPoint();
700		#endif // is_mpi
398	–
399	–	// clean up the forcefield
701
401	–	the_ff->calcRcut();
402	–	the_ff->cleanMe();
403	–
702		}
703
704	<	void SimSetup::initFromBass( void ){
407	<
704	>	void SimSetup::initFromBass(void){
705		int i, j, k;
706		int n_cells;
707		double cellx, celly, cellz;
#	Line 418 | Line 715 | void SimSetup::initFromBass( void ){
715		vel[1] = 0.0;
716		vel[2] = 0.0;
717
718	<	temp1 = (double)tot_nmol / 4.0;
719	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
720	<	temp3 = ceil( temp2 );
718	>	temp1 = (double) tot_nmol / 4.0;
719	>	temp2 = pow(temp1, (1.0 / 3.0));
720	>	temp3 = ceil(temp2);
721
722	<	have_extra =0;
723	<	if( temp2 < temp3 ){ // we have a non-complete lattice
724	<	have_extra =1;
722	>	have_extra = 0;
723	>	if (temp2 < temp3){
724	>	// we have a non-complete lattice
725	>	have_extra = 1;
726
727	<	n_cells = (int)temp3 - 1;
727	>	n_cells = (int) temp3 - 1;
728		cellx = info[0].boxL[0] / temp3;
729		celly = info[0].boxL[1] / temp3;
730		cellz = info[0].boxL[2] / temp3;
731	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
732	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
733	<	n_per_extra = (int)ceil( temp1 );
731	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
732	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
733	>	n_per_extra = (int) ceil(temp1);
734
735	<	if( n_per_extra > 4){
736	<	sprintf( painCave.errMsg,
737	<	"SimSetup error. There has been an error in constructing"
738	<	" the non-complete lattice.\n" );
735	>	if (n_per_extra > 4){
736	>	sprintf(painCave.errMsg,
737	>	"SimSetup error. There has been an error in constructing"
738	>	" the non-complete lattice.\n");
739		painCave.isFatal = 1;
740		simError();
741		}
742		}
743		else{
744	<	n_cells = (int)temp3;
744	>	n_cells = (int) temp3;
745		cellx = info[0].boxL[0] / temp3;
746		celly = info[0].boxL[1] / temp3;
747		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 752 | void SimSetup::initFromBass( void ){
752		current_comp = 0;
753		current_atom_ndx = 0;
754
755	<	for( i=0; i < n_cells ; i++ ){
756	<	for( j=0; j < n_cells; j++ ){
757	<	for( k=0; k < n_cells; k++ ){
755	>	for (i = 0; i < n_cells ; i++){
756	>	for (j = 0; j < n_cells; j++){
757	>	for (k = 0; k < n_cells; k++){
758	>	makeElement(i * cellx, j * celly, k * cellz);
759
760	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
760	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
761
762	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
762	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
763
764	<	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 );
764	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
765		}
766		}
767		}
768
769	<	if( have_extra ){
769	>	if (have_extra){
770		done = 0;
771
772		int start_ndx;
773	<	for( i=0; i < (n_cells+1) && !done; i++ ){
774	<	for( j=0; j < (n_cells+1) && !done; j++ ){
773	>	for (i = 0; i < (n_cells + 1) && !done; i++){
774	>	for (j = 0; j < (n_cells + 1) && !done; j++){
775	>	if (i < n_cells){
776	>	if (j < n_cells){
777	>	start_ndx = n_cells;
778	>	}
779	>	else
780	>	start_ndx = 0;
781	>	}
782	>	else
783	>	start_ndx = 0;
784
785	<	if( i < n_cells ){
785	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
786	>	makeElement(i * cellx, j * celly, k * cellz);
787	>	done = (current_mol >= tot_nmol);
788
789	<	if( j < n_cells ){
790	<	start_ndx = n_cells;
791	<	}
792	<	else start_ndx = 0;
793	<	}
494	<	else start_ndx = 0;
789	>	if (!done && n_per_extra > 1){
790	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
791	>	k * cellz);
792	>	done = (current_mol >= tot_nmol);
793	>	}
794
795	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
795	>	if (!done && n_per_extra > 2){
796	>	makeElement(i * cellx, j * celly + 0.5 * celly,
797	>	k * cellz + 0.5 * cellz);
798	>	done = (current_mol >= tot_nmol);
799	>	}
800
801	<	makeElement( i * cellx,
802	<	j * celly,
803	<	k * cellz );
804	<	done = ( current_mol >= tot_nmol );
805	<
806	<	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	<	}
801	>	if (!done && n_per_extra > 3){
802	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
803	>	k * cellz + 0.5 * cellz);
804	>	done = (current_mol >= tot_nmol);
805	>	}
806	>	}
807		}
808		}
809		}
810
811	<	for( i=0; i<info[0].n_atoms; i++ ){
812	<	info[0].atoms[i]->setVel( vel );
811	>	for (i = 0; i < info[0].n_atoms; i++){
812	>	info[0].atoms[i]->setVel(vel);
813		}
814		}
815
816	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
816	>	void SimSetup::makeElement(double x, double y, double z){
817		int k;
818		AtomStamp* current_atom;
819		DirectionalAtom* dAtom;
820		double rotMat[3][3];
821		double pos[3];
822
823	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
824	<
825	<	current_atom = comp_stamps[current_comp]->getAtom( k );
826	<	if( !current_atom->havePosition() ){
827	<	sprintf( painCave.errMsg,
828	<	"SimSetup:initFromBass error.\n"
829	<	"\tComponent %s, atom %s does not have a position specified.\n"
830	<	"\tThe initialization routine is unable to give a start"
831	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
823	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
824	>	current_atom = comp_stamps[current_comp]->getAtom(k);
825	>	if (!current_atom->havePosition()){
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup:initFromBass error.\n"
828	>	"\tComponent %s, atom %s does not have a position specified.\n"
829	>	"\tThe initialization routine is unable to give a start"
830	>	" position.\n",
831	>	comp_stamps[current_comp]->getID(), current_atom->getType());
832		painCave.isFatal = 1;
833		simError();
834		}
835	<
835	>
836		pos[0] = x + current_atom->getPosX();
837		pos[1] = y + current_atom->getPosY();
838		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
839
840	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
840	>	info[0].atoms[current_atom_ndx]->setPos(pos);
841
842	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
842	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
843	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
844
845		rotMat[0][0] = 1.0;
846		rotMat[0][1] = 0.0;
#	Line 575 | Line 854 | void SimSetup::makeElement( double x, double y, double
854		rotMat[2][1] = 0.0;
855		rotMat[2][2] = 1.0;
856
857	<	dAtom->setA( rotMat );
857	>	dAtom->setA(rotMat);
858		}
859
860		current_atom_ndx++;
#	Line 584 | Line 863 | void SimSetup::makeElement( double x, double y, double
863		current_mol++;
864		current_comp_mol++;
865
866	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
866	>	if (current_comp_mol >= components_nmol[current_comp]){
867		current_comp_mol = 0;
868		current_comp++;
869		}
870		}
871
872
873	<	void SimSetup::gatherInfo( void ){
874	<	int i,j,k;
873	>	void SimSetup::gatherInfo(void){
874	>	int i;
875
876		ensembleCase = -1;
877		ffCase = -1;
878
879		// set the easy ones first
880
881	<	for( i=0; i<nInfo; i++){
881	>	for (i = 0; i < nInfo; i++){
882		info[i].target_temp = globals->getTargetTemp();
883		info[i].dt = globals->getDt();
884		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 888 | void SimSetup::gatherInfo( void ){
888
889		// get the forceField
890
891	<	strcpy( force_field, globals->getForceField() );
891	>	strcpy(force_field, globals->getForceField());
892
893	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
894	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
895	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
893	>	if (!strcasecmp(force_field, "DUFF")){
894	>	ffCase = FF_DUFF;
895	>	}
896	>	else if (!strcasecmp(force_field, "LJ")){
897	>	ffCase = FF_LJ;
898	>	}
899	>	else if (!strcasecmp(force_field, "EAM")){
900	>	ffCase = FF_EAM;
901	>	}
902	>	else if (!strcasecmp(force_field, "WATER")){
903	>	ffCase = FF_H2O;
904	>	}
905		else{
906	<	sprintf( painCave.errMsg,
907	<	"SimSetup Error. Unrecognized force field -> %s\n",
908	<	force_field );
909	<	painCave.isFatal = 1;
623	<	simError();
906	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
907	>	force_field);
908	>	painCave.isFatal = 1;
909	>	simError();
910		}
911
912	<	// get the ensemble
912	>	// get the ensemble
913
914	<	strcpy( ensemble, globals->getEnsemble() );
914	>	strcpy(ensemble, globals->getEnsemble());
915
916	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	<	ensembleCase = NPTi_ENS;
634	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	<	else{
638	<	sprintf( painCave.errMsg,
639	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	<	"reverting to NVE for this simulation.\n",
641	<	ensemble );
642	<	painCave.isFatal = 0;
643	<	simError();
644	<	strcpy( ensemble, "NVE" );
916	>	if (!strcasecmp(ensemble, "NVE")){
917		ensembleCase = NVE_ENS;
646	–	}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
651	–
652	–	// get the mixing rule
653	–
654	–	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	–	info[i].usePBC = globals->getPBC();
918		}
919	<
920	<	// get the components and calculate the tot_nMol and indvidual n_mol
921	<
922	<	the_components = globals->getComponents();
923	<	components_nmol = new int[n_components];
924	<
925	<
926	<	if( !globals->haveNMol() ){
919	>	else if (!strcasecmp(ensemble, "NVT")){
920	>	ensembleCase = NVT_ENS;
921	>	}
922	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
923	>	ensembleCase = NPTi_ENS;
924	>	}
925	>	else if (!strcasecmp(ensemble, "NPTf")){
926	>	ensembleCase = NPTf_ENS;
927	>	}
928	>	else if (!strcasecmp(ensemble, "NPTxyz")){
929	>	ensembleCase = NPTxyz_ENS;
930	>	}
931	>	else{
932	>	sprintf(painCave.errMsg,
933	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
934	>	"\treverting to NVE for this simulation.\n",
935	>	ensemble);
936	>	painCave.isFatal = 0;
937	>	simError();
938	>	strcpy(ensemble, "NVE");
939	>	ensembleCase = NVE_ENS;
940	>	}
941	>
942	>	for (i = 0; i < nInfo; i++){
943	>	strcpy(info[i].ensemble, ensemble);
944	>
945	>	// get the mixing rule
946	>
947	>	strcpy(info[i].mixingRule, globals->getMixingRule());
948	>	info[i].usePBC = globals->getPBC();
949	>	}
950	>
951	>	// get the components and calculate the tot_nMol and indvidual n_mol
952	>
953	>	the_components = globals->getComponents();
954	>	components_nmol = new int[n_components];
955	>
956	>
957	>	if (!globals->haveNMol()){
958		// we don't have the total number of molecules, so we assume it is
959		// given in each component
960
961		tot_nmol = 0;
962	<	for( i=0; i<n_components; i++ ){
963	<
964	<	if( !the_components[i]->haveNMol() ){
965	<	// we have a problem
966	<	sprintf( painCave.errMsg,
967	<	"SimSetup Error. No global NMol or component NMol"
968	<	" given. Cannot calculate the number of atoms.\n" );
969	<	painCave.isFatal = 1;
677	<	simError();
962	>	for (i = 0; i < n_components; i++){
963	>	if (!the_components[i]->haveNMol()){
964	>	// we have a problem
965	>	sprintf(painCave.errMsg,
966	>	"SimSetup Error. No global NMol or component NMol given.\n"
967	>	"\tCannot calculate the number of atoms.\n");
968	>	painCave.isFatal = 1;
969	>	simError();
970		}
971
972		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 974 | void SimSetup::gatherInfo( void ){
974		}
975		}
976		else{
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup error.\n"
979	<	"\tSorry, the ability to specify total"
980	<	" nMols and then give molfractions in the components\n"
981	<	"\tis not currently supported."
982	<	" Please give nMol in the components.\n" );
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup error.\n"
979	>	"\tSorry, the ability to specify total"
980	>	" nMols and then give molfractions in the components\n"
981	>	"\tis not currently supported."
982	>	" Please give nMol in the components.\n");
983		painCave.isFatal = 1;
984		simError();
985		}
986
987	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
988	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
989	+	sprintf(painCave.errMsg,
990	+	"Sample time is not divisible by dt.\n"
991	+	"\tThis will result in samples that are not uniformly\n"
992	+	"\tdistributed in time.  If this is a problem, change\n"
993	+	"\tyour sampleTime variable.\n");
994	+	painCave.isFatal = 0;
995	+	simError();
996	+	}
997	+
998	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
999	+	sprintf(painCave.errMsg,
1000	+	"Status time is not divisible by dt.\n"
1001	+	"\tThis will result in status reports that are not uniformly\n"
1002	+	"\tdistributed in time.  If this is a problem, change \n"
1003	+	"\tyour statusTime variable.\n");
1004	+	painCave.isFatal = 0;
1005	+	simError();
1006	+	}
1007	+
1008	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1009	+	sprintf(painCave.errMsg,
1010	+	"Thermal time is not divisible by dt.\n"
1011	+	"\tThis will result in thermalizations that are not uniformly\n"
1012	+	"\tdistributed in time.  If this is a problem, change \n"
1013	+	"\tyour thermalTime variable.\n");
1014	+	painCave.isFatal = 0;
1015	+	simError();
1016	+	}
1017	+
1018	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1019	+	sprintf(painCave.errMsg,
1020	+	"Reset time is not divisible by dt.\n"
1021	+	"\tThis will result in integrator resets that are not uniformly\n"
1022	+	"\tdistributed in time.  If this is a problem, change\n"
1023	+	"\tyour resetTime variable.\n");
1024	+	painCave.isFatal = 0;
1025	+	simError();
1026	+	}
1027	+
1028		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
1029
1030	<	if( globals->haveSampleTime() ){
1030	>	for (i = 0; i < nInfo; i++){
1031	>	if (globals->haveSampleTime()){
1032		info[i].sampleTime = globals->getSampleTime();
1033		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
1034		}
1035		else{
1036		info[i].sampleTime = globals->getRunTime();
1037		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
1038		}
1039	<
1040	<	if( globals->haveStatusTime() ){
1039	>
1040	>	if (globals->haveStatusTime()){
1041		info[i].statusTime = globals->getStatusTime();
1042		}
1043	<
1044	<	if( globals->haveThermalTime() ){
1043	>
1044	>	if (globals->haveThermalTime()){
1045		info[i].thermalTime = globals->getThermalTime();
1046	+	} else {
1047	+	info[i].thermalTime = globals->getRunTime();
1048		}
1049
1050	<	// check for the temperature set flag
1050	>	info[i].resetIntegrator = 0;
1051	>	if( globals->haveResetTime() ){
1052	>	info[i].resetTime = globals->getResetTime();
1053	>	info[i].resetIntegrator = 1;
1054	>	}
1055
1056	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
1056	>	// check for the temperature set flag
1057
1058	<	// get some of the tricky things that may still be in the globals
1059	<
1060	<	double boxVector[3];
1061	<	if( globals->haveBox() ){
1062	<	boxVector[0] = globals->getBox();
1063	<	boxVector[1] = globals->getBox();
1064	<	boxVector[2] = globals->getBox();
1065	<
1066	<	info[i].setBox( boxVector );
1067	<	}
1068	<	else if( globals->haveDensity() ){
1069	<
1070	<	double vol;
1071	<	vol = (double)tot_nmol / globals->getDensity();
1072	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
1073	<	boxVector[1] = boxVector[0];
1074	<	boxVector[2] = boxVector[0];
1075	<
1076	<	info[i].setBox( boxVector );
1077	<	}
1078	<	else{
1079	<	if( !globals->haveBoxX() ){
1080	<	sprintf( painCave.errMsg,
1081	<	"SimSetup error, no periodic BoxX size given.\n" );
1058	>	if (globals->haveTempSet())
1059	>	info[i].setTemp = globals->getTempSet();
1060	>
1061	>	// check for the extended State init
1062	>
1063	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1064	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065	>
1066	>	// check for thermodynamic integration
1067	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070	>	info[i].thermIntLambda = globals->getThermIntLambda();
1071	>	info[i].thermIntK = globals->getThermIntK();
1072	>
1073	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1074	>	info[i].restraint = myRestraint;
1075	>	}
1076	>	else {
1077	>	sprintf(painCave.errMsg,
1078	>	"SimSetup Error:\n"
1079	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1080	>	"\tthermodynamicIntegrationLambda (and/or\n"
1081	>	"\tthermodynamicIntegrationK) was not specified.\n"
1082	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1083		painCave.isFatal = 1;
1084	<	simError();
1084	>	simError();
1085		}
1086	<	boxVector[0] = globals->getBoxX();
1087	<
1088	<	if( !globals->haveBoxY() ){
1086	>	}
1087	>	else if(globals->getUseLiquidThermInt()) {
1088	>	if (globals->getUseSolidThermInt()) {
1089		sprintf( painCave.errMsg,
1090	<	"SimSetup error, no periodic BoxY size given.\n" );
1091	<	painCave.isFatal = 1;
1090	>	"SimSetup Warning: It appears that you have both solid and\n"
1091	>	"\tliquid thermodynamic integration activated in your .bass\n"
1092	>	"\tfile. To avoid confusion, specify only one technique in\n"
1093	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1094	>	"\twill be assumed for the current simulation. If this is not\n"
1095	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1096	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097	>	painCave.isFatal = 0;
1098		simError();
1099		}
1100	<	boxVector[1] = globals->getBoxY();
1101	<
1102	<	if( !globals->haveBoxZ() ){
1103	<	sprintf( painCave.errMsg,
1104	<	"SimSetup error, no periodic BoxZ size given.\n" );
1100	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102	>	info[i].thermIntLambda = globals->getThermIntLambda();
1103	>	info[i].thermIntK = globals->getThermIntK();
1104	>	}
1105	>	else {
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error:\n"
1108	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1109	>	"\tthermodynamicIntegrationLambda (and/or\n"
1110	>	"\tthermodynamicIntegrationK) was not specified.\n"
1111	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1112		painCave.isFatal = 1;
1113	<	simError();
1113	>	simError();
1114		}
765	–	boxVector[2] = globals->getBoxZ();
766	–
767	–	info[i].setBox( boxVector );
1115		}
1116	<
1116	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1117	>	sprintf(painCave.errMsg,
1118	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1119	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120	>	"\t'true' in your .bass file.  These keywords are set to\n"
1121	>	"\t'false' by default, so your lambda and/or k values are\n"
1122	>	"\tbeing ignored.\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	}
1126		}
1127	+
1128	+	//setup seed for random number generator
1129	+	int seedValue;
1130	+
1131	+	if (globals->haveSeed()){
1132	+	seedValue = globals->getSeed();
1133	+
1134	+	if(seedValue / 1E9 == 0){
1135	+	sprintf(painCave.errMsg,
1136	+	"Seed for sprng library should contain at least 9 digits\n"
1137	+	"OOPSE will generate a seed for user\n");
1138	+	painCave.isFatal = 0;
1139	+	simError();
1140	+
1141	+	//using seed generated by system instead of invalid seed set by user
1142	+	#ifndef IS_MPI
1143	+	seedValue = make_sprng_seed();
1144	+	#else
1145	+	if (worldRank == 0){
1146	+	seedValue = make_sprng_seed();
1147	+	}
1148	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1149	+	#endif
1150	+	}
1151	+	}//end of if branch of globals->haveSeed()
1152	+	else{
1153
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}//end of globals->haveSeed()
1163	+
1164	+	for (int i = 0; i < nInfo; i++){
1165	+	info[i].setSeed(seedValue);
1166	+	}
1167	+
1168		#ifdef IS_MPI
1169	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1169	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1170		MPIcheckPoint();
1171		#endif // is_mpi
776	–
1172		}
1173
1174
1175	<	void SimSetup::finalInfoCheck( void ){
1175	>	void SimSetup::finalInfoCheck(void){
1176		int index;
1177		int usesDipoles;
1178	+	int usesCharges;
1179		int i;
1180
1181	<	for(i=0; i<nInfo; i++){
1181	>	for (i = 0; i < nInfo; i++){
1182		// check electrostatic parameters
1183	<
1183	>
1184		index = 0;
1185		usesDipoles = 0;
1186	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1186	>	while ((index < info[i].n_atoms) && !usesDipoles){
1187		usesDipoles = (info[i].atoms[index])->hasDipole();
1188		index++;
1189		}
1190	<
1190	>	index = 0;
1191	>	usesCharges = 0;
1192	>	while ((index < info[i].n_atoms) && !usesCharges){
1193	>	usesCharges= (info[i].atoms[index])->hasCharge();
1194	>	index++;
1195	>	}
1196		#ifdef IS_MPI
1197		int myUse = usesDipoles;
1198	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1198	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1199		#endif //is_mpi
1200	<
1201	<	double theEcr, theEst;
1202	<
1203	<	if (globals->getUseRF() ) {
1204	<	info[i].useReactionField = 1;
1200	>
1201	>	double theRcut, theRsw;
1202	>
1203	>	if (globals->haveRcut()) {
1204	>	theRcut = globals->getRcut();
1205	>
1206	>	if (globals->haveRsw())
1207	>	theRsw = globals->getRsw();
1208	>	else
1209	>	theRsw = theRcut;
1210
1211	<	if( !globals->haveECR() ){
1212	<	sprintf( painCave.errMsg,
1213	<	"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	<	}
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212	>
1213	>	} else {
1214
1215	<	if( !globals->haveEST() ){
1216	<	sprintf( painCave.errMsg,
1217	<	"SimSetup Warning: using default value of 0.05 * the "
1218	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1219	<	);
1220	<	painCave.isFatal = 0;
1221	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
831	<	}
1215	>	the_ff->calcRcut();
1216	>	theRcut = info[i].getRcut();
1217	>
1218	>	if (globals->haveRsw())
1219	>	theRsw = globals->getRsw();
1220	>	else
1221	>	theRsw = theRcut;
1222
1223	<	info[i].setEcr( theEcr, theEst );
1223	>	info[i].setDefaultRcut(theRcut, theRsw);
1224	>	}
1225	>
1226	>	if (globals->getUseRF()){
1227	>	info[i].useReactionField = 1;
1228
1229	<	if(!globals->haveDielectric() ){
1230	<	sprintf( painCave.errMsg,
1231	<	"SimSetup Error: You are trying to use Reaction Field without"
1232	<	"setting a dielectric constant!\n"
1233	<	);
1234	<	painCave.isFatal = 1;
1235	<	simError();
1229	>	if (!globals->haveRcut()){
1230	>	sprintf(painCave.errMsg,
1231	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1232	>	"\tOOPSE will use a default value of 15.0 angstroms"
1233	>	"\tfor the cutoffRadius.\n");
1234	>	painCave.isFatal = 0;
1235	>	simError();
1236	>	theRcut = 15.0;
1237		}
1238	<	info[i].dielectric = globals->getDielectric();
1239	<	}
1240	<	else {
1241	<	if (usesDipoles) {
1238	>	else{
1239	>	theRcut = globals->getRcut();
1240	>	}
1241	>
1242	>	if (!globals->haveRsw()){
1243	>	sprintf(painCave.errMsg,
1244	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1245	>	"\tOOPSE will use a default value of\n"
1246	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1247	>	painCave.isFatal = 0;
1248	>	simError();
1249	>	theRsw = 0.95 * theRcut;
1250	>	}
1251	>	else{
1252	>	theRsw = globals->getRsw();
1253	>	}
1254	>
1255	>	info[i].setDefaultRcut(theRcut, theRsw);
1256	>
1257	>	if (!globals->haveDielectric()){
1258	>	sprintf(painCave.errMsg,
1259	>	"SimSetup Error: No Dielectric constant was set.\n"
1260	>	"\tYou are trying to use Reaction Field without"
1261	>	"\tsetting a dielectric constant!\n");
1262	>	painCave.isFatal = 1;
1263	>	simError();
1264	>	}
1265	>	info[i].dielectric = globals->getDielectric();
1266	>	}
1267	>	else{
1268	>	if (usesDipoles || usesCharges){
1269	>
1270	>	if (!globals->haveRcut()){
1271	>	sprintf(painCave.errMsg,
1272	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1273	>	"\tOOPSE will use a default value of 15.0 angstroms"
1274	>	"\tfor the cutoffRadius.\n");
1275	>	painCave.isFatal = 0;
1276	>	simError();
1277	>	theRcut = 15.0;
1278	>	}
1279	>	else{
1280	>	theRcut = globals->getRcut();
1281	>	}
1282	>
1283	>	if (!globals->haveRsw()){
1284	>	sprintf(painCave.errMsg,
1285	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1286	>	"\tOOPSE will use a default value of\n"
1287	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1288	>	painCave.isFatal = 0;
1289	>	simError();
1290	>	theRsw = 0.95 * theRcut;
1291	>	}
1292	>	else{
1293	>	theRsw = globals->getRsw();
1294	>	}
1295	>
1296	>	info[i].setDefaultRcut(theRcut, theRsw);
1297
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 );
1298		}
1299	<	}
1299	>	}
1300		}
881	–
1301		#ifdef IS_MPI
1302	<	strcpy( checkPointMsg, "post processing checks out" );
1302	>	strcpy(checkPointMsg, "post processing checks out");
1303		MPIcheckPoint();
1304		#endif // is_mpi
1305
1306	+	// clean up the forcefield
1307	+	the_ff->cleanMe();
1308		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
1309
1310	+	void SimSetup::initSystemCoords(void){
1311	+	int i;
1312	+
1313		char* inName;
1314
1315	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1316
1317	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1318	<
1319	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1320	<
899	<	if( globals->haveInitialConfig() ){
900	<
1317	>	for (i = 0; i < info[0].n_atoms; i++)
1318	>	info[0].atoms[i]->setCoords();
1319	>
1320	>	if (globals->haveInitialConfig()){
1321		InitializeFromFile* fileInit;
1322		#ifdef IS_MPI // is_mpi
1323	<	if( worldRank == 0 ){
1323	>	if (worldRank == 0){
1324		#endif //is_mpi
1325		inName = globals->getInitialConfig();
1326	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
1326	>	fileInit = new InitializeFromFile(inName);
1327		#ifdef IS_MPI
1328	<	}else fileInit = new InitializeFromFile( NULL );
1328	>	}
1329	>	else
1330	>	fileInit = new InitializeFromFile(NULL);
1331		#endif
1332	<	fileInit->readInit( info ); // default velocities on
1333	<
1332	>	fileInit->readInit(info); // default velocities on
1333	>
1334		delete fileInit;
1335		}
1336		else{
1337
917	–	#ifdef IS_MPI
918	–
1338		// no init from bass
1339
1340	<	sprintf( painCave.errMsg,
1341	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1342	<	painCave.isFatal;
1340	>	sprintf(painCave.errMsg,
1341	>	"Cannot intialize a simulation without an initial configuration file.\n");
1342	>	painCave.isFatal = 1;;
1343		simError();
1344
926	–	#else
927	–
928	–	initFromBass();
929	–
930	–
931	–	#endif
1345		}
1346	<
1346	>
1347		#ifdef IS_MPI
1348	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1348	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1349		MPIcheckPoint();
1350		#endif // is_mpi
938	–
1351		}
1352
1353
1354	<	void SimSetup::makeOutNames( void ){
943	<
1354	>	void SimSetup::makeOutNames(void){
1355		int k;
1356
946	–
947	–	for(k=0; k<nInfo; k++){
1357
1358	+	for (k = 0; k < nInfo; k++){
1359		#ifdef IS_MPI
1360	<	if( worldRank == 0 ){
1360	>	if (worldRank == 0){
1361		#endif // is_mpi
1362	<
1363	<	if( globals->haveFinalConfig() ){
1364	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1362	>
1363	>	if (globals->haveFinalConfig()){
1364	>	strcpy(info[k].finalName, globals->getFinalConfig());
1365		}
1366		else{
1367	<	strcpy( info[k].finalName, inFileName );
1368	<	char* endTest;
1369	<	int nameLength = strlen( info[k].finalName );
1370	<	endTest = &(info[k].finalName[nameLength - 5]);
1371	<	if( !strcmp( endTest, ".bass" ) ){
1372	<	strcpy( endTest, ".eor" );
1373	<	}
1374	<	else if( !strcmp( endTest, ".BASS" ) ){
1375	<	strcpy( endTest, ".eor" );
1376	<	}
1377	<	else{
1378	<	endTest = &(info[k].finalName[nameLength - 4]);
1379	<	if( !strcmp( endTest, ".bss" ) ){
1380	<	strcpy( endTest, ".eor" );
1381	<	}
1382	<	else if( !strcmp( endTest, ".mdl" ) ){
1383	<	strcpy( endTest, ".eor" );
1384	<	}
1385	<	else{
1386	<	strcat( info[k].finalName, ".eor" );
1387	<	}
1388	<	}
1367	>	strcpy(info[k].finalName, inFileName);
1368	>	char* endTest;
1369	>	int nameLength = strlen(info[k].finalName);
1370	>	endTest = &(info[k].finalName[nameLength - 5]);
1371	>	if (!strcmp(endTest, ".bass")){
1372	>	strcpy(endTest, ".eor");
1373	>	}
1374	>	else if (!strcmp(endTest, ".BASS")){
1375	>	strcpy(endTest, ".eor");
1376	>	}
1377	>	else{
1378	>	endTest = &(info[k].finalName[nameLength - 4]);
1379	>	if (!strcmp(endTest, ".bss")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else if (!strcmp(endTest, ".mdl")){
1383	>	strcpy(endTest, ".eor");
1384	>	}
1385	>	else{
1386	>	strcat(info[k].finalName, ".eor");
1387	>	}
1388	>	}
1389		}
1390	<
1390	>
1391		// make the sample and status out names
1392	<
1393	<	strcpy( info[k].sampleName, inFileName );
1392	>
1393	>	strcpy(info[k].sampleName, inFileName);
1394		char* endTest;
1395	<	int nameLength = strlen( info[k].sampleName );
1395	>	int nameLength = strlen(info[k].sampleName);
1396		endTest = &(info[k].sampleName[nameLength - 5]);
1397	<	if( !strcmp( endTest, ".bass" ) ){
1398	<	strcpy( endTest, ".dump" );
1397	>	if (!strcmp(endTest, ".bass")){
1398	>	strcpy(endTest, ".dump");
1399		}
1400	<	else if( !strcmp( endTest, ".BASS" ) ){
1401	<	strcpy( endTest, ".dump" );
1400	>	else if (!strcmp(endTest, ".BASS")){
1401	>	strcpy(endTest, ".dump");
1402		}
1403		else{
1404	<	endTest = &(info[k].sampleName[nameLength - 4]);
1405	<	if( !strcmp( endTest, ".bss" ) ){
1406	<	strcpy( endTest, ".dump" );
1407	<	}
1408	<	else if( !strcmp( endTest, ".mdl" ) ){
1409	<	strcpy( endTest, ".dump" );
1410	<	}
1411	<	else{
1412	<	strcat( info[k].sampleName, ".dump" );
1413	<	}
1404	>	endTest = &(info[k].sampleName[nameLength - 4]);
1405	>	if (!strcmp(endTest, ".bss")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else if (!strcmp(endTest, ".mdl")){
1409	>	strcpy(endTest, ".dump");
1410	>	}
1411	>	else{
1412	>	strcat(info[k].sampleName, ".dump");
1413	>	}
1414		}
1415	<
1416	<	strcpy( info[k].statusName, inFileName );
1417	<	nameLength = strlen( info[k].statusName );
1415	>
1416	>	strcpy(info[k].statusName, inFileName);
1417	>	nameLength = strlen(info[k].statusName);
1418		endTest = &(info[k].statusName[nameLength - 5]);
1419	<	if( !strcmp( endTest, ".bass" ) ){
1420	<	strcpy( endTest, ".stat" );
1419	>	if (!strcmp(endTest, ".bass")){
1420	>	strcpy(endTest, ".stat");
1421		}
1422	<	else if( !strcmp( endTest, ".BASS" ) ){
1423	<	strcpy( endTest, ".stat" );
1422	>	else if (!strcmp(endTest, ".BASS")){
1423	>	strcpy(endTest, ".stat");
1424		}
1425		else{
1426	<	endTest = &(info[k].statusName[nameLength - 4]);
1427	<	if( !strcmp( endTest, ".bss" ) ){
1428	<	strcpy( endTest, ".stat" );
1429	<	}
1430	<	else if( !strcmp( endTest, ".mdl" ) ){
1431	<	strcpy( endTest, ".stat" );
1432	<	}
1433	<	else{
1434	<	strcat( info[k].statusName, ".stat" );
1435	<	}
1426	>	endTest = &(info[k].statusName[nameLength - 4]);
1427	>	if (!strcmp(endTest, ".bss")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else if (!strcmp(endTest, ".mdl")){
1431	>	strcpy(endTest, ".stat");
1432	>	}
1433	>	else{
1434	>	strcat(info[k].statusName, ".stat");
1435	>	}
1436		}
1437	<
1437	>
1438	>	strcpy(info[k].rawPotName, inFileName);
1439	>	nameLength = strlen(info[k].rawPotName);
1440	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1441	>	if (!strcmp(endTest, ".bass")){
1442	>	strcpy(endTest, ".raw");
1443	>	}
1444	>	else if (!strcmp(endTest, ".BASS")){
1445	>	strcpy(endTest, ".raw");
1446	>	}
1447	>	else{
1448	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1449	>	if (!strcmp(endTest, ".bss")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else if (!strcmp(endTest, ".mdl")){
1453	>	strcpy(endTest, ".raw");
1454	>	}
1455	>	else{
1456	>	strcat(info[k].rawPotName, ".raw");
1457	>	}
1458	>	}
1459	>
1460		#ifdef IS_MPI
1461	+
1462		}
1463		#endif // is_mpi
1464		}
1465		}
1466
1467
1468	<	void SimSetup::sysObjectsCreation( void ){
1469	<
1470	<	int i,k;
1038	<
1468	>	void SimSetup::sysObjectsCreation(void){
1469	>	int i, k;
1470	>
1471		// create the forceField
1472
1473		createFF();
#	Line 1050 | Line 1482 | void SimSetup::sysObjectsCreation( void ){
1482
1483		#ifdef IS_MPI
1484		// divide the molecules among the processors
1485	<
1485	>
1486		mpiMolDivide();
1487		#endif //is_mpi
1488	<
1488	>
1489		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1490	<
1490	>
1491		makeSysArrays();
1492
1493		// make and initialize the molecules (all but atomic coordinates)
1494	<
1494	>
1495		makeMolecules();
1496	<
1497	<	for(k=0; k<nInfo; k++){
1496	>
1497	>	for (k = 0; k < nInfo; k++){
1498		info[k].identArray = new int[info[k].n_atoms];
1499	<	for(i=0; i<info[k].n_atoms; i++){
1499	>	for (i = 0; i < info[k].n_atoms; i++){
1500		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1501		}
1502		}
1503		}
1504
1505
1506	<	void SimSetup::createFF( void ){
1506	>	void SimSetup::createFF(void){
1507	>	switch (ffCase){
1508	>	case FF_DUFF:
1509	>	the_ff = new DUFF();
1510	>	break;
1511
1512	<	switch( ffCase ){
1512	>	case FF_LJ:
1513	>	the_ff = new LJFF();
1514	>	break;
1515
1516	<	case FF_DUFF:
1517	<	the_ff = new DUFF();
1518	<	break;
1516	>	case FF_EAM:
1517	>	the_ff = new EAM_FF();
1518	>	break;
1519
1520	<	case FF_LJ:
1521	<	the_ff = new LJFF();
1522	<	break;
1520	>	case FF_H2O:
1521	>	the_ff = new WATER();
1522	>	break;
1523
1524	<	case FF_EAM:
1525	<	the_ff = new EAM_FF();
1526	<	break;
1527	<
1528	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	simError();
1524	>	default:
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529		}
1530
1531		#ifdef IS_MPI
1532	<	strcpy( checkPointMsg, "ForceField creation successful" );
1532	>	strcpy(checkPointMsg, "ForceField creation successful");
1533		MPIcheckPoint();
1534		#endif // is_mpi
1101	–
1535		}
1536
1537
1538	<	void SimSetup::compList( void ){
1106	<
1538	>	void SimSetup::compList(void){
1539		int i;
1540		char* id;
1541		LinkedMolStamp* headStamp = new LinkedMolStamp();
1542		LinkedMolStamp* currentStamp = NULL;
1543	<	comp_stamps = new MoleculeStamp*[n_components];
1543	>	comp_stamps = new MoleculeStamp * [n_components];
1544	>	bool haveCutoffGroups;
1545	>
1546	>	haveCutoffGroups = false;
1547
1548		// make an array of molecule stamps that match the components used.
1549		// also extract the used stamps out into a separate linked list
1550	<
1551	<	for(i=0; i<nInfo; i++){
1550	>
1551	>	for (i = 0; i < nInfo; i++){
1552		info[i].nComponents = n_components;
1553		info[i].componentsNmol = components_nmol;
1554		info[i].compStamps = comp_stamps;
1555		info[i].headStamp = headStamp;
1556		}
1122	–
1557
1124	–	for( i=0; i<n_components; i++ ){
1558
1559	+	for (i = 0; i < n_components; i++){
1560		id = the_components[i]->getType();
1561		comp_stamps[i] = NULL;
1562	<
1562	>
1563		// check to make sure the component isn't already in the list
1564
1565	<	comp_stamps[i] = headStamp->match( id );
1566	<	if( comp_stamps[i] == NULL ){
1133	<
1565	>	comp_stamps[i] = headStamp->match(id);
1566	>	if (comp_stamps[i] == NULL){
1567		// extract the component from the list;
1568	<
1569	<	currentStamp = stamps->extractMolStamp( id );
1570	<	if( currentStamp == NULL ){
1571	<	sprintf( painCave.errMsg,
1572	<	"SimSetup error: Component \"%s\" was not found in the "
1573	<	"list of declared molecules\n",
1574	<	id );
1575	<	painCave.isFatal = 1;
1576	<	simError();
1568	>
1569	>	currentStamp = stamps->extractMolStamp(id);
1570	>	if (currentStamp == NULL){
1571	>	sprintf(painCave.errMsg,
1572	>	"SimSetup error: Component \"%s\" was not found in the "
1573	>	"list of declared molecules\n",
1574	>	id);
1575	>	painCave.isFatal = 1;
1576	>	simError();
1577		}
1578	<
1579	<	headStamp->add( currentStamp );
1580	<	comp_stamps[i] = headStamp->match( id );
1578	>
1579	>	headStamp->add(currentStamp);
1580	>	comp_stamps[i] = headStamp->match(id);
1581		}
1582	+
1583	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1584	+	haveCutoffGroups = true;
1585		}
1586	+
1587	+	for (i = 0; i < nInfo; i++)
1588	+	info[i].haveCutoffGroups = haveCutoffGroups;
1589
1590		#ifdef IS_MPI
1591	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1591	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1592		MPIcheckPoint();
1593		#endif // is_mpi
1594	+	}
1595
1596	+	void SimSetup::calcSysValues(void){
1597	+	int i, j;
1598	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1599
1600	<	}
1600	>	int* molMembershipArray;
1601	>	CutoffGroupStamp* cg;
1602
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1603		tot_atoms = 0;
1604		tot_bonds = 0;
1605		tot_bends = 0;
1606		tot_torsions = 0;
1607	<	for( i=0; i<n_components; i++ ){
1608	<
1609	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1610	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1611	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1607	>	tot_rigid = 0;
1608	>	tot_groups = 0;
1609	>	for (i = 0; i < n_components; i++){
1610	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1611	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1612	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1613		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1614	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1615	+
1616	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1617	+	atomsingroups = 0;
1618	+	for (j=0; j < ncutgroups; j++) {
1619	+	cg = comp_stamps[i]->getCutoffGroup(j);
1620	+	atomsingroups += cg->getNMembers();
1621	+	}
1622	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1623	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1624		}
1625
1626		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1627		molMembershipArray = new int[tot_atoms];
1628	<
1629	<	for(i=0; i<nInfo; i++){
1628	>
1629	>	for (i = 0; i < nInfo; i++){
1630		info[i].n_atoms = tot_atoms;
1631		info[i].n_bonds = tot_bonds;
1632		info[i].n_bends = tot_bends;
1633		info[i].n_torsions = tot_torsions;
1634		info[i].n_SRI = tot_SRI;
1635		info[i].n_mol = tot_nmol;
1636	<
1636	>	info[i].ngroup = tot_groups;
1637		info[i].molMembershipArray = molMembershipArray;
1638	<	}
1638	>	}
1639		}
1640
1641		#ifdef IS_MPI
1642
1643	<	void SimSetup::mpiMolDivide( void ){
1194	<
1643	>	void SimSetup::mpiMolDivide(void){
1644		int i, j, k;
1645		int localMol, allMol;
1646		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1647	+	int local_rigid, local_groups;
1648	+	vector<int> globalMolIndex;
1649	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1650	+	CutoffGroupStamp* cg;
1651
1652	<	mpiSim = new mpiSimulation( info );
1200	<
1201	<	globalIndex = mpiSim->divideLabor();
1652	>	mpiSim = new mpiSimulation(info);
1653
1654	+	mpiSim->divideLabor();
1655	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1658	+
1659		// set up the local variables
1660	<
1660	>
1661		mol2proc = mpiSim->getMolToProcMap();
1662		molCompType = mpiSim->getMolComponentType();
1663	<
1663	>
1664		allMol = 0;
1665		localMol = 0;
1666		local_atoms = 0;
1667		local_bonds = 0;
1668		local_bends = 0;
1669		local_torsions = 0;
1670	<	globalAtomIndex = 0;
1670	>	local_rigid = 0;
1671	>	local_groups = 0;
1672	>	globalAtomCounter = 0;
1673
1674	+	for (i = 0; i < n_components; i++){
1675	+	for (j = 0; j < components_nmol[i]; j++){
1676	+	if (mol2proc[allMol] == worldRank){
1677	+	local_atoms += comp_stamps[i]->getNAtoms();
1678	+	local_bonds += comp_stamps[i]->getNBonds();
1679	+	local_bends += comp_stamps[i]->getNBends();
1680	+	local_torsions += comp_stamps[i]->getNTorsions();
1681	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1682
1683	<	for( i=0; i<n_components; i++ ){
1683	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1684	>	atomsingroups = 0;
1685	>	for (k=0; k < ncutgroups; k++) {
1686	>	cg = comp_stamps[i]->getCutoffGroup(k);
1687	>	atomsingroups += cg->getNMembers();
1688	>	}
1689	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1690	>	ncutgroups;
1691	>	local_groups += ngroupsinstamp;
1692
1693	<	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++;
1693	>	localMol++;
1694		}
1695	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1696	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1697	<	globalAtomIndex++;
1695	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1696	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1697	>	globalAtomCounter++;
1698		}
1699
1700	<	allMol++;
1700	>	allMol++;
1701		}
1702		}
1703		local_SRI = local_bonds + local_bends + local_torsions;
1704	+
1705	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1706
1707	<	info[0].n_atoms = mpiSim->getMyNlocal();
1708	<
1709	<	if( local_atoms != info[0].n_atoms ){
1710	<	sprintf( painCave.errMsg,
1711	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	<	" localAtom (%d) are not equal.\n",
1245	<	info[0].n_atoms,
1246	<	local_atoms );
1707	>	if (local_atoms != info[0].n_atoms){
1708	>	sprintf(painCave.errMsg,
1709	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1710	>	"\tlocalAtom (%d) are not equal.\n",
1711	>	info[0].n_atoms, local_atoms);
1712		painCave.isFatal = 1;
1713		simError();
1714		}
1715
1716	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1717	+	if (local_groups != info[0].ngroup){
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1720	+	"\tlocalGroups (%d) are not equal.\n",
1721	+	info[0].ngroup, local_groups);
1722	+	painCave.isFatal = 1;
1723	+	simError();
1724	+	}
1725	+
1726		info[0].n_bonds = local_bonds;
1727		info[0].n_bends = local_bends;
1728		info[0].n_torsions = local_torsions;
1729		info[0].n_SRI = local_SRI;
1730		info[0].n_mol = localMol;
1731
1732	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1732	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1733		MPIcheckPoint();
1734		}
1735	<
1735	>
1736		#endif // is_mpi
1737
1738
1739	<	void SimSetup::makeSysArrays( void ){
1740	<	int i, j, k, l;
1739	>	void SimSetup::makeSysArrays(void){
1740	>
1741	>	#ifndef IS_MPI
1742	>	int k, j;
1743	>	#endif // is_mpi
1744	>	int i, l;
1745
1746		Atom** the_atoms;
1747		Molecule* the_molecules;
1269	–	Exclude** the_excludes;
1748
1749	<
1272	<	for(l=0; l<nInfo; l++){
1273	<
1749	>	for (l = 0; l < nInfo; l++){
1750		// create the atom and short range interaction arrays
1751	<
1752	<	the_atoms = new Atom*[info[l].n_atoms];
1751	>
1752	>	the_atoms = new Atom * [info[l].n_atoms];
1753		the_molecules = new Molecule[info[l].n_mol];
1754		int molIndex;
1755
1756		// initialize the molecule's stampID's
1757	<
1757	>
1758		#ifdef IS_MPI
1759	<
1760	<
1759	>
1760	>
1761		molIndex = 0;
1762	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1763	<
1764	<	if(mol2proc[i] == worldRank ){
1765	<	the_molecules[molIndex].setStampID( molCompType[i] );
1766	<	the_molecules[molIndex].setMyIndex( molIndex );
1767	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
1762	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1763	>	if (mol2proc[i] == worldRank){
1764	>	the_molecules[molIndex].setStampID(molCompType[i]);
1765	>	the_molecules[molIndex].setMyIndex(molIndex);
1766	>	the_molecules[molIndex].setGlobalIndex(i);
1767	>	molIndex++;
1768		}
1769		}
1770	<
1770	>
1771		#else // is_mpi
1772	<
1772	>
1773		molIndex = 0;
1774	<	globalAtomIndex = 0;
1775	<	for(i=0; i<n_components; i++){
1776	<	for(j=0; j<components_nmol[i]; j++ ){
1777	<	the_molecules[molIndex].setStampID( i );
1778	<	the_molecules[molIndex].setMyIndex( molIndex );
1779	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1780	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1781	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1782	<	globalAtomIndex++;
1783	<	}
1784	<	molIndex++;
1774	>	globalAtomCounter = 0;
1775	>	for (i = 0; i < n_components; i++){
1776	>	for (j = 0; j < components_nmol[i]; j++){
1777	>	the_molecules[molIndex].setStampID(i);
1778	>	the_molecules[molIndex].setMyIndex(molIndex);
1779	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1780	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1781	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1782	>	globalAtomCounter++;
1783	>	}
1784	>	molIndex++;
1785		}
1786		}
1312	–
1313	–
1314	–	#endif // is_mpi
1787
1788
1789	<	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	<	}
1789	>	#endif // is_mpi
1790
1791	+	info[l].globalExcludes = new int;
1792	+	info[l].globalExcludes[0] = 0;
1793	+
1794		// set the arrays into the SimInfo object
1795
1796		info[l].atoms = the_atoms;
1797		info[l].molecules = the_molecules;
1798		info[l].nGlobalExcludes = 0;
1343	–	info[l].excludes = the_excludes;
1344	–
1345	–	the_ff->setSimInfo( info );
1799
1800	+	the_ff->setSimInfo(info);
1801		}
1802		}
1803
1804	<	void SimSetup::makeIntegrator( void ){
1351	<
1804	>	void SimSetup::makeIntegrator(void){
1805		int k;
1806
1807	<	NVT<RealIntegrator>*  myNVT = NULL;
1808	<	NPTi<RealIntegrator>* myNPTi = NULL;
1809	<	NPTf<RealIntegrator>* myNPTf = NULL;
1810	<	NPTim<RealIntegrator>* myNPTim = NULL;
1811	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1812	<
1813	<	for(k=0; k<nInfo; k++){
1814	<
1815	<	switch( ensembleCase ){
1816	<
1817	<	case NVE_ENS:
1818	<	if (globals->haveZconstraints()){
1819	<	setupZConstraint(info[k]);
1820	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1807	>	NVE<RealIntegrator>* myNVE = NULL;
1808	>	NVT<RealIntegrator>* myNVT = NULL;
1809	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1810	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1811	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1812	>
1813	>	for (k = 0; k < nInfo; k++){
1814	>	switch (ensembleCase){
1815	>	case NVE_ENS:
1816	>	if (globals->haveZconstraints()){
1817	>	setupZConstraint(info[k]);
1818	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1819	>	}
1820	>	else{
1821	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1822		}
1823	+
1824	+	info->the_integrator = myNVE;
1825	+	break;
1826
1827	<	else
1828	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1829	<	break;
1830	<
1831	<	case NVT_ENS:
1832	<	if (globals->haveZconstraints()){
1833	<	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 );
1381	<
1382	<	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 );
1827	>	case NVT_ENS:
1828	>	if (globals->haveZconstraints()){
1829	>	setupZConstraint(info[k]);
1830	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1831	>	}
1832	>	else
1833	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1834
1835	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	<
1406	<	if (globals->haveTargetPressure())
1407	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	<	else {
1409	<	sprintf( painCave.errMsg,
1410	<	"SimSetup error: If you use a constant pressure\n"
1411	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	<	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 );
1835	>	myNVT->setTargetTemp(globals->getTargetTemp());
1836
1837	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1838	<
1839	<	if (globals->haveTargetPressure())
1840	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1841	<	else {
1842	<	sprintf( painCave.errMsg,
1843	<	"SimSetup error: If you use a constant pressure\n"
1844	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1845	<	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 );
1837	>	if (globals->haveTauThermostat())
1838	>	myNVT->setTauThermostat(globals->getTauThermostat());
1839	>	else{
1840	>	sprintf(painCave.errMsg,
1841	>	"SimSetup error: If you use the NVT\n"
1842	>	"\tensemble, you must set tauThermostat.\n");
1843	>	painCave.isFatal = 1;
1844	>	simError();
1845	>	}
1846
1847	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1848	<
1488	<	if (globals->haveTargetPressure())
1489	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	<	else {
1491	<	sprintf( painCave.errMsg,
1492	<	"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 );
1847	>	info->the_integrator = myNVT;
1848	>	break;
1849
1850	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1851	<
1852	<	if (globals->haveTargetPressure())
1853	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1854	<	else {
1855	<	sprintf( painCave.errMsg,
1856	<	"SimSetup error: If you use a constant pressure\n"
1857	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1858	<	painCave.isFatal = 1;
1859	<	simError();
1860	<	}
1861	<
1862	<	if( globals->haveTauThermostat() )
1863	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1864	<	else{
1865	<	sprintf( painCave.errMsg,
1866	<	"SimSetup error: If you use an NPT\n"
1867	<	"    ensemble, you must set tauThermostat.\n");
1868	<	painCave.isFatal = 1;
1869	<	simError();
1870	<	}
1871	<
1872	<	if( globals->haveTauBarostat() )
1873	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1874	<	else{
1875	<	sprintf( painCave.errMsg,
1876	<	"SimSetup error: If you use an NPT\n"
1877	<	"    ensemble, you must set tauBarostat.\n");
1878	<	painCave.isFatal = 1;
1879	<	simError();
1880	<	}
1881	<	break;
1882	<
1883	<	default:
1884	<	sprintf( painCave.errMsg,
1885	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1886	<	painCave.isFatal = 1;
1887	<	simError();
1850	>	case NPTi_ENS:
1851	>	if (globals->haveZconstraints()){
1852	>	setupZConstraint(info[k]);
1853	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1854	>	}
1855	>	else
1856	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1857	>
1858	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1859	>
1860	>	if (globals->haveTargetPressure())
1861	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1862	>	else{
1863	>	sprintf(painCave.errMsg,
1864	>	"SimSetup error: If you use a constant pressure\n"
1865	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1866	>	painCave.isFatal = 1;
1867	>	simError();
1868	>	}
1869	>
1870	>	if (globals->haveTauThermostat())
1871	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1872	>	else{
1873	>	sprintf(painCave.errMsg,
1874	>	"SimSetup error: If you use an NPT\n"
1875	>	"\tensemble, you must set tauThermostat.\n");
1876	>	painCave.isFatal = 1;
1877	>	simError();
1878	>	}
1879	>
1880	>	if (globals->haveTauBarostat())
1881	>	myNPTi->setTauBarostat(globals->getTauBarostat());
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 = myNPTi;
1891	>	break;
1892	>
1893	>	case NPTf_ENS:
1894	>	if (globals->haveZconstraints()){
1895	>	setupZConstraint(info[k]);
1896	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	>	}
1898	>	else
1899	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	>
1901	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1902	>
1903	>	if (globals->haveTargetPressure())
1904	>	myNPTf->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	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1915	>
1916	>	else{
1917	>	sprintf(painCave.errMsg,
1918	>	"SimSetup error: If you use an NPT\n"
1919	>	"\tensemble, you must set tauThermostat.\n");
1920	>	painCave.isFatal = 1;
1921	>	simError();
1922	>	}
1923	>
1924	>	if (globals->haveTauBarostat())
1925	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1926	>
1927	>	else{
1928	>	sprintf(painCave.errMsg,
1929	>	"SimSetup error: If you use an NPT\n"
1930	>	"\tensemble, you must set tauBarostat.\n");
1931	>	painCave.isFatal = 1;
1932	>	simError();
1933	>	}
1934	>
1935	>	info->the_integrator = myNPTf;
1936	>	break;
1937	>
1938	>	case NPTxyz_ENS:
1939	>	if (globals->haveZconstraints()){
1940	>	setupZConstraint(info[k]);
1941	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1942	>	}
1943	>	else
1944	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1945	>
1946	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1947	>
1948	>	if (globals->haveTargetPressure())
1949	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1950	>	else{
1951	>	sprintf(painCave.errMsg,
1952	>	"SimSetup error: If you use a constant pressure\n"
1953	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1954	>	painCave.isFatal = 1;
1955	>	simError();
1956	>	}
1957	>
1958	>	if (globals->haveTauThermostat())
1959	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1960	>	else{
1961	>	sprintf(painCave.errMsg,
1962	>	"SimSetup error: If you use an NPT\n"
1963	>	"\tensemble, you must set tauThermostat.\n");
1964	>	painCave.isFatal = 1;
1965	>	simError();
1966	>	}
1967	>
1968	>	if (globals->haveTauBarostat())
1969	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1970	>	else{
1971	>	sprintf(painCave.errMsg,
1972	>	"SimSetup error: If you use an NPT\n"
1973	>	"\tensemble, you must set tauBarostat.\n");
1974	>	painCave.isFatal = 1;
1975	>	simError();
1976	>	}
1977	>
1978	>	info->the_integrator = myNPTxyz;
1979	>	break;
1980	>
1981	>	default:
1982	>	sprintf(painCave.errMsg,
1983	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1984	>	painCave.isFatal = 1;
1985	>	simError();
1986		}
1987		}
1988		}
1989
1990	<	void SimSetup::initFortran( void ){
1570	<
1990	>	void SimSetup::initFortran(void){
1991		info[0].refreshSim();
1992	<
1993	<	if( !strcmp( info[0].mixingRule, "standard") ){
1994	<	the_ff->initForceField( LB_MIXING_RULE );
1992	>
1993	>	if (!strcmp(info[0].mixingRule, "standard")){
1994	>	the_ff->initForceField(LB_MIXING_RULE);
1995		}
1996	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1997	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1996	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1997	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1998		}
1999		else{
2000	<	sprintf( painCave.errMsg,
2001	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
2000	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2001	>	info[0].mixingRule);
2002		painCave.isFatal = 1;
2003		simError();
2004		}
2005
2006
2007		#ifdef IS_MPI
2008	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
2008	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2009		MPIcheckPoint();
2010		#endif // is_mpi
2011	+	}
2012
2013	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2014	+	int nZConstraints;
2015	+	ZconStamp** zconStamp;
2016	+
2017	+	if (globals->haveZconstraintTime()){
2018	+	//add sample time of z-constraint  into SimInfo's property list
2019	+	DoubleData* zconsTimeProp = new DoubleData();
2020	+	zconsTimeProp->setID(ZCONSTIME_ID);
2021	+	zconsTimeProp->setData(globals->getZconsTime());
2022	+	theInfo.addProperty(zconsTimeProp);
2023	+	}
2024	+	else{
2025	+	sprintf(painCave.errMsg,
2026	+	"ZConstraint error: If you use a ZConstraint,\n"
2027	+	"\tyou must set zconsTime.\n");
2028	+	painCave.isFatal = 1;
2029	+	simError();
2030	+	}
2031	+
2032	+	//push zconsTol into siminfo, if user does not specify
2033	+	//value for zconsTol, a default value will be used
2034	+	DoubleData* zconsTol = new DoubleData();
2035	+	zconsTol->setID(ZCONSTOL_ID);
2036	+	if (globals->haveZconsTol()){
2037	+	zconsTol->setData(globals->getZconsTol());
2038	+	}
2039	+	else{
2040	+	double defaultZConsTol = 0.01;
2041	+	sprintf(painCave.errMsg,
2042	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2043	+	"\tOOPSE will use a default value of %f.\n"
2044	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2045	+	defaultZConsTol);
2046	+	painCave.isFatal = 0;
2047	+	simError();
2048	+
2049	+	zconsTol->setData(defaultZConsTol);
2050	+	}
2051	+	theInfo.addProperty(zconsTol);
2052	+
2053	+	//set Force Subtraction Policy
2054	+	StringData* zconsForcePolicy = new StringData();
2055	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2056	+
2057	+	if (globals->haveZconsForcePolicy()){
2058	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2059	+	}
2060	+	else{
2061	+	sprintf(painCave.errMsg,
2062	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2063	+	"\tOOPSE will use PolicyByMass.\n"
2064	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2065	+	painCave.isFatal = 0;
2066	+	simError();
2067	+	zconsForcePolicy->setData("BYMASS");
2068	+	}
2069	+
2070	+	theInfo.addProperty(zconsForcePolicy);
2071	+
2072	+	//set zcons gap
2073	+	DoubleData* zconsGap = new DoubleData();
2074	+	zconsGap->setID(ZCONSGAP_ID);
2075	+
2076	+	if (globals->haveZConsGap()){
2077	+	zconsGap->setData(globals->getZconsGap());
2078	+	theInfo.addProperty(zconsGap);
2079	+	}
2080	+
2081	+	//set zcons fixtime
2082	+	DoubleData* zconsFixtime = new DoubleData();
2083	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2084	+
2085	+	if (globals->haveZConsFixTime()){
2086	+	zconsFixtime->setData(globals->getZconsFixtime());
2087	+	theInfo.addProperty(zconsFixtime);
2088	+	}
2089	+
2090	+	//set zconsUsingSMD
2091	+	IntData* zconsUsingSMD = new IntData();
2092	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2093	+
2094	+	if (globals->haveZConsUsingSMD()){
2095	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2096	+	theInfo.addProperty(zconsUsingSMD);
2097	+	}
2098	+
2099	+	//Determine the name of ouput file and add it into SimInfo's property list
2100	+	//Be careful, do not use inFileName, since it is a pointer which
2101	+	//point to a string at master node, and slave nodes do not contain that string
2102	+
2103	+	string zconsOutput(theInfo.finalName);
2104	+
2105	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2106	+
2107	+	StringData* zconsFilename = new StringData();
2108	+	zconsFilename->setID(ZCONSFILENAME_ID);
2109	+	zconsFilename->setData(zconsOutput);
2110	+
2111	+	theInfo.addProperty(zconsFilename);
2112	+
2113	+	//setup index, pos and other parameters of z-constraint molecules
2114	+	nZConstraints = globals->getNzConstraints();
2115	+	theInfo.nZconstraints = nZConstraints;
2116	+
2117	+	zconStamp = globals->getZconStamp();
2118	+	ZConsParaItem tempParaItem;
2119	+
2120	+	ZConsParaData* zconsParaData = new ZConsParaData();
2121	+	zconsParaData->setID(ZCONSPARADATA_ID);
2122	+
2123	+	for (int i = 0; i < nZConstraints; i++){
2124	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2125	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2126	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2127	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2128	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2129	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2130	+	zconsParaData->addItem(tempParaItem);
2131	+	}
2132	+
2133	+	//check the uniqueness of index
2134	+	if(!zconsParaData->isIndexUnique()){
2135	+	sprintf(painCave.errMsg,
2136	+	"ZConstraint Error: molIndex is not unique!\n");
2137	+	painCave.isFatal = 1;
2138	+	simError();
2139	+	}
2140	+
2141	+	//sort the parameters by index of molecules
2142	+	zconsParaData->sortByIndex();
2143	+
2144	+	//push data into siminfo, therefore, we can retrieve later
2145	+	theInfo.addProperty(zconsParaData);
2146		}
2147
2148	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
2149	<	{
2150	<	int nZConstraints;
2151	<	ZconStamp** zconStamp;
2152	<
2153	<	if(globals->haveZconstraintTime()){
2154	<
2155	<	//add sample time of z-constraint  into SimInfo's property list
2156	<	DoubleData* zconsTimeProp = new DoubleData();
2157	<	zconsTimeProp->setID(ZCONSTIME_ID);
2158	<	zconsTimeProp->setData(globals->getZconsTime());
2159	<	theInfo.addProperty(zconsTimeProp);
2148	>	void SimSetup::makeMinimizer(){
2149	>
2150	>	OOPSEMinimizer* myOOPSEMinimizer;
2151	>	MinimizerParameterSet* param;
2152	>	char minimizerName[100];
2153	>
2154	>	for (int i = 0; i < nInfo; i++){
2155	>
2156	>	//prepare parameter set for minimizer
2157	>	param = new MinimizerParameterSet();
2158	>	param->setDefaultParameter();
2159	>
2160	>	if (globals->haveMinimizer()){
2161	>	param->setFTol(globals->getMinFTol());
2162		}
2163	<	else{
2164	<	sprintf( painCave.errMsg,
2165	<	"ZConstraint error: If you use an ZConstraint\n"
1612	<	" , you must set sample time.\n");
1613	<	painCave.isFatal = 1;
1614	<	simError();
2163	>
2164	>	if (globals->haveMinGTol()){
2165	>	param->setGTol(globals->getMinGTol());
2166		}
2167
2168	<	//push zconsTol into siminfo, if user does not specify
2169	<	//value for zconsTol, a default value will be used
1619	<	DoubleData* zconsTol = new DoubleData();
1620	<	zconsTol->setID(ZCONSTOL_ID);
1621	<	if(globals->haveZconsTol()){
1622	<	zconsTol->setData(globals->getZconsTol());
2168	>	if (globals->haveMinMaxIter()){
2169	>	param->setMaxIteration(globals->getMinMaxIter());
2170		}
1624	–	else{
1625	–	double defaultZConsTol = 0.01;
1626	–	sprintf( painCave.errMsg,
1627	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	–	" , default value %f is used.\n", defaultZConsTol);
1629	–	painCave.isFatal = 0;
1630	–	simError();
2171
2172	<	zconsTol->setData(defaultZConsTol);
2173	<	}
2174	<	theInfo.addProperty(zconsTol);
2172	>	if (globals->haveMinWriteFrq()){
2173	>	param->setMaxIteration(globals->getMinMaxIter());
2174	>	}
2175
2176	<	//set Force Substraction Policy
2177	<	StringData* zconsForcePolicy =  new StringData();
2178	<	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	<
1640	<	if(globals->haveZconsForcePolicy()){
1641	<	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	<	}
1643	<	else{
1644	<	sprintf( painCave.errMsg,
1645	<	"ZConstraint Warning: User does not set force substraction policy, "
1646	<	"average force substraction policy is used\n");
1647	<	painCave.isFatal = 0;
1648	<	simError();
1649	<	zconsForcePolicy->setData("BYNUMBER");
1650	<	}
1651	<
1652	<	theInfo.addProperty(zconsForcePolicy);
1653	<
1654	<	//Determine the name of ouput file and add it into SimInfo's property list
1655	<	//Be careful, do not use inFileName, since it is a pointer which
1656	<	//point to a string at master node, and slave nodes do not contain that string
2176	>	if (globals->haveMinWriteFrq()){
2177	>	param->setWriteFrq(globals->getMinWriteFrq());
2178	>	}
2179
2180	<	string zconsOutput(theInfo.finalName);
2181	<
2182	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	<
1662	<	StringData* zconsFilename = new StringData();
1663	<	zconsFilename->setID(ZCONSFILENAME_ID);
1664	<	zconsFilename->setData(zconsOutput);
1665	<
1666	<	theInfo.addProperty(zconsFilename);
1667	<
1668	<	//setup index, pos and other parameters of z-constraint molecules
1669	<	nZConstraints = globals->getNzConstraints();
1670	<	theInfo.nZconstraints = nZConstraints;
1671	<
1672	<	zconStamp = globals->getZconStamp();
1673	<	ZConsParaItem tempParaItem;
2180	>	if (globals->haveMinStepSize()){
2181	>	param->setStepSize(globals->getMinStepSize());
2182	>	}
2183
2184	<	ZConsParaData* zconsParaData = new ZConsParaData();
2185	<	zconsParaData->setID(ZCONSPARADATA_ID);
2186	<
1678	<	for(int i = 0; i < nZConstraints; i++){
1679	<	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	<	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	<	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	<	tempParaItem.kRatio = zconStamp[i]->getKratio();
2184	>	if (globals->haveMinLSMaxIter()){
2185	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2186	>	}
2187
2188	<	zconsParaData->addItem(tempParaItem);
2188	>	if (globals->haveMinLSTol()){
2189	>	param->setLineSearchTol(globals->getMinLSTol());
2190	>	}
2191	>
2192	>	strcpy(minimizerName, globals->getMinimizer());
2193	>
2194	>	if (!strcasecmp(minimizerName, "CG")){
2195	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2196		}
2197	+	else if (!strcasecmp(minimizerName, "SD")){
2198	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2199	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2200	+	}
2201	+	else{
2202	+	sprintf(painCave.errMsg,
2203	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2204	+	painCave.isFatal = 0;
2205	+	simError();
2206
2207	<	//sort the parameters by index of molecules
2208	<	zconsParaData->sortByIndex();
2209	<
2210	<	//push data into siminfo, therefore, we can retrieve later
2211	<	theInfo.addProperty(zconsParaData);
2212	<
2207	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2208	>	}
2209	>	info[i].the_integrator = myOOPSEMinimizer;
2210	>
2211	>	//store the minimizer into simInfo
2212	>	info[i].the_minimizer = myOOPSEMinimizer;
2213	>	info[i].has_minimizer = true;
2214	>	}
2215	>
2216		}

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