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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 14 | Line 21
21
22		// some defines for ensemble and Forcefield  cases
23
24	<	#define NVE_ENS   0
25	<	#define NVT_ENS   1
26	<	#define NPTi_ENS  2
27	<	#define NPTf_ENS  3
28	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
24	>	#define NVE_ENS        0
25	>	#define NVT_ENS        1
26	>	#define NPTi_ENS       2
27	>	#define NPTf_ENS       3
28	>	#define NPTxyz_ENS     4
29
30
31	<	#define FF_DUFF 0
32	<	#define FF_LJ   1
31	>	#define FF_DUFF  0
32	>	#define FF_LJ    1
33	>	#define FF_EAM   2
34	>	#define FF_H2O   3
35
36	+	using namespace std;
37
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 41 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
81	–	int i, j, k, globalAtomIndex;
82	–
127		// gather all of the information from the Bass file
128	<
128	>
129		gatherInfo();
130
131		// creation of complex system objects
#	Line 89 | Line 133 | void SimSetup::createSim( void ){
133		sysObjectsCreation();
134
135		// check on the post processing info
136	<
136	>
137		finalInfoCheck();
138
139		// initialize the system coordinates
140
141	<	initSystemCoords();
142	<
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	+	if( !(globals->getUseInitTime()) )
145	+	info[0].currentTime = 0.0;
146	+	}
147	+
148		// make the output filenames
149
150		makeOutNames();
103	–
104	–	// make the integrator
151
106	–	makeIntegrator();
107	–
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 113 | Line 157 | void SimSetup::createSim( void ){
157
158		initFortran();
159
160	+	if (globals->haveMinimizer())
161	+	// make minimizer
162	+	makeMinimizer();
163	+	else
164	+	// make the integrator
165	+	makeIntegrator();
166
117	–
167		}
168
169
170	<	void SimSetup::makeMolecules( void ){
171	<
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI, 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
142	–
212		// init the atoms
213
214	<	double ux, uy, uz, u, uSqr;
146	<
147	<	atomOffset = 0;
148	<	excludeOffset = 0;
149	<	for(i=0; i<info->n_mol; i++){
150	<
151	<	stampID = the_molecules[i].getStampID();
214	>	int nMembers, nNew, rb1, rb2;
215
216	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
217	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
155	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
156	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
157	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
159	–	molInfo.myAtoms = &the_atoms[atomOffset];
160	–	molInfo.myExcludes = &the_excludes[excludeOffset];
161	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
162	–	molInfo.myBends = new Bend*[molInfo.nBends];
163	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
164	–
165	–	theBonds = new bond_pair[molInfo.nBonds];
166	–	theBends = new bend_set[molInfo.nBends];
167	–	theTorsions = new torsion_set[molInfo.nTorsions];
168	–
169	–	// make the Atoms
170	–
171	–	for(j=0; j<molInfo.nAtoms; j++){
172	–
173	–	currentAtom = comp_stamps[stampID]->getAtom( j );
174	–	if( currentAtom->haveOrientation() ){
175	–
176	–	dAtom = new DirectionalAtom(j + atomOffset);
177	–	info->n_oriented++;
178	–	molInfo.myAtoms[j] = dAtom;
179	–
180	–	ux = currentAtom->getOrntX();
181	–	uy = currentAtom->getOrntY();
182	–	uz = currentAtom->getOrntZ();
183	–
184	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
185	–
186	–	u = sqrt( uSqr );
187	–	ux = ux / u;
188	–	uy = uy / u;
189	–	uz = uz / u;
190	–
191	–	dAtom->setSUx( ux );
192	–	dAtom->setSUy( uy );
193	–	dAtom->setSUz( uz );
194	–	}
195	–	else{
196	–	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197	–	}
198	–	molInfo.myAtoms[j]->setType( currentAtom->getType() );
199	–
219		#ifdef IS_MPI
220	<
221	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
222	<
223	<	#endif // is_mpi
224	<	}
225	<
226	<	// make the bonds
227	<	for(j=0; j<molInfo.nBonds; j++){
209	<
210	<	currentBond = comp_stamps[stampID]->getBond( j );
211	<	theBonds[j].a = currentBond->getA() + atomOffset;
212	<	theBonds[j].b = currentBond->getB() + atomOffset;
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	<	exI = theBonds[j].a;
230	<	exJ = theBonds[j].b;
229	>	atomOffset = 0;
230	>	groupOffset = 0;
231
232	<	// exclude_I must always be the smaller of the pair
233	<	if( exI > exJ ){
234	<	tempEx = exI;
235	<	exI = exJ;
236	<	exJ = tempEx;
237	<	}
238	<	#ifdef IS_MPI
239	<	tempEx = exI;
240	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
241	<	tempEx = exJ;
242	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
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();
239	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241	>
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
230	<	#else  // isn't MPI
244	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
247	<	#endif  //is_mpi
248	<	}
249	<	excludeOffset += molInfo.nBonds;
246	>	if (molInfo.nBonds > 0)
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	>	else
249	>	molInfo.myBonds = NULL;
250
251	<	//make the bends
252	<	for(j=0; j<molInfo.nBends; j++){
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
265	<	currentBend = comp_stamps[stampID]->getBend( j );
266	<	theBends[j].a = currentBend->getA() + atomOffset;
267	<	theBends[j].b = currentBend->getB() + atomOffset;
268	<	theBends[j].c = currentBend->getC() + atomOffset;
269	<
270	<	if( currentBend->haveExtras() ){
271	<
272	<	extras = currentBend->getExtras();
273	<	current_extra = extras;
274	<
275	<	while( current_extra != NULL ){
276	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
277	<
278	<	switch( current_extra->getType() ){
279	<
280	<	case 0:
281	<	theBends[j].ghost =
282	<	current_extra->getInt() + atomOffset;
283	<	theBends[j].isGhost = 1;
284	<	break;
285	<
286	<	case 1:
287	<	theBends[j].ghost =
288	<	(int)current_extra->getDouble() + atomOffset;
289	<	theBends[j].isGhost = 1;
290	<	break;
291	<
292	<	default:
293	<	sprintf( painCave.errMsg,
294	<	"SimSetup Error: ghostVectorSource was neither a "
295	<	"double nor an int.\n"
296	<	"-->Bend[%d] in %s\n",
297	<	j, comp_stamps[stampID]->getID() );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<	}
302	<
303	<	else{
304	<
305	<	sprintf( painCave.errMsg,
306	<	"SimSetup Error: unhandled bend assignment:\n"
307	<	"    -->%s in Bend[%d] in %s\n",
308	<	current_extra->getlhs(),
309	<	j, comp_stamps[stampID]->getID() );
310	<	painCave.isFatal = 1;
311	<	simError();
312	<	}
313	<
314	<	current_extra = current_extra->getNext();
315	<	}
265	>	// make the Atoms
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	>	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	>	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	<
319	<	if( !theBends[j].isGhost ){
320	<
321	<	exI = theBends[j].a;
322	<	exJ = theBends[j].c;
318	>
319	>	//make the bends
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	>	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	<	else{
403	<
404	<	exI = theBends[j].a;
405	<	exJ = theBends[j].b;
406	<	}
407	<
408	<	// exclude_I must always be the smaller of the pair
409	<	if( exI > exJ ){
410	<	tempEx = exI;
411	<	exI = exJ;
412	<	exJ = tempEx;
413	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
418	<	tempEx = exJ;
419	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
420	<
421	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
422	<	#else  // isn't MPI
423	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
424	<	#endif  //is_mpi
425	<	}
321	<	excludeOffset += molInfo.nBends;
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	<	for(j=0; j<molInfo.nTorsions; j++){
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	>
435
436	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
326	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
436	>	molInfo.myRigidBodies.clear();
437
438	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
438	>	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	<	// exclude_I must always be the smaller of the pair
441	<	if( exI > exJ ){
442	<	tempEx = exI;
443	<	exI = exJ;
444	<	exJ = tempEx;
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	+
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	<	tempEx = exI;
520	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
521	<	tempEx = exJ;
522	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(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[groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = groupOffset;
538	>	#endif
539	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
540	>	cutoffAtomSet.insert(tempI);
541	>	}
542	>
543	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
544	>	groupOffset++;
545	>
546	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547
548	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
549	<	#else  // isn't MPI
550	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
551	<	#endif  //is_mpi
548	>
549	>	// create a cutoff group for every atom in current molecule which
550	>	// does not belong to cutoffgroup defined at mdl file
551	>
552	>	for(j = 0; j < molInfo.nAtoms; j++){
553	>
554	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555	>	myCutoffGroup = new CutoffGroup();
556	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557	>
558	>	#ifdef IS_MPI
559	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562	>	#else
563	>	myCutoffGroup->setGlobalIndex(groupOffset);
564	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
565	>	info[k].globalGroupMembership[globalID] = groupOffset;
566	>	#endif
567	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
568	>	groupOffset++;
569	>	}
570	>	}
571	>
572	>	// After this is all set up, scan through the atoms to
573	>	// see if they can be added to the integrableObjects:
574	>
575	>	molInfo.myIntegrableObjects.clear();
576	>
577	>
578	>	for (j = 0; j < molInfo.nAtoms; j++){
579	>
580	>	#ifdef IS_MPI
581	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
582	>	#else
583	>	slJ = j+atomOffset;
584	>	#endif
585	>
586	>	// if they aren't on the skip list, then they can be integrated
587	>
588	>	if (skipList.find(slJ) == skipList.end()) {
589	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
590	>	info[k].integrableObjects.push_back(mySD);
591	>	molInfo.myIntegrableObjects.push_back(mySD);
592	>	}
593	>	}
594	>
595	>	// all rigid bodies are integrated:
596	>
597	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
598	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
599	>	info[k].integrableObjects.push_back(mySD);
600	>	molInfo.myIntegrableObjects.push_back(mySD);
601	>	}
602	>
603	>
604	>	/*
605	>
606	>	//creat ConstraintPair.
607	>	molInfo.myConstraintPair.clear();
608	>
609	>	for (j = 0; j < molInfo.nBonds; j++){
610	>
611	>	//if both atoms are in the same rigid body, just skip it
612	>	currentBond = comp_stamps[stampID]->getBond(j);
613	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
614	>
615	>	tempI = currentBond->getA() + atomOffset;
616	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
617	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
618	>	else
619	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
620	>
621	>	tempJ =  currentBond->getB() + atomOffset;
622	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
623	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
624	>	else
625	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
626	>
627	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>	}
631	>
632	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
633	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
634	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
635	>
636	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
637	>
638	>	for(size_t m = 0; m < jointAtoms.size(); m++){
639	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
640	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
641	>
642	>	consPair = new JointConstraintPair(consElement1, consElement2);
643	>	molInfo.myConstraintPairs.push_back(consPair);
644	>	}
645	>
646	>	}
647	>	}
648	>
649	>	*/
650	>	// send the arrays off to the forceField for init.
651	>
652	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
653	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
654	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
655	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
656	>	theTorsions);
657	>
658	>	info[k].molecules[i].initialize(molInfo);
659	>
660	>
661	>	atomOffset += molInfo.nAtoms;
662	>	delete[] theBonds;
663	>	delete[] theBends;
664	>	delete[] theTorsions;
665		}
351	–	excludeOffset += molInfo.nTorsions;
666
353	–
354	–	// send the arrays off to the forceField for init.
667
356	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
668
669	+	#ifdef IS_MPI
670	+	// Since the globalGroupMembership has been zero filled and we've only
671	+	// poked values into the atoms we know, we can do an Allreduce
672	+	// to get the full globalGroupMembership array (We think).
673	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674	+	// docs said we could.
675
676	<	the_molecules[i].initialize( molInfo );
676	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
677
678	+	MPI_Allreduce(info[k].globalGroupMembership,
679	+	ggMjunk,
680	+	mpiSim->getNAtomsGlobal(),
681	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682
683	<	atomOffset += molInfo.nAtoms;
684	<	delete[] theBonds;
685	<	delete[] theBends;
686	<	delete[] theTorsions;
683	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684	>	info[k].globalGroupMembership[i] = ggMjunk[i];
685	>
686	>	delete[] ggMjunk;
687	>
688	>	#endif
689	>
690	>
691	>
692		}
693
694		#ifdef IS_MPI
695	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
695	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
696		MPIcheckPoint();
697		#endif // is_mpi
698
376	–	// clean up the forcefield
377	–	the_ff->calcRcut();
378	–	the_ff->cleanMe();
379	–
699		}
700
701	<	void SimSetup::initFromBass( void ){
383	<
701	>	void SimSetup::initFromBass(void){
702		int i, j, k;
703		int n_cells;
704		double cellx, celly, cellz;
#	Line 389 | Line 707 | void SimSetup::initFromBass( void ){
707		int n_extra;
708		int have_extra, done;
709
710	<	temp1 = (double)tot_nmol / 4.0;
711	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
712	<	temp3 = ceil( temp2 );
710	>	double vel[3];
711	>	vel[0] = 0.0;
712	>	vel[1] = 0.0;
713	>	vel[2] = 0.0;
714
715	<	have_extra =0;
716	<	if( temp2 < temp3 ){ // we have a non-complete lattice
717	<	have_extra =1;
715	>	temp1 = (double) tot_nmol / 4.0;
716	>	temp2 = pow(temp1, (1.0 / 3.0));
717	>	temp3 = ceil(temp2);
718
719	<	n_cells = (int)temp3 - 1;
720	<	cellx = info->boxL[0] / temp3;
721	<	celly = info->boxL[1] / temp3;
722	<	cellz = info->boxL[2] / temp3;
404	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406	<	n_per_extra = (int)ceil( temp1 );
719	>	have_extra = 0;
720	>	if (temp2 < temp3){
721	>	// we have a non-complete lattice
722	>	have_extra = 1;
723
724	<	if( n_per_extra > 4){
725	<	sprintf( painCave.errMsg,
726	<	"SimSetup error. There has been an error in constructing"
727	<	" the non-complete lattice.\n" );
724	>	n_cells = (int) temp3 - 1;
725	>	cellx = info[0].boxL[0] / temp3;
726	>	celly = info[0].boxL[1] / temp3;
727	>	cellz = info[0].boxL[2] / temp3;
728	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
729	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
730	>	n_per_extra = (int) ceil(temp1);
731	>
732	>	if (n_per_extra > 4){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error. There has been an error in constructing"
735	>	" the non-complete lattice.\n");
736		painCave.isFatal = 1;
737		simError();
738		}
739		}
740		else{
741	<	n_cells = (int)temp3;
742	<	cellx = info->boxL[0] / temp3;
743	<	celly = info->boxL[1] / temp3;
744	<	cellz = info->boxL[2] / temp3;
741	>	n_cells = (int) temp3;
742	>	cellx = info[0].boxL[0] / temp3;
743	>	celly = info[0].boxL[1] / temp3;
744	>	cellz = info[0].boxL[2] / temp3;
745		}
746
747		current_mol = 0;
#	Line 425 | Line 749 | void SimSetup::initFromBass( void ){
749		current_comp = 0;
750		current_atom_ndx = 0;
751
752	<	for( i=0; i < n_cells ; i++ ){
753	<	for( j=0; j < n_cells; j++ ){
754	<	for( k=0; k < n_cells; k++ ){
752	>	for (i = 0; i < n_cells ; i++){
753	>	for (j = 0; j < n_cells; j++){
754	>	for (k = 0; k < n_cells; k++){
755	>	makeElement(i * cellx, j * celly, k * cellz);
756
757	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
757	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
758
759	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
759	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
760
761	<	makeElement( i * cellx,
441	<	j * celly + 0.5 * celly,
442	<	k * cellz + 0.5 * cellz );
443	<
444	<	makeElement( i * cellx + 0.5 * cellx,
445	<	j * celly,
446	<	k * cellz + 0.5 * cellz );
761	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
762		}
763		}
764		}
765
766	<	if( have_extra ){
766	>	if (have_extra){
767		done = 0;
768
769		int start_ndx;
770	<	for( i=0; i < (n_cells+1) && !done; i++ ){
771	<	for( j=0; j < (n_cells+1) && !done; j++ ){
770	>	for (i = 0; i < (n_cells + 1) && !done; i++){
771	>	for (j = 0; j < (n_cells + 1) && !done; j++){
772	>	if (i < n_cells){
773	>	if (j < n_cells){
774	>	start_ndx = n_cells;
775	>	}
776	>	else
777	>	start_ndx = 0;
778	>	}
779	>	else
780	>	start_ndx = 0;
781
782	<	if( i < n_cells ){
782	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
783	>	makeElement(i * cellx, j * celly, k * cellz);
784	>	done = (current_mol >= tot_nmol);
785
786	<	if( j < n_cells ){
787	<	start_ndx = n_cells;
788	<	}
789	<	else start_ndx = 0;
790	<	}
465	<	else start_ndx = 0;
786	>	if (!done && n_per_extra > 1){
787	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
788	>	k * cellz);
789	>	done = (current_mol >= tot_nmol);
790	>	}
791
792	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
792	>	if (!done && n_per_extra > 2){
793	>	makeElement(i * cellx, j * celly + 0.5 * celly,
794	>	k * cellz + 0.5 * cellz);
795	>	done = (current_mol >= tot_nmol);
796	>	}
797
798	<	makeElement( i * cellx,
799	<	j * celly,
800	<	k * cellz );
801	<	done = ( current_mol >= tot_nmol );
802	<
803	<	if( !done && n_per_extra > 1 ){
475	<	makeElement( i * cellx + 0.5 * cellx,
476	<	j * celly + 0.5 * celly,
477	<	k * cellz );
478	<	done = ( current_mol >= tot_nmol );
479	<	}
480	<
481	<	if( !done && n_per_extra > 2){
482	<	makeElement( i * cellx,
483	<	j * celly + 0.5 * celly,
484	<	k * cellz + 0.5 * cellz );
485	<	done = ( current_mol >= tot_nmol );
486	<	}
487	<
488	<	if( !done && n_per_extra > 3){
489	<	makeElement( i * cellx + 0.5 * cellx,
490	<	j * celly,
491	<	k * cellz + 0.5 * cellz );
492	<	done = ( current_mol >= tot_nmol );
493	<	}
494	<	}
798	>	if (!done && n_per_extra > 3){
799	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
800	>	k * cellz + 0.5 * cellz);
801	>	done = (current_mol >= tot_nmol);
802	>	}
803	>	}
804		}
805		}
806		}
807
808	<
809	<	for( i=0; i<info->n_atoms; i++ ){
501	<	info->atoms[i]->set_vx( 0.0 );
502	<	info->atoms[i]->set_vy( 0.0 );
503	<	info->atoms[i]->set_vz( 0.0 );
808	>	for (i = 0; i < info[0].n_atoms; i++){
809	>	info[0].atoms[i]->setVel(vel);
810		}
811		}
812
813	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
813	>	void SimSetup::makeElement(double x, double y, double z){
814		int k;
815		AtomStamp* current_atom;
816		DirectionalAtom* dAtom;
817		double rotMat[3][3];
818	+	double pos[3];
819
820	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
821	<
822	<	current_atom = comp_stamps[current_comp]->getAtom( k );
823	<	if( !current_atom->havePosition() ){
824	<	sprintf( painCave.errMsg,
825	<	"SimSetup:initFromBass error.\n"
826	<	"\tComponent %s, atom %s does not have a position specified.\n"
827	<	"\tThe initialization routine is unable to give a start"
828	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
820	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
821	>	current_atom = comp_stamps[current_comp]->getAtom(k);
822	>	if (!current_atom->havePosition()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup:initFromBass error.\n"
825	>	"\tComponent %s, atom %s does not have a position specified.\n"
826	>	"\tThe initialization routine is unable to give a start"
827	>	" position.\n",
828	>	comp_stamps[current_comp]->getID(), current_atom->getType());
829		painCave.isFatal = 1;
830		simError();
831		}
832
833	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
834	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
835	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
833	>	pos[0] = x + current_atom->getPosX();
834	>	pos[1] = y + current_atom->getPosY();
835	>	pos[2] = z + current_atom->getPosZ();
836
837	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
837	>	info[0].atoms[current_atom_ndx]->setPos(pos);
838
839	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
839	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
840	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
841
842		rotMat[0][0] = 1.0;
843		rotMat[0][1] = 0.0;
#	Line 546 | Line 851 | void SimSetup::makeElement( double x, double y, double
851		rotMat[2][1] = 0.0;
852		rotMat[2][2] = 1.0;
853
854	<	dAtom->setA( rotMat );
854	>	dAtom->setA(rotMat);
855		}
856
857		current_atom_ndx++;
#	Line 555 | Line 860 | void SimSetup::makeElement( double x, double y, double
860		current_mol++;
861		current_comp_mol++;
862
863	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
863	>	if (current_comp_mol >= components_nmol[current_comp]){
864		current_comp_mol = 0;
865		current_comp++;
866		}
867		}
868
869
870	<	void SimSetup::gatherInfo( void ){
871	<	int i,j,k;
870	>	void SimSetup::gatherInfo(void){
871	>	int i;
872
873		ensembleCase = -1;
874		ffCase = -1;
875
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
876		// set the easy ones first
877	<	info->target_temp = globals->getTargetTemp();
878	<	info->dt = globals->getDt();
879	<	info->run_time = globals->getRunTime();
877	>
878	>	for (i = 0; i < nInfo; i++){
879	>	info[i].target_temp = globals->getTargetTemp();
880	>	info[i].dt = globals->getDt();
881	>	info[i].run_time = globals->getRunTime();
882	>	}
883		n_components = globals->getNComponents();
884
885
886		// get the forceField
887
888	<	strcpy( force_field, globals->getForceField() );
888	>	strcpy(force_field, globals->getForceField());
889
890	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
891	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
589	<	else{
590	<	sprintf( painCave.errMsg,
591	<	"SimSetup Error. Unrecognized force field -> %s\n",
592	<	force_field );
593	<	painCave.isFatal = 1;
594	<	simError();
890	>	if (!strcasecmp(force_field, "DUFF")){
891	>	ffCase = FF_DUFF;
892		}
893	<
894	<	// get the ensemble
895	<
896	<	strcpy( ensemble, globals->getEnsemble() );
897	<
898	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
899	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
900	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
901	<	ensembleCase = NPTi_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
893	>	else if (!strcasecmp(force_field, "LJ")){
894	>	ffCase = FF_LJ;
895	>	}
896	>	else if (!strcasecmp(force_field, "EAM")){
897	>	ffCase = FF_EAM;
898	>	}
899	>	else if (!strcasecmp(force_field, "WATER")){
900	>	ffCase = FF_H2O;
901	>	}
902		else{
903	<	sprintf( painCave.errMsg,
904	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
905	<	"reverting to NVE for this simulation.\n",
906	<	ensemble );
907	<	painCave.isFatal = 0;
908	<	simError();
909	<	strcpy( ensemble, "NVE" );
903	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
904	>	force_field);
905	>	painCave.isFatal = 1;
906	>	simError();
907	>	}
908	>
909	>	// get the ensemble
910	>
911	>	strcpy(ensemble, globals->getEnsemble());
912	>
913	>	if (!strcasecmp(ensemble, "NVE")){
914		ensembleCase = NVE_ENS;
915	+	}
916	+	else if (!strcasecmp(ensemble, "NVT")){
917	+	ensembleCase = NVT_ENS;
918	+	}
919	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
920	+	ensembleCase = NPTi_ENS;
921	+	}
922	+	else if (!strcasecmp(ensemble, "NPTf")){
923	+	ensembleCase = NPTf_ENS;
924	+	}
925	+	else if (!strcasecmp(ensemble, "NPTxyz")){
926	+	ensembleCase = NPTxyz_ENS;
927	+	}
928	+	else{
929	+	sprintf(painCave.errMsg,
930	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
931	+	"\treverting to NVE for this simulation.\n",
932	+	ensemble);
933	+	painCave.isFatal = 0;
934	+	simError();
935	+	strcpy(ensemble, "NVE");
936	+	ensembleCase = NVE_ENS;
937		}
618	–	strcpy( info->ensemble, ensemble );
938
939	<	// get the mixing rule
939	>	for (i = 0; i < nInfo; i++){
940	>	strcpy(info[i].ensemble, ensemble);
941
942	<	strcpy( info->mixingRule, globals->getMixingRule() );
943	<	info->usePBC = globals->getPBC();
944	<
945	<
942	>	// get the mixing rule
943	>
944	>	strcpy(info[i].mixingRule, globals->getMixingRule());
945	>	info[i].usePBC = globals->getPBC();
946	>	}
947	>
948		// get the components and calculate the tot_nMol and indvidual n_mol
949	<
949	>
950		the_components = globals->getComponents();
951		components_nmol = new int[n_components];
952
953
954	<	if( !globals->haveNMol() ){
954	>	if (!globals->haveNMol()){
955		// we don't have the total number of molecules, so we assume it is
956		// given in each component
957
958		tot_nmol = 0;
959	<	for( i=0; i<n_components; i++ ){
960	<
961	<	if( !the_components[i]->haveNMol() ){
962	<	// we have a problem
963	<	sprintf( painCave.errMsg,
964	<	"SimSetup Error. No global NMol or component NMol"
965	<	" given. Cannot calculate the number of atoms.\n" );
966	<	painCave.isFatal = 1;
645	<	simError();
959	>	for (i = 0; i < n_components; i++){
960	>	if (!the_components[i]->haveNMol()){
961	>	// we have a problem
962	>	sprintf(painCave.errMsg,
963	>	"SimSetup Error. No global NMol or component NMol given.\n"
964	>	"\tCannot calculate the number of atoms.\n");
965	>	painCave.isFatal = 1;
966	>	simError();
967		}
968
969		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 971 | void SimSetup::gatherInfo( void ){
971		}
972		}
973		else{
974	<	sprintf( painCave.errMsg,
975	<	"SimSetup error.\n"
976	<	"\tSorry, the ability to specify total"
977	<	" nMols and then give molfractions in the components\n"
978	<	"\tis not currently supported."
979	<	" Please give nMol in the components.\n" );
974	>	sprintf(painCave.errMsg,
975	>	"SimSetup error.\n"
976	>	"\tSorry, the ability to specify total"
977	>	" nMols and then give molfractions in the components\n"
978	>	"\tis not currently supported."
979	>	" Please give nMol in the components.\n");
980		painCave.isFatal = 1;
981		simError();
982		}
983
984	<	// set the status, sample, and thermal kick times
985	<
986	<	if( globals->haveSampleTime() ){
987	<	info->sampleTime = globals->getSampleTime();
988	<	info->statusTime = info->sampleTime;
989	<	info->thermalTime = info->sampleTime;
984	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
985	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
986	>	sprintf(painCave.errMsg,
987	>	"Sample time is not divisible by dt.\n"
988	>	"\tThis will result in samples that are not uniformly\n"
989	>	"\tdistributed in time.  If this is a problem, change\n"
990	>	"\tyour sampleTime variable.\n");
991	>	painCave.isFatal = 0;
992	>	simError();
993		}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
994
995	<	if( globals->haveStatusTime() ){
996	<	info->statusTime = globals->getStatusTime();
995	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
996	>	sprintf(painCave.errMsg,
997	>	"Status time is not divisible by dt.\n"
998	>	"\tThis will result in status reports that are not uniformly\n"
999	>	"\tdistributed in time.  If this is a problem, change \n"
1000	>	"\tyour statusTime variable.\n");
1001	>	painCave.isFatal = 0;
1002	>	simError();
1003		}
1004
1005	<	if( globals->haveThermalTime() ){
1006	<	info->thermalTime = globals->getThermalTime();
1007	<	}
1005	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1006	>	sprintf(painCave.errMsg,
1007	>	"Thermal time is not divisible by dt.\n"
1008	>	"\tThis will result in thermalizations that are not uniformly\n"
1009	>	"\tdistributed in time.  If this is a problem, change \n"
1010	>	"\tyour thermalTime variable.\n");
1011	>	painCave.isFatal = 0;
1012	>	simError();
1013	>	}
1014
1015	<	// check for the temperature set flag
1015	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1016	>	sprintf(painCave.errMsg,
1017	>	"Reset time is not divisible by dt.\n"
1018	>	"\tThis will result in integrator resets that are not uniformly\n"
1019	>	"\tdistributed in time.  If this is a problem, change\n"
1020	>	"\tyour resetTime variable.\n");
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	}
1024
1025	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
1025	>	// set the status, sample, and thermal kick times
1026
1027	<	// get some of the tricky things that may still be in the globals
1027	>	for (i = 0; i < nInfo; i++){
1028	>	if (globals->haveSampleTime()){
1029	>	info[i].sampleTime = globals->getSampleTime();
1030	>	info[i].statusTime = info[i].sampleTime;
1031	>	}
1032	>	else{
1033	>	info[i].sampleTime = globals->getRunTime();
1034	>	info[i].statusTime = info[i].sampleTime;
1035	>	}
1036
1037	<	double boxVector[3];
1038	<	if( globals->haveBox() ){
692	<	boxVector[0] = globals->getBox();
693	<	boxVector[1] = globals->getBox();
694	<	boxVector[2] = globals->getBox();
695	<
696	<	info->setBox( boxVector );
697	<	}
698	<	else if( globals->haveDensity() ){
699	<
700	<	double vol;
701	<	vol = (double)tot_nmol / globals->getDensity();
702	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	<	boxVector[1] = boxVector[0];
704	<	boxVector[2] = boxVector[0];
705	<
706	<	info->setBox( boxVector );
707	<	}
708	<	else{
709	<	if( !globals->haveBoxX() ){
710	<	sprintf( painCave.errMsg,
711	<	"SimSetup error, no periodic BoxX size given.\n" );
712	<	painCave.isFatal = 1;
713	<	simError();
1037	>	if (globals->haveStatusTime()){
1038	>	info[i].statusTime = globals->getStatusTime();
1039		}
715	–	boxVector[0] = globals->getBoxX();
1040
1041	<	if( !globals->haveBoxY() ){
1042	<	sprintf( painCave.errMsg,
1043	<	"SimSetup error, no periodic BoxY size given.\n" );
1044	<	painCave.isFatal = 1;
721	<	simError();
1041	>	if (globals->haveThermalTime()){
1042	>	info[i].thermalTime = globals->getThermalTime();
1043	>	} else {
1044	>	info[i].thermalTime = globals->getRunTime();
1045		}
723	–	boxVector[1] = globals->getBoxY();
1046
1047	<	if( !globals->haveBoxZ() ){
1048	<	sprintf( painCave.errMsg,
1049	<	"SimSetup error, no periodic BoxZ size given.\n" );
1050	<	painCave.isFatal = 1;
729	<	simError();
1047	>	info[i].resetIntegrator = 0;
1048	>	if( globals->haveResetTime() ){
1049	>	info[i].resetTime = globals->getResetTime();
1050	>	info[i].resetIntegrator = 1;
1051		}
731	–	boxVector[2] = globals->getBoxZ();
1052
1053	<	info->setBox( boxVector );
1053	>	// check for the temperature set flag
1054	>
1055	>	if (globals->haveTempSet())
1056	>	info[i].setTemp = globals->getTempSet();
1057	>
1058	>	// check for the extended State init
1059	>
1060	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1061	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062	>
1063	>	// check for thermodynamic integration
1064	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067	>	info[i].thermIntLambda = globals->getThermIntLambda();
1068	>	info[i].thermIntK = globals->getThermIntK();
1069	>
1070	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1071	>	info[i].restraint = myRestraint;
1072	>	}
1073	>	else {
1074	>	sprintf(painCave.errMsg,
1075	>	"SimSetup Error:\n"
1076	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1077	>	"\tthermodynamicIntegrationLambda (and/or\n"
1078	>	"\tthermodynamicIntegrationK) was not specified.\n"
1079	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1080	>	painCave.isFatal = 1;
1081	>	simError();
1082	>	}
1083	>	}
1084	>	else if(globals->getUseLiquidThermInt()) {
1085	>	if (globals->getUseSolidThermInt()) {
1086	>	sprintf( painCave.errMsg,
1087	>	"SimSetup Warning: It appears that you have both solid and\n"
1088	>	"\tliquid thermodynamic integration activated in your .bass\n"
1089	>	"\tfile. To avoid confusion, specify only one technique in\n"
1090	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1091	>	"\twill be assumed for the current simulation. If this is not\n"
1092	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1093	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094	>	painCave.isFatal = 0;
1095	>	simError();
1096	>	}
1097	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099	>	info[i].thermIntLambda = globals->getThermIntLambda();
1100	>	info[i].thermIntK = globals->getThermIntK();
1101	>	}
1102	>	else {
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup Error:\n"
1105	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1106	>	"\tthermodynamicIntegrationLambda (and/or\n"
1107	>	"\tthermodynamicIntegrationK) was not specified.\n"
1108	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111	>	}
1112	>	}
1113	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1116	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117	>	"\t'true' in your .bass file.  These keywords are set to\n"
1118	>	"\t'false' by default, so your lambda and/or k values are\n"
1119	>	"\tbeing ignored.\n");
1120	>	painCave.isFatal = 0;
1121	>	simError();
1122	>	}
1123		}
1124	+
1125	+	//setup seed for random number generator
1126	+	int seedValue;
1127
1128	+	if (globals->haveSeed()){
1129	+	seedValue = globals->getSeed();
1130
1131	+	if(seedValue / 1E9 == 0){
1132	+	sprintf(painCave.errMsg,
1133	+	"Seed for sprng library should contain at least 9 digits\n"
1134	+	"OOPSE will generate a seed for user\n");
1135	+	painCave.isFatal = 0;
1136	+	simError();
1137	+
1138	+	//using seed generated by system instead of invalid seed set by user
1139	+	#ifndef IS_MPI
1140	+	seedValue = make_sprng_seed();
1141	+	#else
1142	+	if (worldRank == 0){
1143	+	seedValue = make_sprng_seed();
1144	+	}
1145	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1146	+	#endif
1147	+	}
1148	+	}//end of if branch of globals->haveSeed()
1149	+	else{
1150
1151	+	#ifndef IS_MPI
1152	+	seedValue = make_sprng_seed();
1153	+	#else
1154	+	if (worldRank == 0){
1155	+	seedValue = make_sprng_seed();
1156	+	}
1157	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1158	+	#endif
1159	+	}//end of globals->haveSeed()
1160	+
1161	+	for (int i = 0; i < nInfo; i++){
1162	+	info[i].setSeed(seedValue);
1163	+	}
1164	+
1165		#ifdef IS_MPI
1166	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1166	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1167		MPIcheckPoint();
1168		#endif // is_mpi
742	–
1169		}
1170
1171
1172	<	void SimSetup::finalInfoCheck( void ){
1172	>	void SimSetup::finalInfoCheck(void){
1173		int index;
1174		int usesDipoles;
1175	<
1175	>	int usesCharges;
1176	>	int i;
1177
1178	<	// check electrostatic parameters
1179	<
1180	<	index = 0;
1181	<	usesDipoles = 0;
1182	<	while( (index < info->n_atoms) && !usesDipoles ){
1183	<	usesDipoles = ((info->atoms)[index])->hasDipole();
1184	<	index++;
1185	<	}
1186	<
1178	>	for (i = 0; i < nInfo; i++){
1179	>	// check electrostatic parameters
1180	>
1181	>	index = 0;
1182	>	usesDipoles = 0;
1183	>	while ((index < info[i].n_atoms) && !usesDipoles){
1184	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1185	>	index++;
1186	>	}
1187	>	index = 0;
1188	>	usesCharges = 0;
1189	>	while ((index < info[i].n_atoms) && !usesCharges){
1190	>	usesCharges= (info[i].atoms[index])->hasCharge();
1191	>	index++;
1192	>	}
1193		#ifdef IS_MPI
1194	<	int myUse = usesDipoles;
1195	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1194	>	int myUse = usesDipoles;
1195	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1196		#endif //is_mpi
1197
1198	<	double theEcr, theEst;
1198	>	double theRcut, theRsw;
1199
1200	<	if (globals->getUseRF() ) {
1201	<	info->useReactionField = 1;
769	<
770	<	if( !globals->haveECR() ){
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup Warning: using default value of 1/2 the smallest "
773	<	"box length for the electrostaticCutoffRadius.\n"
774	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
784	<	}
1200	>	if (globals->haveRcut()) {
1201	>	theRcut = globals->getRcut();
1202
1203	<	if( !globals->haveEST() ){
1204	<	sprintf( painCave.errMsg,
1205	<	"SimSetup Warning: using default value of 0.05 * the "
1206	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1207	<	);
1208	<	painCave.isFatal = 0;
1209	<	simError();
793	<	theEst = 0.05 * theEcr;
1203	>	if (globals->haveRsw())
1204	>	theRsw = globals->getRsw();
1205	>	else
1206	>	theRsw = theRcut;
1207	>
1208	>	info[i].setDefaultRcut(theRcut, theRsw);
1209	>
1210		} else {
1211	<	theEst= globals->getEST();
1212	<	}
1211	>
1212	>	the_ff->calcRcut();
1213	>	theRcut = info[i].getRcut();
1214
1215	<	info->setEcr( theEcr, theEst );
1216	<
1217	<	if(!globals->haveDielectric() ){
1218	<	sprintf( painCave.errMsg,
1219	<	"SimSetup Error: You are trying to use Reaction Field without"
1220	<	"setting a dielectric constant!\n"
804	<	);
805	<	painCave.isFatal = 1;
806	<	simError();
1215	>	if (globals->haveRsw())
1216	>	theRsw = globals->getRsw();
1217	>	else
1218	>	theRsw = theRcut;
1219	>
1220	>	info[i].setDefaultRcut(theRcut, theRsw);
1221		}
1222	<	info->dielectric = globals->getDielectric();
1223	<	}
1224	<	else {
811	<	if (usesDipoles) {
1222	>
1223	>	if (globals->getUseRF()){
1224	>	info[i].useReactionField = 1;
1225
1226	<	if( !globals->haveECR() ){
1227	<	sprintf( painCave.errMsg,
1228	<	"SimSetup Warning: using default value of 1/2 the smallest "
1229	<	"box length for the electrostaticCutoffRadius.\n"
1230	<	"I hope you have a very fast processor!\n");
1231	<	painCave.isFatal = 0;
1232	<	simError();
1233	<	double smallest;
821	<	smallest = info->boxL[0];
822	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
1226	>	if (!globals->haveRcut()){
1227	>	sprintf(painCave.errMsg,
1228	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	>	"\tOOPSE will use a default value of 15.0 angstroms"
1230	>	"\tfor the cutoffRadius.\n");
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	theRcut = 15.0;
1234		}
1235	<
1236	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the "
833	<	"electrostaticSkinThickness\n"
834	<	);
835	<	painCave.isFatal = 0;
836	<	simError();
837	<	theEst = 0.05 * theEcr;
838	<	} else {
839	<	theEst= globals->getEST();
1235	>	else{
1236	>	theRcut = globals->getRcut();
1237		}
1238
1239	<	info->setEcr( theEcr, theEst );
1239	>	if (!globals->haveRsw()){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	>	"\tOOPSE will use a default value of\n"
1243	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	>	painCave.isFatal = 0;
1245	>	simError();
1246	>	theRsw = 0.95 * theRcut;
1247	>	}
1248	>	else{
1249	>	theRsw = globals->getRsw();
1250	>	}
1251	>
1252	>	info[i].setDefaultRcut(theRcut, theRsw);
1253	>
1254	>	if (!globals->haveDielectric()){
1255	>	sprintf(painCave.errMsg,
1256	>	"SimSetup Error: No Dielectric constant was set.\n"
1257	>	"\tYou are trying to use Reaction Field without"
1258	>	"\tsetting a dielectric constant!\n");
1259	>	painCave.isFatal = 1;
1260	>	simError();
1261	>	}
1262	>	info[i].dielectric = globals->getDielectric();
1263		}
1264	<	}
1264	>	else{
1265	>	if (usesDipoles || usesCharges){
1266
1267	+	if (!globals->haveRcut()){
1268	+	sprintf(painCave.errMsg,
1269	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1270	+	"\tOOPSE will use a default value of 15.0 angstroms"
1271	+	"\tfor the cutoffRadius.\n");
1272	+	painCave.isFatal = 0;
1273	+	simError();
1274	+	theRcut = 15.0;
1275	+	}
1276	+	else{
1277	+	theRcut = globals->getRcut();
1278	+	}
1279	+
1280	+	if (!globals->haveRsw()){
1281	+	sprintf(painCave.errMsg,
1282	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1283	+	"\tOOPSE will use a default value of\n"
1284	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1285	+	painCave.isFatal = 0;
1286	+	simError();
1287	+	theRsw = 0.95 * theRcut;
1288	+	}
1289	+	else{
1290	+	theRsw = globals->getRsw();
1291	+	}
1292	+
1293	+	info[i].setDefaultRcut(theRcut, theRsw);
1294	+
1295	+	}
1296	+	}
1297	+	}
1298		#ifdef IS_MPI
1299	<	strcpy( checkPointMsg, "post processing checks out" );
1299	>	strcpy(checkPointMsg, "post processing checks out");
1300		MPIcheckPoint();
1301		#endif // is_mpi
1302
1303	+	// clean up the forcefield
1304	+	the_ff->cleanMe();
1305		}
1306	+
1307	+	void SimSetup::initSystemCoords(void){
1308	+	int i;
1309
1310	<	void SimSetup::initSystemCoords( void ){
1310	>	char* inName;
1311
1312	<	if( globals->haveInitialConfig() ){
1313	<
1314	<	InitializeFromFile* fileInit;
1312	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1313	>
1314	>	for (i = 0; i < info[0].n_atoms; i++)
1315	>	info[0].atoms[i]->setCoords();
1316	>
1317	>	if (globals->haveInitialConfig()){
1318	>	InitializeFromFile* fileInit;
1319		#ifdef IS_MPI // is_mpi
1320	<	if( worldRank == 0 ){
1320	>	if (worldRank == 0){
1321		#endif //is_mpi
1322	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1322	>	inName = globals->getInitialConfig();
1323	>	fileInit = new InitializeFromFile(inName);
1324		#ifdef IS_MPI
1325	<	}else fileInit = new InitializeFromFile( NULL );
1325	>	}
1326	>	else
1327	>	fileInit = new InitializeFromFile(NULL);
1328		#endif
1329	<	fileInit->read_xyz( info ); // default velocities on
1329	>	fileInit->readInit(info); // default velocities on
1330
1331	<	delete fileInit;
1332	<	}
1333	<	else{
1331	>	delete fileInit;
1332	>	}
1333	>	else{
1334	>
1335	>	// no init from bass
1336	>
1337	>	sprintf(painCave.errMsg,
1338	>	"Cannot intialize a simulation without an initial configuration file.\n");
1339	>	painCave.isFatal = 1;;
1340	>	simError();
1341	>
1342	>	}
1343
871	–	#ifdef IS_MPI
872	–
873	–	// no init from bass
874	–
875	–	sprintf( painCave.errMsg,
876	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	–	painCave.isFatal;
878	–	simError();
879	–
880	–	#else
881	–
882	–	initFromBass();
883	–
884	–
885	–	#endif
886	–	}
887	–
1344		#ifdef IS_MPI
1345	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1345	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1346		MPIcheckPoint();
1347		#endif // is_mpi
892	–
1348		}
1349
1350
1351	<	void SimSetup::makeOutNames( void ){
1351	>	void SimSetup::makeOutNames(void){
1352	>	int k;
1353
1354	+
1355	+	for (k = 0; k < nInfo; k++){
1356		#ifdef IS_MPI
1357	<	if( worldRank == 0 ){
1357	>	if (worldRank == 0){
1358		#endif // is_mpi
1359	<
1360	<	if( globals->haveFinalConfig() ){
1361	<	strcpy( info->finalName, globals->getFinalConfig() );
1362	<	}
1363	<	else{
1364	<	strcpy( info->finalName, inFileName );
1359	>
1360	>	if (globals->haveFinalConfig()){
1361	>	strcpy(info[k].finalName, globals->getFinalConfig());
1362	>	}
1363	>	else{
1364	>	strcpy(info[k].finalName, inFileName);
1365	>	char* endTest;
1366	>	int nameLength = strlen(info[k].finalName);
1367	>	endTest = &(info[k].finalName[nameLength - 5]);
1368	>	if (!strcmp(endTest, ".bass")){
1369	>	strcpy(endTest, ".eor");
1370	>	}
1371	>	else if (!strcmp(endTest, ".BASS")){
1372	>	strcpy(endTest, ".eor");
1373	>	}
1374	>	else{
1375	>	endTest = &(info[k].finalName[nameLength - 4]);
1376	>	if (!strcmp(endTest, ".bss")){
1377	>	strcpy(endTest, ".eor");
1378	>	}
1379	>	else if (!strcmp(endTest, ".mdl")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else{
1383	>	strcat(info[k].finalName, ".eor");
1384	>	}
1385	>	}
1386	>	}
1387	>
1388	>	// make the sample and status out names
1389	>
1390	>	strcpy(info[k].sampleName, inFileName);
1391		char* endTest;
1392	<	int nameLength = strlen( info->finalName );
1393	<	endTest = &(info->finalName[nameLength - 5]);
1394	<	if( !strcmp( endTest, ".bass" ) ){
1395	<	strcpy( endTest, ".eor" );
1392	>	int nameLength = strlen(info[k].sampleName);
1393	>	endTest = &(info[k].sampleName[nameLength - 5]);
1394	>	if (!strcmp(endTest, ".bass")){
1395	>	strcpy(endTest, ".dump");
1396		}
1397	<	else if( !strcmp( endTest, ".BASS" ) ){
1398	<	strcpy( endTest, ".eor" );
1397	>	else if (!strcmp(endTest, ".BASS")){
1398	>	strcpy(endTest, ".dump");
1399		}
1400		else{
1401	<	endTest = &(info->finalName[nameLength - 4]);
1402	<	if( !strcmp( endTest, ".bss" ) ){
1403	<	strcpy( endTest, ".eor" );
1404	<	}
1405	<	else if( !strcmp( endTest, ".mdl" ) ){
1406	<	strcpy( endTest, ".eor" );
1407	<	}
1408	<	else{
1409	<	strcat( info->finalName, ".eor" );
1410	<	}
1401	>	endTest = &(info[k].sampleName[nameLength - 4]);
1402	>	if (!strcmp(endTest, ".bss")){
1403	>	strcpy(endTest, ".dump");
1404	>	}
1405	>	else if (!strcmp(endTest, ".mdl")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else{
1409	>	strcat(info[k].sampleName, ".dump");
1410	>	}
1411		}
1412	<	}
1413	<
1414	<	// make the sample and status out names
1415	<
1416	<	strcpy( info->sampleName, inFileName );
1417	<	char* endTest;
934	<	int nameLength = strlen( info->sampleName );
935	<	endTest = &(info->sampleName[nameLength - 5]);
936	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
945	<	strcpy( endTest, ".dump" );
1412	>
1413	>	strcpy(info[k].statusName, inFileName);
1414	>	nameLength = strlen(info[k].statusName);
1415	>	endTest = &(info[k].statusName[nameLength - 5]);
1416	>	if (!strcmp(endTest, ".bass")){
1417	>	strcpy(endTest, ".stat");
1418		}
1419	<	else if( !strcmp( endTest, ".mdl" ) ){
1420	<	strcpy( endTest, ".dump" );
1419	>	else if (!strcmp(endTest, ".BASS")){
1420	>	strcpy(endTest, ".stat");
1421		}
1422		else{
1423	<	strcat( info->sampleName, ".dump" );
1423	>	endTest = &(info[k].statusName[nameLength - 4]);
1424	>	if (!strcmp(endTest, ".bss")){
1425	>	strcpy(endTest, ".stat");
1426	>	}
1427	>	else if (!strcmp(endTest, ".mdl")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else{
1431	>	strcat(info[k].statusName, ".stat");
1432	>	}
1433		}
1434	<	}
1435	<
1436	<	strcpy( info->statusName, inFileName );
1437	<	nameLength = strlen( info->statusName );
1438	<	endTest = &(info->statusName[nameLength - 5]);
1439	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".stat" );
1434	>
1435	>	strcpy(info[k].rawPotName, inFileName);
1436	>	nameLength = strlen(info[k].rawPotName);
1437	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1438	>	if (!strcmp(endTest, ".bass")){
1439	>	strcpy(endTest, ".raw");
1440		}
1441	<	else if( !strcmp( endTest, ".mdl" ) ){
1442	<	strcpy( endTest, ".stat" );
1441	>	else if (!strcmp(endTest, ".BASS")){
1442	>	strcpy(endTest, ".raw");
1443		}
1444		else{
1445	<	strcat( info->statusName, ".stat" );
1445	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1446	>	if (!strcmp(endTest, ".bss")){
1447	>	strcpy(endTest, ".raw");
1448	>	}
1449	>	else if (!strcmp(endTest, ".mdl")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else{
1453	>	strcat(info[k].rawPotName, ".raw");
1454	>	}
1455		}
1456	<	}
976	<
1456	>
1457		#ifdef IS_MPI
978	–	}
979	–	#endif // is_mpi
1458
1459	+	}
1460	+	#endif // is_mpi
1461	+	}
1462		}
1463
1464
1465	<	void SimSetup::sysObjectsCreation( void ){
1465	>	void SimSetup::sysObjectsCreation(void){
1466	>	int i, k;
1467
986	–	int i;
987	–
1468		// create the forceField
1469
1470		createFF();
#	Line 999 | Line 1479 | void SimSetup::sysObjectsCreation( void ){
1479
1480		#ifdef IS_MPI
1481		// divide the molecules among the processors
1482	<
1482	>
1483		mpiMolDivide();
1484		#endif //is_mpi
1485	<
1485	>
1486		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1487	<
1487	>
1488		makeSysArrays();
1489
1490		// make and initialize the molecules (all but atomic coordinates)
1491	<
1491	>
1492		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1017	–
1493
1494	<
1494	>	for (k = 0; k < nInfo; k++){
1495	>	info[k].identArray = new int[info[k].n_atoms];
1496	>	for (i = 0; i < info[k].n_atoms; i++){
1497	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1498	>	}
1499	>	}
1500		}
1501
1502
1503	<	void SimSetup::createFF( void ){
1503	>	void SimSetup::createFF(void){
1504	>	switch (ffCase){
1505	>	case FF_DUFF:
1506	>	the_ff = new DUFF();
1507	>	break;
1508
1509	<	switch( ffCase ){
1509	>	case FF_LJ:
1510	>	the_ff = new LJFF();
1511	>	break;
1512
1513	<	case FF_DUFF:
1514	<	the_ff = new DUFF();
1515	<	break;
1513	>	case FF_EAM:
1514	>	the_ff = new EAM_FF();
1515	>	break;
1516
1517	<	case FF_LJ:
1518	<	the_ff = new LJFF();
1519	<	break;
1517	>	case FF_H2O:
1518	>	the_ff = new WATER();
1519	>	break;
1520
1521	<	default:
1522	<	sprintf( painCave.errMsg,
1523	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1524	<	painCave.isFatal = 1;
1525	<	simError();
1521	>	default:
1522	>	sprintf(painCave.errMsg,
1523	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1524	>	painCave.isFatal = 1;
1525	>	simError();
1526		}
1527
1528		#ifdef IS_MPI
1529	<	strcpy( checkPointMsg, "ForceField creation successful" );
1529	>	strcpy(checkPointMsg, "ForceField creation successful");
1530		MPIcheckPoint();
1531		#endif // is_mpi
1046	–
1532		}
1533
1534
1535	<	void SimSetup::compList( void ){
1051	<
1535	>	void SimSetup::compList(void){
1536		int i;
1537	+	char* id;
1538	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1539	+	LinkedMolStamp* currentStamp = NULL;
1540	+	comp_stamps = new MoleculeStamp * [n_components];
1541	+	bool haveCutoffGroups;
1542
1543	<	comp_stamps = new MoleculeStamp*[n_components];
1544	<
1543	>	haveCutoffGroups = false;
1544	>
1545		// make an array of molecule stamps that match the components used.
1546		// also extract the used stamps out into a separate linked list
1547
1548	<	info->nComponents = n_components;
1549	<	info->componentsNmol = components_nmol;
1550	<	info->compStamps = comp_stamps;
1551	<	info->headStamp = new LinkedMolStamp();
1552	<
1553	<	char* id;
1065	<	LinkedMolStamp* headStamp = info->headStamp;
1066	<	LinkedMolStamp* currentStamp = NULL;
1067	<	for( i=0; i<n_components; i++ ){
1548	>	for (i = 0; i < nInfo; i++){
1549	>	info[i].nComponents = n_components;
1550	>	info[i].componentsNmol = components_nmol;
1551	>	info[i].compStamps = comp_stamps;
1552	>	info[i].headStamp = headStamp;
1553	>	}
1554
1555	+
1556	+	for (i = 0; i < n_components; i++){
1557		id = the_components[i]->getType();
1558		comp_stamps[i] = NULL;
1559	<
1559	>
1560		// check to make sure the component isn't already in the list
1561
1562	<	comp_stamps[i] = headStamp->match( id );
1563	<	if( comp_stamps[i] == NULL ){
1076	<
1562	>	comp_stamps[i] = headStamp->match(id);
1563	>	if (comp_stamps[i] == NULL){
1564		// extract the component from the list;
1565	<
1566	<	currentStamp = stamps->extractMolStamp( id );
1567	<	if( currentStamp == NULL ){
1568	<	sprintf( painCave.errMsg,
1569	<	"SimSetup error: Component \"%s\" was not found in the "
1570	<	"list of declared molecules\n",
1571	<	id );
1572	<	painCave.isFatal = 1;
1573	<	simError();
1565	>
1566	>	currentStamp = stamps->extractMolStamp(id);
1567	>	if (currentStamp == NULL){
1568	>	sprintf(painCave.errMsg,
1569	>	"SimSetup error: Component \"%s\" was not found in the "
1570	>	"list of declared molecules\n",
1571	>	id);
1572	>	painCave.isFatal = 1;
1573	>	simError();
1574		}
1575	<
1576	<	headStamp->add( currentStamp );
1577	<	comp_stamps[i] = headStamp->match( id );
1575	>
1576	>	headStamp->add(currentStamp);
1577	>	comp_stamps[i] = headStamp->match(id);
1578		}
1579	+
1580	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1581	+	haveCutoffGroups = true;
1582		}
1583	+
1584	+	for (i = 0; i < nInfo; i++)
1585	+	info[i].haveCutoffGroups = haveCutoffGroups;
1586
1587		#ifdef IS_MPI
1588	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1588	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1589		MPIcheckPoint();
1590		#endif // is_mpi
1098	–
1099	–
1591		}
1592
1593	<	void SimSetup::calcSysValues( void ){
1594	<	int i, j, k;
1593	>	void SimSetup::calcSysValues(void){
1594	>	int i, j;
1595	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1596
1597	+	int* molMembershipArray;
1598	+	CutoffGroupStamp* cg;
1599
1600		tot_atoms = 0;
1601		tot_bonds = 0;
1602		tot_bends = 0;
1603		tot_torsions = 0;
1604	<	for( i=0; i<n_components; i++ ){
1605	<
1606	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1607	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1608	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1604	>	tot_rigid = 0;
1605	>	tot_groups = 0;
1606	>	for (i = 0; i < n_components; i++){
1607	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1608	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1609	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1610		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1611	<	}
1611	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1612
1613	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1614	+	atomsingroups = 0;
1615	+	for (j=0; j < ncutgroups; j++) {
1616	+	cg = comp_stamps[i]->getCutoffGroup(j);
1617	+	atomsingroups += cg->getNMembers();
1618	+	}
1619	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1620	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1621	+	}
1622	+
1623		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1624	+	molMembershipArray = new int[tot_atoms];
1625
1626	<	info->n_atoms = tot_atoms;
1627	<	info->n_bonds = tot_bonds;
1628	<	info->n_bends = tot_bends;
1629	<	info->n_torsions = tot_torsions;
1630	<	info->n_SRI = tot_SRI;
1631	<	info->n_mol = tot_nmol;
1632	<
1633	<	info->molMembershipArray = new int[tot_atoms];
1626	>	for (i = 0; i < nInfo; i++){
1627	>	info[i].n_atoms = tot_atoms;
1628	>	info[i].n_bonds = tot_bonds;
1629	>	info[i].n_bends = tot_bends;
1630	>	info[i].n_torsions = tot_torsions;
1631	>	info[i].n_SRI = tot_SRI;
1632	>	info[i].n_mol = tot_nmol;
1633	>	info[i].ngroup = tot_groups;
1634	>	info[i].molMembershipArray = molMembershipArray;
1635	>	}
1636		}
1637
1130	–
1638		#ifdef IS_MPI
1639
1640	<	void SimSetup::mpiMolDivide( void ){
1134	<
1640	>	void SimSetup::mpiMolDivide(void){
1641		int i, j, k;
1642		int localMol, allMol;
1643		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1644	+	int local_rigid, local_groups;
1645	+	vector<int> globalMolIndex;
1646	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1647	+	CutoffGroupStamp* cg;
1648
1649	<	mpiSim = new mpiSimulation( info );
1140	<
1141	<	globalIndex = mpiSim->divideLabor();
1649	>	mpiSim = new mpiSimulation(info);
1650
1651	+	mpiSim->divideLabor();
1652	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1655	+
1656		// set up the local variables
1657	<
1657	>
1658		mol2proc = mpiSim->getMolToProcMap();
1659		molCompType = mpiSim->getMolComponentType();
1660	<
1660	>
1661		allMol = 0;
1662		localMol = 0;
1663		local_atoms = 0;
1664		local_bonds = 0;
1665		local_bends = 0;
1666		local_torsions = 0;
1667	<	globalAtomIndex = 0;
1667	>	local_rigid = 0;
1668	>	local_groups = 0;
1669	>	globalAtomCounter = 0;
1670
1671	+	for (i = 0; i < n_components; i++){
1672	+	for (j = 0; j < components_nmol[i]; j++){
1673	+	if (mol2proc[allMol] == worldRank){
1674	+	local_atoms += comp_stamps[i]->getNAtoms();
1675	+	local_bonds += comp_stamps[i]->getNBonds();
1676	+	local_bends += comp_stamps[i]->getNBends();
1677	+	local_torsions += comp_stamps[i]->getNTorsions();
1678	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1679
1680	<	for( i=0; i<n_components; i++ ){
1680	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1681	>	atomsingroups = 0;
1682	>	for (k=0; k < ncutgroups; k++) {
1683	>	cg = comp_stamps[i]->getCutoffGroup(k);
1684	>	atomsingroups += cg->getNMembers();
1685	>	}
1686	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1687	>	ncutgroups;
1688	>	local_groups += ngroupsinstamp;
1689
1690	<	for( j=0; j<components_nmol[i]; j++ ){
1160	<
1161	<	if( mol2proc[allMol] == worldRank ){
1162	<
1163	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1164	<	local_bonds +=    comp_stamps[i]->getNBonds();
1165	<	local_bends +=    comp_stamps[i]->getNBends();
1166	<	local_torsions += comp_stamps[i]->getNTorsions();
1167	<	localMol++;
1690	>	localMol++;
1691		}
1692	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1693	<	info->molMembershipArray[globalAtomIndex] = allMol;
1694	<	globalAtomIndex++;
1692	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1693	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1694	>	globalAtomCounter++;
1695		}
1696
1697	<	allMol++;
1697	>	allMol++;
1698		}
1699		}
1700		local_SRI = local_bonds + local_bends + local_torsions;
1701	+
1702	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1703
1704	<	info->n_atoms = mpiSim->getMyNlocal();
1705	<
1706	<	if( local_atoms != info->n_atoms ){
1707	<	sprintf( painCave.errMsg,
1708	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1184	<	" localAtom (%d) are not equal.\n",
1185	<	info->n_atoms,
1186	<	local_atoms );
1704	>	if (local_atoms != info[0].n_atoms){
1705	>	sprintf(painCave.errMsg,
1706	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1707	>	"\tlocalAtom (%d) are not equal.\n",
1708	>	info[0].n_atoms, local_atoms);
1709		painCave.isFatal = 1;
1710		simError();
1711		}
1712
1713	<	info->n_bonds = local_bonds;
1714	<	info->n_bends = local_bends;
1715	<	info->n_torsions = local_torsions;
1716	<	info->n_SRI = local_SRI;
1717	<	info->n_mol = localMol;
1713	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1714	>	if (local_groups != info[0].ngroup){
1715	>	sprintf(painCave.errMsg,
1716	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1717	>	"\tlocalGroups (%d) are not equal.\n",
1718	>	info[0].ngroup, local_groups);
1719	>	painCave.isFatal = 1;
1720	>	simError();
1721	>	}
1722	>
1723	>	info[0].n_bonds = local_bonds;
1724	>	info[0].n_bends = local_bends;
1725	>	info[0].n_torsions = local_torsions;
1726	>	info[0].n_SRI = local_SRI;
1727	>	info[0].n_mol = localMol;
1728
1729	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1729	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1730		MPIcheckPoint();
1731		}
1732	<
1732	>
1733		#endif // is_mpi
1734
1735
1736	<	void SimSetup::makeSysArrays( void ){
1737	<	int i, j, k;
1736	>	void SimSetup::makeSysArrays(void){
1737	>
1738	>	#ifndef IS_MPI
1739	>	int k, j;
1740	>	#endif // is_mpi
1741	>	int i, l;
1742
1743	+	Atom** the_atoms;
1744	+	Molecule* the_molecules;
1745
1746	<	// create the atom and short range interaction arrays
1746	>	for (l = 0; l < nInfo; l++){
1747	>	// create the atom and short range interaction arrays
1748
1749	<	Atom::createArrays(info->n_atoms);
1750	<	the_atoms = new Atom*[info->n_atoms];
1751	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1749	>	the_atoms = new Atom * [info[l].n_atoms];
1750	>	the_molecules = new Molecule[info[l].n_mol];
1751	>	int molIndex;
1752
1753	<	// initialize the molecule's stampID's
1753	>	// initialize the molecule's stampID's
1754
1755		#ifdef IS_MPI
1218	–
1756
1757	<	molIndex = 0;
1758	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1759	<
1760	<	if(mol2proc[i] == worldRank ){
1761	<	the_molecules[molIndex].setStampID( molCompType[i] );
1762	<	the_molecules[molIndex].setMyIndex( molIndex );
1763	<	the_molecules[molIndex].setGlobalIndex( i );
1764	<	molIndex++;
1757	>
1758	>	molIndex = 0;
1759	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1760	>	if (mol2proc[i] == worldRank){
1761	>	the_molecules[molIndex].setStampID(molCompType[i]);
1762	>	the_molecules[molIndex].setMyIndex(molIndex);
1763	>	the_molecules[molIndex].setGlobalIndex(i);
1764	>	molIndex++;
1765	>	}
1766		}
1229	–	}
1767
1768		#else // is_mpi
1769	<
1770	<	molIndex = 0;
1771	<	globalAtomIndex = 0;
1772	<	for(i=0; i<n_components; i++){
1773	<	for(j=0; j<components_nmol[i]; j++ ){
1774	<	the_molecules[molIndex].setStampID( i );
1775	<	the_molecules[molIndex].setMyIndex( molIndex );
1776	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1777	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1778	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1779	<	globalAtomIndex++;
1769	>
1770	>	molIndex = 0;
1771	>	globalAtomCounter = 0;
1772	>	for (i = 0; i < n_components; i++){
1773	>	for (j = 0; j < components_nmol[i]; j++){
1774	>	the_molecules[molIndex].setStampID(i);
1775	>	the_molecules[molIndex].setMyIndex(molIndex);
1776	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1777	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1778	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1779	>	globalAtomCounter++;
1780	>	}
1781	>	molIndex++;
1782		}
1244	–	molIndex++;
1783		}
1246	–	}
1247	–
1784
1785	+
1786		#endif // is_mpi
1787
1788	<
1789	<	if( info->n_SRI ){
1788	>	info[l].globalExcludes = new int;
1789	>	info[l].globalExcludes[0] = 0;
1790
1791	<	Exclude::createArray(info->n_SRI);
1792	<	the_excludes = new Exclude*[info->n_SRI];
1793	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1794	<	info->globalExcludes = new int;
1795	<	info->n_exclude = info->n_SRI;
1259	<	}
1260	<	else{
1791	>	// set the arrays into the SimInfo object
1792	>
1793	>	info[l].atoms = the_atoms;
1794	>	info[l].molecules = the_molecules;
1795	>	info[l].nGlobalExcludes = 0;
1796
1797	<	Exclude::createArray( 1 );
1263	<	the_excludes = new Exclude*;
1264	<	the_excludes[0] = new Exclude(0);
1265	<	the_excludes[0]->setPair( 0,0 );
1266	<	info->globalExcludes = new int;
1267	<	info->globalExcludes[0] = 0;
1268	<	info->n_exclude = 0;
1797	>	the_ff->setSimInfo(info);
1798		}
1799	+	}
1800
1801	<	// set the arrays into the SimInfo object
1801	>	void SimSetup::makeIntegrator(void){
1802	>	int k;
1803
1804	<	info->atoms = the_atoms;
1805	<	info->molecules = the_molecules;
1806	<	info->nGlobalExcludes = 0;
1807	<	info->excludes = the_excludes;
1804	>	NVE<RealIntegrator>* myNVE = NULL;
1805	>	NVT<RealIntegrator>* myNVT = NULL;
1806	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1807	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1808	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1809	>
1810	>	for (k = 0; k < nInfo; k++){
1811	>	switch (ensembleCase){
1812	>	case NVE_ENS:
1813	>	if (globals->haveZconstraints()){
1814	>	setupZConstraint(info[k]);
1815	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1816	>	}
1817	>	else{
1818	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1819	>	}
1820	>
1821	>	info->the_integrator = myNVE;
1822	>	break;
1823
1824	<	the_ff->setSimInfo( info );
1824	>	case NVT_ENS:
1825	>	if (globals->haveZconstraints()){
1826	>	setupZConstraint(info[k]);
1827	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1828	>	}
1829	>	else
1830	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1831
1832	<	}
1832	>	myNVT->setTargetTemp(globals->getTargetTemp());
1833
1834	<	void SimSetup::makeIntegrator( void ){
1834	>	if (globals->haveTauThermostat())
1835	>	myNVT->setTauThermostat(globals->getTauThermostat());
1836	>	else{
1837	>	sprintf(painCave.errMsg,
1838	>	"SimSetup error: If you use the NVT\n"
1839	>	"\tensemble, you must set tauThermostat.\n");
1840	>	painCave.isFatal = 1;
1841	>	simError();
1842	>	}
1843
1844	<	NVT*  myNVT = NULL;
1845	<	NPTi* myNPTi = NULL;
1286	<	NPTf* myNPTf = NULL;
1287	<	NPTim* myNPTim = NULL;
1288	<	NPTfm* myNPTfm = NULL;
1844	>	info->the_integrator = myNVT;
1845	>	break;
1846
1847	<	switch( ensembleCase ){
1847	>	case NPTi_ENS:
1848	>	if (globals->haveZconstraints()){
1849	>	setupZConstraint(info[k]);
1850	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1851	>	}
1852	>	else
1853	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1854
1855	<	case NVE_ENS:
1293	<	new NVE( info, the_ff );
1294	<	break;
1855	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1856
1857	<	case NVT_ENS:
1858	<	myNVT = new NVT( info, the_ff );
1859	<	myNVT->setTargetTemp(globals->getTargetTemp());
1857	>	if (globals->haveTargetPressure())
1858	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1859	>	else{
1860	>	sprintf(painCave.errMsg,
1861	>	"SimSetup error: If you use a constant pressure\n"
1862	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1863	>	painCave.isFatal = 1;
1864	>	simError();
1865	>	}
1866
1867	<	if (globals->haveTauThermostat())
1868	<	myNVT->setTauThermostat(globals->getTauThermostat());
1867	>	if (globals->haveTauThermostat())
1868	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1869	>	else{
1870	>	sprintf(painCave.errMsg,
1871	>	"SimSetup error: If you use an NPT\n"
1872	>	"\tensemble, you must set tauThermostat.\n");
1873	>	painCave.isFatal = 1;
1874	>	simError();
1875	>	}
1876
1877	<	else {
1878	<	sprintf( painCave.errMsg,
1879	<	"SimSetup error: If you use the NVT\n"
1880	<	"    ensemble, you must set tauThermostat.\n");
1881	<	painCave.isFatal = 1;
1882	<	simError();
1883	<	}
1884	<	break;
1877	>	if (globals->haveTauBarostat())
1878	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1879	>	else{
1880	>	sprintf(painCave.errMsg,
1881	>	"SimSetup error: If you use an NPT\n"
1882	>	"\tensemble, you must set tauBarostat.\n");
1883	>	painCave.isFatal = 1;
1884	>	simError();
1885	>	}
1886
1887	<	case NPTi_ENS:
1888	<	myNPTi = new NPTi( info, the_ff );
1314	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1887	>	info->the_integrator = myNPTi;
1888	>	break;
1889
1890	<	if (globals->haveTargetPressure())
1891	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1892	<	else {
1893	<	sprintf( painCave.errMsg,
1894	<	"SimSetup error: If you use a constant pressure\n"
1895	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1896	<	painCave.isFatal = 1;
1323	<	simError();
1324	<	}
1325	<
1326	<	if( globals->haveTauThermostat() )
1327	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	<	else{
1329	<	sprintf( painCave.errMsg,
1330	<	"SimSetup error: If you use an NPT\n"
1331	<	"    ensemble, you must set tauThermostat.\n");
1332	<	painCave.isFatal = 1;
1333	<	simError();
1334	<	}
1890	>	case NPTf_ENS:
1891	>	if (globals->haveZconstraints()){
1892	>	setupZConstraint(info[k]);
1893	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1894	>	}
1895	>	else
1896	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1897
1898	<	if( globals->haveTauBarostat() )
1337	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	<	else{
1339	<	sprintf( painCave.errMsg,
1340	<	"SimSetup error: If you use an NPT\n"
1341	<	"    ensemble, you must set tauBarostat.\n");
1342	<	painCave.isFatal = 1;
1343	<	simError();
1344	<	}
1345	<	break;
1898	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1899
1900	<	case NPTf_ENS:
1901	<	myNPTf = new NPTf( info, the_ff );
1902	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1903	<
1904	<	if (globals->haveTargetPressure())
1905	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1906	<	else {
1907	<	sprintf( painCave.errMsg,
1908	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	<	painCave.isFatal = 1;
1358	<	simError();
1359	<	}
1900	>	if (globals->haveTargetPressure())
1901	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1902	>	else{
1903	>	sprintf(painCave.errMsg,
1904	>	"SimSetup error: If you use a constant pressure\n"
1905	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1906	>	painCave.isFatal = 1;
1907	>	simError();
1908	>	}
1909
1910	<	if( globals->haveTauThermostat() )
1911	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1363	<	else{
1364	<	sprintf( painCave.errMsg,
1365	<	"SimSetup error: If you use an NPT\n"
1366	<	"    ensemble, you must set tauThermostat.\n");
1367	<	painCave.isFatal = 1;
1368	<	simError();
1369	<	}
1910	>	if (globals->haveTauThermostat())
1911	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1912
1913	<	if( globals->haveTauBarostat() )
1914	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1915	<	else{
1916	<	sprintf( painCave.errMsg,
1917	<	"SimSetup error: If you use an NPT\n"
1918	<	"    ensemble, you must set tauBarostat.\n");
1919	<	painCave.isFatal = 1;
1378	<	simError();
1379	<	}
1380	<	break;
1381	<
1382	<	case NPTim_ENS:
1383	<	myNPTim = new NPTim( info, the_ff );
1384	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1913	>	else{
1914	>	sprintf(painCave.errMsg,
1915	>	"SimSetup error: If you use an NPT\n"
1916	>	"\tensemble, you must set tauThermostat.\n");
1917	>	painCave.isFatal = 1;
1918	>	simError();
1919	>	}
1920
1921	<	if (globals->haveTargetPressure())
1922	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1388	<	else {
1389	<	sprintf( painCave.errMsg,
1390	<	"SimSetup error: If you use a constant pressure\n"
1391	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1392	<	painCave.isFatal = 1;
1393	<	simError();
1394	<	}
1395	<
1396	<	if( globals->haveTauThermostat() )
1397	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	<	else{
1399	<	sprintf( painCave.errMsg,
1400	<	"SimSetup error: If you use an NPT\n"
1401	<	"    ensemble, you must set tauThermostat.\n");
1402	<	painCave.isFatal = 1;
1403	<	simError();
1404	<	}
1921	>	if (globals->haveTauBarostat())
1922	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1923
1924	<	if( globals->haveTauBarostat() )
1925	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1926	<	else{
1927	<	sprintf( painCave.errMsg,
1928	<	"SimSetup error: If you use an NPT\n"
1929	<	"    ensemble, you must set tauBarostat.\n");
1930	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<	break;
1924	>	else{
1925	>	sprintf(painCave.errMsg,
1926	>	"SimSetup error: If you use an NPT\n"
1927	>	"\tensemble, you must set tauBarostat.\n");
1928	>	painCave.isFatal = 1;
1929	>	simError();
1930	>	}
1931
1932	<	case NPTfm_ENS:
1933	<	myNPTfm = new NPTfm( info, the_ff );
1419	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1932	>	info->the_integrator = myNPTf;
1933	>	break;
1934
1935	<	if (globals->haveTargetPressure())
1936	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1937	<	else {
1938	<	sprintf( painCave.errMsg,
1939	<	"SimSetup error: If you use a constant pressure\n"
1940	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1941	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1430	<
1431	<	if( globals->haveTauThermostat() )
1432	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	<	else{
1434	<	sprintf( painCave.errMsg,
1435	<	"SimSetup error: If you use an NPT\n"
1436	<	"    ensemble, you must set tauThermostat.\n");
1437	<	painCave.isFatal = 1;
1438	<	simError();
1439	<	}
1935	>	case NPTxyz_ENS:
1936	>	if (globals->haveZconstraints()){
1937	>	setupZConstraint(info[k]);
1938	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1939	>	}
1940	>	else
1941	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1942
1943	<	if( globals->haveTauBarostat() )
1442	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	<	else{
1444	<	sprintf( painCave.errMsg,
1445	<	"SimSetup error: If you use an NPT\n"
1446	<	"    ensemble, you must set tauBarostat.\n");
1447	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1450	<	break;
1943	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1944
1945	<	default:
1946	<	sprintf( painCave.errMsg,
1947	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1948	<	painCave.isFatal = 1;
1949	<	simError();
1950	<	}
1945	>	if (globals->haveTargetPressure())
1946	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1947	>	else{
1948	>	sprintf(painCave.errMsg,
1949	>	"SimSetup error: If you use a constant pressure\n"
1950	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1951	>	painCave.isFatal = 1;
1952	>	simError();
1953	>	}
1954
1955	+	if (globals->haveTauThermostat())
1956	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1957	+	else{
1958	+	sprintf(painCave.errMsg,
1959	+	"SimSetup error: If you use an NPT\n"
1960	+	"\tensemble, you must set tauThermostat.\n");
1961	+	painCave.isFatal = 1;
1962	+	simError();
1963	+	}
1964	+
1965	+	if (globals->haveTauBarostat())
1966	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1967	+	else{
1968	+	sprintf(painCave.errMsg,
1969	+	"SimSetup error: If you use an NPT\n"
1970	+	"\tensemble, you must set tauBarostat.\n");
1971	+	painCave.isFatal = 1;
1972	+	simError();
1973	+	}
1974	+
1975	+	info->the_integrator = myNPTxyz;
1976	+	break;
1977	+
1978	+	default:
1979	+	sprintf(painCave.errMsg,
1980	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1981	+	painCave.isFatal = 1;
1982	+	simError();
1983	+	}
1984	+	}
1985		}
1986
1987	<	void SimSetup::initFortran( void ){
1987	>	void SimSetup::initFortran(void){
1988	>	info[0].refreshSim();
1989
1990	<	info->refreshSim();
1991	<
1465	<	if( !strcmp( info->mixingRule, "standard") ){
1466	<	the_ff->initForceField( LB_MIXING_RULE );
1990	>	if (!strcmp(info[0].mixingRule, "standard")){
1991	>	the_ff->initForceField(LB_MIXING_RULE);
1992		}
1993	<	else if( !strcmp( info->mixingRule, "explicit") ){
1994	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1993	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1994	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1995		}
1996		else{
1997	<	sprintf( painCave.errMsg,
1998	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	<	info->mixingRule );
1997	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1998	>	info[0].mixingRule);
1999		painCave.isFatal = 1;
2000		simError();
2001		}
2002
2003
2004		#ifdef IS_MPI
2005	<	strcpy( checkPointMsg,
1482	<	"Successfully intialized the mixingRule for Fortran." );
2005	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2006		MPIcheckPoint();
2007		#endif // is_mpi
2008	+	}
2009
2010	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2011	+	int nZConstraints;
2012	+	ZconStamp** zconStamp;
2013	+
2014	+	if (globals->haveZconstraintTime()){
2015	+	//add sample time of z-constraint  into SimInfo's property list
2016	+	DoubleData* zconsTimeProp = new DoubleData();
2017	+	zconsTimeProp->setID(ZCONSTIME_ID);
2018	+	zconsTimeProp->setData(globals->getZconsTime());
2019	+	theInfo.addProperty(zconsTimeProp);
2020	+	}
2021	+	else{
2022	+	sprintf(painCave.errMsg,
2023	+	"ZConstraint error: If you use a ZConstraint,\n"
2024	+	"\tyou must set zconsTime.\n");
2025	+	painCave.isFatal = 1;
2026	+	simError();
2027	+	}
2028	+
2029	+	//push zconsTol into siminfo, if user does not specify
2030	+	//value for zconsTol, a default value will be used
2031	+	DoubleData* zconsTol = new DoubleData();
2032	+	zconsTol->setID(ZCONSTOL_ID);
2033	+	if (globals->haveZconsTol()){
2034	+	zconsTol->setData(globals->getZconsTol());
2035	+	}
2036	+	else{
2037	+	double defaultZConsTol = 0.01;
2038	+	sprintf(painCave.errMsg,
2039	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2040	+	"\tOOPSE will use a default value of %f.\n"
2041	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2042	+	defaultZConsTol);
2043	+	painCave.isFatal = 0;
2044	+	simError();
2045	+
2046	+	zconsTol->setData(defaultZConsTol);
2047	+	}
2048	+	theInfo.addProperty(zconsTol);
2049	+
2050	+	//set Force Subtraction Policy
2051	+	StringData* zconsForcePolicy = new StringData();
2052	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2053	+
2054	+	if (globals->haveZconsForcePolicy()){
2055	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2056	+	}
2057	+	else{
2058	+	sprintf(painCave.errMsg,
2059	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2060	+	"\tOOPSE will use PolicyByMass.\n"
2061	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2062	+	painCave.isFatal = 0;
2063	+	simError();
2064	+	zconsForcePolicy->setData("BYMASS");
2065	+	}
2066	+
2067	+	theInfo.addProperty(zconsForcePolicy);
2068	+
2069	+	//set zcons gap
2070	+	DoubleData* zconsGap = new DoubleData();
2071	+	zconsGap->setID(ZCONSGAP_ID);
2072	+
2073	+	if (globals->haveZConsGap()){
2074	+	zconsGap->setData(globals->getZconsGap());
2075	+	theInfo.addProperty(zconsGap);
2076	+	}
2077	+
2078	+	//set zcons fixtime
2079	+	DoubleData* zconsFixtime = new DoubleData();
2080	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2081	+
2082	+	if (globals->haveZConsFixTime()){
2083	+	zconsFixtime->setData(globals->getZconsFixtime());
2084	+	theInfo.addProperty(zconsFixtime);
2085	+	}
2086	+
2087	+	//set zconsUsingSMD
2088	+	IntData* zconsUsingSMD = new IntData();
2089	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2090	+
2091	+	if (globals->haveZConsUsingSMD()){
2092	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2093	+	theInfo.addProperty(zconsUsingSMD);
2094	+	}
2095	+
2096	+	//Determine the name of ouput file and add it into SimInfo's property list
2097	+	//Be careful, do not use inFileName, since it is a pointer which
2098	+	//point to a string at master node, and slave nodes do not contain that string
2099	+
2100	+	string zconsOutput(theInfo.finalName);
2101	+
2102	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2103	+
2104	+	StringData* zconsFilename = new StringData();
2105	+	zconsFilename->setID(ZCONSFILENAME_ID);
2106	+	zconsFilename->setData(zconsOutput);
2107	+
2108	+	theInfo.addProperty(zconsFilename);
2109	+
2110	+	//setup index, pos and other parameters of z-constraint molecules
2111	+	nZConstraints = globals->getNzConstraints();
2112	+	theInfo.nZconstraints = nZConstraints;
2113	+
2114	+	zconStamp = globals->getZconStamp();
2115	+	ZConsParaItem tempParaItem;
2116	+
2117	+	ZConsParaData* zconsParaData = new ZConsParaData();
2118	+	zconsParaData->setID(ZCONSPARADATA_ID);
2119	+
2120	+	for (int i = 0; i < nZConstraints; i++){
2121	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2122	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2123	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2124	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2125	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2126	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2127	+	zconsParaData->addItem(tempParaItem);
2128	+	}
2129	+
2130	+	//check the uniqueness of index
2131	+	if(!zconsParaData->isIndexUnique()){
2132	+	sprintf(painCave.errMsg,
2133	+	"ZConstraint Error: molIndex is not unique!\n");
2134	+	painCave.isFatal = 1;
2135	+	simError();
2136	+	}
2137	+
2138	+	//sort the parameters by index of molecules
2139	+	zconsParaData->sortByIndex();
2140	+
2141	+	//push data into siminfo, therefore, we can retrieve later
2142	+	theInfo.addProperty(zconsParaData);
2143		}
2144	+
2145	+	void SimSetup::makeMinimizer(){
2146	+
2147	+	OOPSEMinimizer* myOOPSEMinimizer;
2148	+	MinimizerParameterSet* param;
2149	+	char minimizerName[100];
2150	+
2151	+	for (int i = 0; i < nInfo; i++){
2152	+
2153	+	//prepare parameter set for minimizer
2154	+	param = new MinimizerParameterSet();
2155	+	param->setDefaultParameter();
2156	+
2157	+	if (globals->haveMinimizer()){
2158	+	param->setFTol(globals->getMinFTol());
2159	+	}
2160	+
2161	+	if (globals->haveMinGTol()){
2162	+	param->setGTol(globals->getMinGTol());
2163	+	}
2164	+
2165	+	if (globals->haveMinMaxIter()){
2166	+	param->setMaxIteration(globals->getMinMaxIter());
2167	+	}
2168	+
2169	+	if (globals->haveMinWriteFrq()){
2170	+	param->setMaxIteration(globals->getMinMaxIter());
2171	+	}
2172	+
2173	+	if (globals->haveMinWriteFrq()){
2174	+	param->setWriteFrq(globals->getMinWriteFrq());
2175	+	}
2176	+
2177	+	if (globals->haveMinStepSize()){
2178	+	param->setStepSize(globals->getMinStepSize());
2179	+	}
2180	+
2181	+	if (globals->haveMinLSMaxIter()){
2182	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2183	+	}
2184	+
2185	+	if (globals->haveMinLSTol()){
2186	+	param->setLineSearchTol(globals->getMinLSTol());
2187	+	}
2188	+
2189	+	strcpy(minimizerName, globals->getMinimizer());
2190	+
2191	+	if (!strcasecmp(minimizerName, "CG")){
2192	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2193	+	}
2194	+	else if (!strcasecmp(minimizerName, "SD")){
2195	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2196	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2197	+	}
2198	+	else{
2199	+	sprintf(painCave.errMsg,
2200	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2201	+	painCave.isFatal = 0;
2202	+	simError();
2203	+
2204	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2205	+	}
2206	+	info[i].the_integrator = myOOPSEMinimizer;
2207	+
2208	+	//store the minimizer into simInfo
2209	+	info[i].the_minimizer = myOOPSEMinimizer;
2210	+	info[i].has_minimizer = true;
2211	+	}
2212	+
2213	+	}

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