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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 616 by mmeineke, Tue Jul 15 18:52:16 2003 UTC vs.
Revision 1261 by gezelter, Fri Jun 11 14:14:10 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	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
#	Line 14 | Line 22
22
23		// some defines for ensemble and Forcefield  cases
24
25	<	#define NVE_ENS   0
26	<	#define NVT_ENS   1
27	<	#define NPTi_ENS  2
28	<	#define NPTf_ENS  3
29	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
25	>	#define NVE_ENS        0
26	>	#define NVT_ENS        1
27	>	#define NPTi_ENS       2
28	>	#define NPTf_ENS       3
29	>	#define NPTxyz_ENS     4
30
31
32	<	#define FF_DUFF 0
33	<	#define FF_LJ   1
32	>	#define FF_DUFF  0
33	>	#define FF_LJ    1
34	>	#define FF_EAM   2
35	>	#define FF_H2O   3
36
37	+	using namespace std;
38
39	+	/**
40	+	* Check whether dividend is divisble by divisor or not
41	+	*/
42	+	bool isDivisible(double dividend, double divisor){
43	+	double tolerance = 0.000001;
44	+	double quotient;
45	+	double diff;
46	+	int intQuotient;
47	+
48	+	quotient = dividend / divisor;
49	+
50	+	if (quotient < 0)
51	+	quotient = -quotient;
52	+
53	+	intQuotient = int (quotient + tolerance);
54	+
55	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
56	+
57	+	if (diff <= tolerance)
58	+	return true;
59	+	else
60	+	return false;
61	+	}
62	+
63		SimSetup::SimSetup(){
64	+
65	+	initSuspend = false;
66	+	isInfoArray = 0;
67	+	nInfo = 1;
68	+
69		stamps = new MakeStamps();
70		globals = new Globals();
71	<
71	>
72	>
73		#ifdef IS_MPI
74	<	strcpy( checkPointMsg, "SimSetup creation successful" );
74	>	strcpy(checkPointMsg, "SimSetup creation successful");
75		MPIcheckPoint();
76		#endif // IS_MPI
77		}
#	Line 41 | Line 81 | SimSetup::~SimSetup(){
81		delete globals;
82		}
83
84	<	void SimSetup::parseFile( char* fileName ){
84	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
85	>	info = the_info;
86	>	nInfo = theNinfo;
87	>	isInfoArray = 1;
88	>	initSuspend = true;
89	>	}
90
91	+
92	+	void SimSetup::parseFile(char* fileName){
93		#ifdef IS_MPI
94	<	if( worldRank == 0 ){
94	>	if (worldRank == 0){
95		#endif // is_mpi
96	<
96	>
97		inFileName = fileName;
98	<	set_interface_stamps( stamps, globals );
99	<
98	>	set_interface_stamps(stamps, globals);
99	>
100		#ifdef IS_MPI
101		mpiEventInit();
102		#endif
103
104	<	yacc_BASS( fileName );
104	>	yacc_BASS(fileName);
105
106		#ifdef IS_MPI
107		throwMPIEvent(NULL);
108		}
109	<	else receiveParse();
109	>	else{
110	>	receiveParse();
111	>	}
112		#endif
113
114		}
115
116		#ifdef IS_MPI
117		void SimSetup::receiveParse(void){
118	<
119	<	set_interface_stamps( stamps, globals );
120	<	mpiEventInit();
121	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
118	>	set_interface_stamps(stamps, globals);
119	>	mpiEventInit();
120	>	MPIcheckPoint();
121	>	mpiEventLoop();
122		}
123
124		#endif // is_mpi
125
126	<	void SimSetup::createSim( void ){
126	>	void SimSetup::createSim(void){
127
81	–	int i, j, k, globalAtomIndex;
82	–
128		// gather all of the information from the Bass file
129	<
129	>
130		gatherInfo();
131
132		// creation of complex system objects
#	Line 89 | Line 134 | void SimSetup::createSim( void ){
134		sysObjectsCreation();
135
136		// check on the post processing info
137	<
137	>
138		finalInfoCheck();
139
140		// initialize the system coordinates
141
142	<	initSystemCoords();
143	<
142	>	if ( !initSuspend ){
143	>	initSystemCoords();
144
145	+	if( !(globals->getUseInitTime()) )
146	+	info[0].currentTime = 0.0;
147	+	}
148	+
149		// make the output filenames
150
151		makeOutNames();
103	–
104	–	// make the integrator
152
106	–	makeIntegrator();
107	–
153		#ifdef IS_MPI
154		mpiSim->mpiRefresh();
155		#endif
#	Line 113 | Line 158 | void SimSetup::createSim( void ){
158
159		initFortran();
160
161	+	//creat constraint manager
162	+	for(int i = 0; i < nInfo; i++)
163	+	info[i].consMan = new ConstraintManager(&info[i]);
164
165	+	if (globals->haveMinimizer())
166	+	// make minimizer
167	+	makeMinimizer();
168	+	else
169	+	// make the integrator
170	+	makeIntegrator();
171
172		}
173
174
175	<	void SimSetup::makeMolecules( void ){
176	<
177	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
175	>	void SimSetup::makeMolecules(void){
176	>	int i, j, k;
177	>	int exI, exJ, exK, exL, slI, slJ;
178	>	int tempI, tempJ, tempK, tempL;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181		molInit molInfo;
182		DirectionalAtom* dAtom;
183	+	RigidBody* myRB;
184	+	StuntDouble* mySD;
185		LinkedAssign* extras;
186		LinkedAssign* current_extra;
187		AtomStamp* currentAtom;
188		BondStamp* currentBond;
189		BendStamp* currentBend;
190		TorsionStamp* currentTorsion;
191	+	RigidBodyStamp* currentRigidBody;
192	+	CutoffGroupStamp* currentCutoffGroup;
193	+	CutoffGroup* myCutoffGroup;
194	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196
197		bond_pair* theBonds;
198		bend_set* theBends;
199		torsion_set* theTorsions;
200
201	<
201	>	set<int> skipList;
202	>
203	>	double phi, theta, psi;
204	>	char* molName;
205	>	char rbName[100];
206	>
207	>	ConstraintPair* consPair; //constraint pair
208	>	ConstraintElement* consElement1;  //first element of constraint pair
209	>	ConstraintElement* consElement2;  //second element of constraint pair
210	>	int whichRigidBody;
211	>	int consAtomIndex;  //index of constraint atom in rigid body's atom array
212	>	vector<pair<int, int> > jointAtoms;
213	>	double bondLength2;
214		//init the forceField paramters
215
216		the_ff->readParams();
217
142	–
218		// init the atoms
219
220	<	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();
220	>	int nMembers, nNew, rb1, rb2;
221
222	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
223	<	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;
222	>	for (k = 0; k < nInfo; k++){
223	>	the_ff->setSimInfo(&(info[k]));
224
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	–
225		#ifdef IS_MPI
226	<
227	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
228	<
229	<	#endif // is_mpi
230	<	}
231	<
232	<	// make the bonds
233	<	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;
226	>	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	>	info[k].globalGroupMembership[i] = 0;
229	>	#else
230	>	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	>	for (i = 0; i < info[k].n_atoms; i++)
232	>	info[k].globalGroupMembership[i] = 0;
233	>	#endif
234
235	<	exI = theBonds[j].a;
236	<	exJ = theBonds[j].b;
235	>	atomOffset = 0;
236	>	groupOffset = 0;
237
238	<	// exclude_I must always be the smaller of the pair
239	<	if( exI > exJ ){
240	<	tempEx = exI;
220	<	exI = exJ;
221	<	exJ = tempEx;
222	<	}
223	<	#ifdef IS_MPI
224	<	tempEx = exI;
225	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
226	<	tempEx = exJ;
227	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
228	<
229	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
230	<	#else  // isn't MPI
238	>	for (i = 0; i < info[k].n_mol; i++){
239	>	stampID = info[k].molecules[i].getStampID();
240	>	molName = comp_stamps[stampID]->getID();
241
242	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
243	<	#endif  //is_mpi
244	<	}
245	<	excludeOffset += molInfo.nBonds;
242	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
245	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247
248	<	//make the bends
238	<	for(j=0; j<molInfo.nBends; j++){
248	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249
250	<	currentBend = comp_stamps[stampID]->getBend( j );
251	<	theBends[j].a = currentBend->getA() + atomOffset;
252	<	theBends[j].b = currentBend->getB() + atomOffset;
253	<	theBends[j].c = currentBend->getC() + atomOffset;
254	<
255	<	if( currentBend->haveExtras() ){
256	<
257	<	extras = currentBend->getExtras();
258	<	current_extra = extras;
259	<
260	<	while( current_extra != NULL ){
261	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
262	<
263	<	switch( current_extra->getType() ){
264	<
265	<	case 0:
266	<	theBends[j].ghost =
267	<	current_extra->getInt() + atomOffset;
268	<	theBends[j].isGhost = 1;
269	<	break;
260	<
261	<	case 1:
262	<	theBends[j].ghost =
263	<	(int)current_extra->getDouble() + atomOffset;
264	<	theBends[j].isGhost = 1;
265	<	break;
266	<
267	<	default:
268	<	sprintf( painCave.errMsg,
269	<	"SimSetup Error: ghostVectorSource was neither a "
270	<	"double nor an int.\n"
271	<	"-->Bend[%d] in %s\n",
272	<	j, comp_stamps[stampID]->getID() );
273	<	painCave.isFatal = 1;
274	<	simError();
275	<	}
276	<	}
277	<
278	<	else{
279	<
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup Error: unhandled bend assignment:\n"
282	<	"    -->%s in Bend[%d] in %s\n",
283	<	current_extra->getlhs(),
284	<	j, comp_stamps[stampID]->getID() );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
288	<
289	<	current_extra = current_extra->getNext();
290	<	}
291	<	}
292	<
293	<	if( !theBends[j].isGhost ){
294	<
295	<	exI = theBends[j].a;
296	<	exJ = theBends[j].c;
297	<	}
298	<	else{
299	<
300	<	exI = theBends[j].a;
301	<	exJ = theBends[j].b;
302	<	}
250	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
251	>
252	>	if (molInfo.nBonds > 0)
253	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	>	else
255	>	molInfo.myBonds = NULL;
256	>
257	>	if (molInfo.nBends > 0)
258	>	molInfo.myBends = new Bend*[molInfo.nBends];
259	>	else
260	>	molInfo.myBends = NULL;
261	>
262	>	if (molInfo.nTorsions > 0)
263	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	>	else
265	>	molInfo.myTorsions = NULL;
266	>
267	>	theBonds = new bond_pair[molInfo.nBonds];
268	>	theBends = new bend_set[molInfo.nBends];
269	>	theTorsions = new torsion_set[molInfo.nTorsions];
270
271	<	// exclude_I must always be the smaller of the pair
272	<	if( exI > exJ ){
273	<	tempEx = exI;
274	<	exI = exJ;
275	<	exJ = tempEx;
271	>	// make the Atoms
272	>
273	>	for (j = 0; j < molInfo.nAtoms; j++){
274	>	currentAtom = comp_stamps[stampID]->getAtom(j);
275	>
276	>	if (currentAtom->haveOrientation()){
277	>	dAtom = new DirectionalAtom((j + atomOffset),
278	>	info[k].getConfiguration());
279	>	info[k].n_oriented++;
280	>	molInfo.myAtoms[j] = dAtom;
281	>
282	>	// Directional Atoms have standard unit vectors which are oriented
283	>	// in space using the three Euler angles.  We assume the standard
284	>	// unit vector was originally along the z axis below.
285	>
286	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
287	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
288	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
289	>
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292	>	}
293	>	else{
294	>
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296	>
297	>	}
298	>
299	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
300	>	#ifdef IS_MPI
301	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302	>	#endif // is_mpi
303	>	}
304	>
305	>	// make the bonds
306	>	for (j = 0; j < molInfo.nBonds; j++){
307	>	currentBond = comp_stamps[stampID]->getBond(j);
308	>	theBonds[j].a = currentBond->getA() + atomOffset;
309	>	theBonds[j].b = currentBond->getB() + atomOffset;
310	>
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313	>
314	>	#ifdef IS_MPI
315	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
316	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
317	>	#else
318	>	exI = tempI + 1;
319	>	exJ = tempJ + 1;
320	>	#endif
321	>
322	>	info[k].excludes->addPair(exI, exJ);
323		}
324	+
325	+	//make the bends
326	+	for (j = 0; j < molInfo.nBends; j++){
327	+	currentBend = comp_stamps[stampID]->getBend(j);
328	+	theBends[j].a = currentBend->getA() + atomOffset;
329	+	theBends[j].b = currentBend->getB() + atomOffset;
330	+	theBends[j].c = currentBend->getC() + atomOffset;
331	+
332	+	if (currentBend->haveExtras()){
333	+	extras = currentBend->getExtras();
334	+	current_extra = extras;
335	+
336	+	while (current_extra != NULL){
337	+	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
338	+	switch (current_extra->getType()){
339	+	case 0:
340	+	theBends[j].ghost = current_extra->getInt() + atomOffset;
341	+	theBends[j].isGhost = 1;
342	+	break;
343	+
344	+	case 1:
345	+	theBends[j].ghost = (int) current_extra->getDouble() +
346	+	atomOffset;
347	+	theBends[j].isGhost = 1;
348	+	break;
349	+
350	+	default:
351	+	sprintf(painCave.errMsg,
352	+	"SimSetup Error: ghostVectorSource was neither a "
353	+	"double nor an int.\n"
354	+	"-->Bend[%d] in %s\n",
355	+	j, comp_stamps[stampID]->getID());
356	+	painCave.isFatal = 1;
357	+	simError();
358	+	}
359	+	}
360	+	else{
361	+	sprintf(painCave.errMsg,
362	+	"SimSetup Error: unhandled bend assignment:\n"
363	+	"    -->%s in Bend[%d] in %s\n",
364	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
365	+	painCave.isFatal = 1;
366	+	simError();
367	+	}
368	+
369	+	current_extra = current_extra->getNext();
370	+	}
371	+	}
372	+
373	+	if (theBends[j].isGhost) {
374	+
375	+	tempI = theBends[j].a;
376	+	tempJ = theBends[j].b;
377	+
378		#ifdef IS_MPI
379	<	tempEx = exI;
380	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
381	<	tempEx = exJ;
382	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
383	<
384	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
385	<	#else  // isn't MPI
318	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319	<	#endif  //is_mpi
320	<	}
321	<	excludeOffset += molInfo.nBends;
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386
387	<	for(j=0; j<molInfo.nTorsions; j++){
387	>	} else {
388	>
389	>	tempI = theBends[j].a;
390	>	tempJ = theBends[j].b;
391	>	tempK = theBends[j].c;
392	>
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	#endif
402	>
403	>	info[k].excludes->addPair(exI, exK);
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exJ, exK);
406	>	}
407	>	}
408	>
409	>	for (j = 0; j < molInfo.nTorsions; j++){
410	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
411	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
412	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
413	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
414	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
415	>
416	>	tempI = theTorsions[j].a;
417	>	tempJ = theTorsions[j].b;
418	>	tempK = theTorsions[j].c;
419	>	tempL = theTorsions[j].d;
420	>
421	>	#ifdef IS_MPI
422	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
423	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
424	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
425	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
426	>	#else
427	>	exI = tempI + 1;
428	>	exJ = tempJ + 1;
429	>	exK = tempK + 1;
430	>	exL = tempL + 1;
431	>	#endif
432	>
433	>	info[k].excludes->addPair(exI, exJ);
434	>	info[k].excludes->addPair(exI, exK);
435	>	info[k].excludes->addPair(exI, exL);
436	>	info[k].excludes->addPair(exJ, exK);
437	>	info[k].excludes->addPair(exJ, exL);
438	>	info[k].excludes->addPair(exK, exL);
439	>	}
440	>
441
442	<	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;
442	>	molInfo.myRigidBodies.clear();
443
444	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
444	>	for (j = 0; j < molInfo.nRigidBodies; j++){
445
446	<	// exclude_I must always be the smaller of the pair
447	<	if( exI > exJ ){
448	<	tempEx = exI;
449	<	exI = exJ;
450	<	exJ = tempEx;
446	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
447	>	nMembers = currentRigidBody->getNMembers();
448	>
449	>	// Create the Rigid Body:
450	>
451	>	myRB = new RigidBody();
452	>
453	>	sprintf(rbName,"%s_RB_%d", molName, j);
454	>	myRB->setType(rbName);
455	>
456	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
457	>
458	>	// molI is atom numbering inside this molecule
459	>	molI = currentRigidBody->getMember(rb1);
460	>
461	>	// tempI is atom numbering on local processor
462	>	tempI = molI + atomOffset;
463	>
464	>	// currentAtom is the AtomStamp (which we need for
465	>	// rigid body reference positions)
466	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
467	>
468	>	// When we add to the rigid body, add the atom itself and
469	>	// the stamp info:
470	>
471	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
472	>
473	>	// Add this atom to the Skip List for the integrators
474	>	#ifdef IS_MPI
475	>	slI = info[k].atoms[tempI]->getGlobalIndex();
476	>	#else
477	>	slI = tempI;
478	>	#endif
479	>	skipList.insert(slI);
480	>
481	>	}
482	>
483	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
484	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
485	>
486	>	tempI = currentRigidBody->getMember(rb1);
487	>	tempJ = currentRigidBody->getMember(rb2);
488	>
489	>	// Some explanation is required here.
490	>	// Fortran indexing starts at 1, while c indexing starts at 0
491	>	// Also, in parallel computations, the GlobalIndex is
492	>	// used for the exclude list:
493	>
494	>	#ifdef IS_MPI
495	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497	>	#else
498	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500	>	#endif
501	>
502	>	info[k].excludes->addPair(exI, exJ);
503	>
504	>	}
505	>	}
506	>
507	>	molInfo.myRigidBodies.push_back(myRB);
508	>	info[k].rigidBodies.push_back(myRB);
509		}
510	+
511	+
512	+	//create cutoff group for molecule
513	+
514	+	cutoffAtomSet.clear();
515	+	molInfo.myCutoffGroups.clear();
516	+
517	+	for (j = 0; j < nCutoffGroups; j++){
518	+
519	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	+	nMembers = currentCutoffGroup->getNMembers();
521	+
522	+	myCutoffGroup = new CutoffGroup();
523	+
524		#ifdef IS_MPI
525	<	tempEx = exI;
526	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
527	<	tempEx = exJ;
528	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
525	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	>	#else
527	>	myCutoffGroup->setGlobalIndex(groupOffset);
528	>	#endif
529	>
530	>	for (int cg = 0; cg < nMembers; cg++) {
531	>
532	>	// molI is atom numbering inside this molecule
533	>	molI = currentCutoffGroup->getMember(cg);
534	>
535	>	// tempI is atom numbering on local processor
536	>	tempI = molI + atomOffset;
537	>
538	>	#ifdef IS_MPI
539	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	>	#else
542	>	globalID = info[k].atoms[tempI]->getIndex();
543	>	info[k].globalGroupMembership[globalID] = groupOffset;
544	>	#endif
545	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	>	cutoffAtomSet.insert(tempI);
547	>	}
548	>
549	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	>	groupOffset++;
551	>
552	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553
554	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
555	<	#else  // isn't MPI
556	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
557	<	#endif  //is_mpi
554	>
555	>	// create a cutoff group for every atom in current molecule which
556	>	// does not belong to cutoffgroup defined at mdl file
557	>
558	>	for(j = 0; j < molInfo.nAtoms; j++){
559	>
560	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	>	myCutoffGroup = new CutoffGroup();
562	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	>
564	>	#ifdef IS_MPI
565	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	>	#else
569	>	myCutoffGroup->setGlobalIndex(groupOffset);
570	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	>	info[k].globalGroupMembership[globalID] = groupOffset;
572	>	#endif
573	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	>	groupOffset++;
575	>	}
576	>	}
577	>
578	>	// After this is all set up, scan through the atoms to
579	>	// see if they can be added to the integrableObjects:
580	>
581	>	molInfo.myIntegrableObjects.clear();
582	>
583	>
584	>	for (j = 0; j < molInfo.nAtoms; j++){
585	>
586	>	#ifdef IS_MPI
587	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	>	#else
589	>	slJ = j+atomOffset;
590	>	#endif
591	>
592	>	// if they aren't on the skip list, then they can be integrated
593	>
594	>	if (skipList.find(slJ) == skipList.end()) {
595	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	>	info[k].integrableObjects.push_back(mySD);
597	>	molInfo.myIntegrableObjects.push_back(mySD);
598	>	}
599	>	}
600	>
601	>	// all rigid bodies are integrated:
602	>
603	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	>	info[k].integrableObjects.push_back(mySD);
606	>	molInfo.myIntegrableObjects.push_back(mySD);
607	>	}
608	>
609	>	// send the arrays off to the forceField for init.
610	>
611	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
612	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
613	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
614	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615	>	theTorsions);
616	>
617	>
618	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620	>
621	>	for (j = 0; j < molInfo.nBonds; j++){
622	>
623	>	//if bond is constrained bond, add it into constraint pair
624	>	if(molInfo.myBonds[j]->is_constrained()){
625	>
626	>	//if both atoms are in the same rigid body, just skip it
627	>	currentBond = comp_stamps[stampID]->getBond(j);
628	>
629	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630	>
631	>	tempI = currentBond->getA() + atomOffset;
632	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	>	else
635	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636	>
637	>	tempJ =  currentBond->getB() + atomOffset;
638	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	>	else
641	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642	>
643	>	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	>	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645	>
646	>	molInfo.myConstraintPairs.push_back(consPair);
647	>	}
648	>	}//end if(molInfo.myBonds[j]->is_constrained())
649	>	}
650	>
651	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	>
655	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656	>
657	>	for(size_t m = 0; m < jointAtoms.size(); m++){
658	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660	>
661	>	consPair = new JointConstraintPair(consElement1, consElement2);
662	>	molInfo.myConstraintPairs.push_back(consPair);
663	>	}
664	>
665	>	}
666	>	}
667	>
668	>
669	>	info[k].molecules[i].initialize(molInfo);
670	>
671	>
672	>	atomOffset += molInfo.nAtoms;
673	>	delete[] theBonds;
674	>	delete[] theBends;
675	>	delete[] theTorsions;
676		}
351	–	excludeOffset += molInfo.nTorsions;
677
353	–
354	–	// send the arrays off to the forceField for init.
678
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 );
679
680	+	#ifdef IS_MPI
681	+	// Since the globalGroupMembership has been zero filled and we've only
682	+	// poked values into the atoms we know, we can do an Allreduce
683	+	// to get the full globalGroupMembership array (We think).
684	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	+	// docs said we could.
686
687	<	the_molecules[i].initialize( molInfo );
687	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688
689	+	MPI_Allreduce(info[k].globalGroupMembership,
690	+	ggMjunk,
691	+	mpiSim->getNAtomsGlobal(),
692	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693
694	<	atomOffset += molInfo.nAtoms;
695	<	delete[] theBonds;
696	<	delete[] theBends;
697	<	delete[] theTorsions;
694	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	>	info[k].globalGroupMembership[i] = ggMjunk[i];
696	>
697	>	delete[] ggMjunk;
698	>
699	>	#endif
700	>
701	>
702	>
703		}
704
705		#ifdef IS_MPI
706	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
706	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
707		MPIcheckPoint();
708		#endif // is_mpi
709
376	–	// clean up the forcefield
377	–	the_ff->calcRcut();
378	–	the_ff->cleanMe();
379	–
710		}
711
712	<	void SimSetup::initFromBass( void ){
383	<
712	>	void SimSetup::initFromBass(void){
713		int i, j, k;
714		int n_cells;
715		double cellx, celly, cellz;
#	Line 389 | Line 718 | void SimSetup::initFromBass( void ){
718		int n_extra;
719		int have_extra, done;
720
721	<	temp1 = (double)tot_nmol / 4.0;
722	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
723	<	temp3 = ceil( temp2 );
721	>	double vel[3];
722	>	vel[0] = 0.0;
723	>	vel[1] = 0.0;
724	>	vel[2] = 0.0;
725
726	<	have_extra =0;
727	<	if( temp2 < temp3 ){ // we have a non-complete lattice
728	<	have_extra =1;
726	>	temp1 = (double) tot_nmol / 4.0;
727	>	temp2 = pow(temp1, (1.0 / 3.0));
728	>	temp3 = ceil(temp2);
729
730	<	n_cells = (int)temp3 - 1;
731	<	cellx = info->boxLx / temp3;
732	<	celly = info->boxLy / temp3;
733	<	cellz = info->boxLz / 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 );
730	>	have_extra = 0;
731	>	if (temp2 < temp3){
732	>	// we have a non-complete lattice
733	>	have_extra = 1;
734
735	<	if( n_per_extra > 4){
736	<	sprintf( painCave.errMsg,
737	<	"SimSetup error. There has been an error in constructing"
738	<	" the non-complete lattice.\n" );
735	>	n_cells = (int) temp3 - 1;
736	>	cellx = info[0].boxL[0] / temp3;
737	>	celly = info[0].boxL[1] / temp3;
738	>	cellz = info[0].boxL[2] / temp3;
739	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
740	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
741	>	n_per_extra = (int) ceil(temp1);
742	>
743	>	if (n_per_extra > 4){
744	>	sprintf(painCave.errMsg,
745	>	"SimSetup error. There has been an error in constructing"
746	>	" the non-complete lattice.\n");
747		painCave.isFatal = 1;
748		simError();
749		}
750		}
751		else{
752	<	n_cells = (int)temp3;
753	<	cellx = info->boxLx / temp3;
754	<	celly = info->boxLy / temp3;
755	<	cellz = info->boxLz / temp3;
752	>	n_cells = (int) temp3;
753	>	cellx = info[0].boxL[0] / temp3;
754	>	celly = info[0].boxL[1] / temp3;
755	>	cellz = info[0].boxL[2] / temp3;
756		}
757
758		current_mol = 0;
#	Line 425 | Line 760 | void SimSetup::initFromBass( void ){
760		current_comp = 0;
761		current_atom_ndx = 0;
762
763	<	for( i=0; i < n_cells ; i++ ){
764	<	for( j=0; j < n_cells; j++ ){
765	<	for( k=0; k < n_cells; k++ ){
763	>	for (i = 0; i < n_cells ; i++){
764	>	for (j = 0; j < n_cells; j++){
765	>	for (k = 0; k < n_cells; k++){
766	>	makeElement(i * cellx, j * celly, k * cellz);
767
768	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
768	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
769
770	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
770	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
771
772	<	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 );
772	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
773		}
774		}
775		}
776
777	<	if( have_extra ){
777	>	if (have_extra){
778		done = 0;
779
780		int start_ndx;
781	<	for( i=0; i < (n_cells+1) && !done; i++ ){
782	<	for( j=0; j < (n_cells+1) && !done; j++ ){
781	>	for (i = 0; i < (n_cells + 1) && !done; i++){
782	>	for (j = 0; j < (n_cells + 1) && !done; j++){
783	>	if (i < n_cells){
784	>	if (j < n_cells){
785	>	start_ndx = n_cells;
786	>	}
787	>	else
788	>	start_ndx = 0;
789	>	}
790	>	else
791	>	start_ndx = 0;
792
793	<	if( i < n_cells ){
793	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
794	>	makeElement(i * cellx, j * celly, k * cellz);
795	>	done = (current_mol >= tot_nmol);
796
797	<	if( j < n_cells ){
798	<	start_ndx = n_cells;
799	<	}
800	<	else start_ndx = 0;
801	<	}
465	<	else start_ndx = 0;
797	>	if (!done && n_per_extra > 1){
798	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
799	>	k * cellz);
800	>	done = (current_mol >= tot_nmol);
801	>	}
802
803	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
803	>	if (!done && n_per_extra > 2){
804	>	makeElement(i * cellx, j * celly + 0.5 * celly,
805	>	k * cellz + 0.5 * cellz);
806	>	done = (current_mol >= tot_nmol);
807	>	}
808
809	<	makeElement( i * cellx,
810	<	j * celly,
811	<	k * cellz );
812	<	done = ( current_mol >= tot_nmol );
813	<
814	<	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	<	}
809	>	if (!done && n_per_extra > 3){
810	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
811	>	k * cellz + 0.5 * cellz);
812	>	done = (current_mol >= tot_nmol);
813	>	}
814	>	}
815		}
816		}
817		}
818
819	<
820	<	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 );
819	>	for (i = 0; i < info[0].n_atoms; i++){
820	>	info[0].atoms[i]->setVel(vel);
821		}
822		}
823
824	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
824	>	void SimSetup::makeElement(double x, double y, double z){
825		int k;
826		AtomStamp* current_atom;
827		DirectionalAtom* dAtom;
828		double rotMat[3][3];
829	+	double pos[3];
830
831	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
832	<
833	<	current_atom = comp_stamps[current_comp]->getAtom( k );
834	<	if( !current_atom->havePosition() ){
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup:initFromBass error.\n"
837	<	"\tComponent %s, atom %s does not have a position specified.\n"
838	<	"\tThe initialization routine is unable to give a start"
839	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
831	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
832	>	current_atom = comp_stamps[current_comp]->getAtom(k);
833	>	if (!current_atom->havePosition()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup:initFromBass error.\n"
836	>	"\tComponent %s, atom %s does not have a position specified.\n"
837	>	"\tThe initialization routine is unable to give a start"
838	>	" position.\n",
839	>	comp_stamps[current_comp]->getID(), current_atom->getType());
840		painCave.isFatal = 1;
841		simError();
842		}
843
844	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
845	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
846	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
844	>	pos[0] = x + current_atom->getPosX();
845	>	pos[1] = y + current_atom->getPosY();
846	>	pos[2] = z + current_atom->getPosZ();
847
848	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
848	>	info[0].atoms[current_atom_ndx]->setPos(pos);
849
850	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
850	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
851	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
852
853		rotMat[0][0] = 1.0;
854		rotMat[0][1] = 0.0;
#	Line 546 | Line 862 | void SimSetup::makeElement( double x, double y, double
862		rotMat[2][1] = 0.0;
863		rotMat[2][2] = 1.0;
864
865	<	dAtom->setA( rotMat );
865	>	dAtom->setA(rotMat);
866		}
867
868		current_atom_ndx++;
#	Line 555 | Line 871 | void SimSetup::makeElement( double x, double y, double
871		current_mol++;
872		current_comp_mol++;
873
874	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
874	>	if (current_comp_mol >= components_nmol[current_comp]){
875		current_comp_mol = 0;
876		current_comp++;
877		}
878		}
879
880
881	<	void SimSetup::gatherInfo( void ){
882	<	int i,j,k;
881	>	void SimSetup::gatherInfo(void){
882	>	int i;
883
884		ensembleCase = -1;
885		ffCase = -1;
886
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
887		// set the easy ones first
888	<	info->target_temp = globals->getTargetTemp();
889	<	info->dt = globals->getDt();
890	<	info->run_time = globals->getRunTime();
888	>
889	>	for (i = 0; i < nInfo; i++){
890	>	info[i].target_temp = globals->getTargetTemp();
891	>	info[i].dt = globals->getDt();
892	>	info[i].run_time = globals->getRunTime();
893	>	}
894		n_components = globals->getNComponents();
895
896
897		// get the forceField
898
899	<	strcpy( force_field, globals->getForceField() );
899	>	strcpy(force_field, globals->getForceField());
900
901	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
902	<	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();
901	>	if (!strcasecmp(force_field, "DUFF")){
902	>	ffCase = FF_DUFF;
903		}
904	<
904	>	else if (!strcasecmp(force_field, "LJ")){
905	>	ffCase = FF_LJ;
906	>	}
907	>	else if (!strcasecmp(force_field, "EAM")){
908	>	ffCase = FF_EAM;
909	>	}
910	>	else if (!strcasecmp(force_field, "WATER")){
911	>	ffCase = FF_H2O;
912	>	}
913	>	else{
914	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915	>	force_field);
916	>	painCave.isFatal = 1;
917	>	simError();
918	>	}
919	>	if (globals->haveForceFieldVariant()) {
920	>	strcpy(forcefield_variant, globals->getForceFieldVariant());
921	>	has_forcefield_variant = 1;
922	>	}
923	>
924		// get the ensemble
925
926	<	strcpy( ensemble, globals->getEnsemble() );
926	>	strcpy(ensemble, globals->getEnsemble());
927
928	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
929	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
930	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
928	>	if (!strcasecmp(ensemble, "NVE")){
929	>	ensembleCase = NVE_ENS;
930	>	}
931	>	else if (!strcasecmp(ensemble, "NVT")){
932	>	ensembleCase = NVT_ENS;
933	>	}
934	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
935		ensembleCase = NPTi_ENS;
936	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
937	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
938	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
936	>	}
937	>	else if (!strcasecmp(ensemble, "NPTf")){
938	>	ensembleCase = NPTf_ENS;
939	>	}
940	>	else if (!strcasecmp(ensemble, "NPTxyz")){
941	>	ensembleCase = NPTxyz_ENS;
942	>	}
943		else{
944	<	sprintf( painCave.errMsg,
945	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
946	<	"reverting to NVE for this simulation.\n",
947	<	ensemble );
948	<	painCave.isFatal = 0;
949	<	simError();
950	<	strcpy( ensemble, "NVE" );
951	<	ensembleCase = NVE_ENS;
944	>	sprintf(painCave.errMsg,
945	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
946	>	"\treverting to NVE for this simulation.\n",
947	>	ensemble);
948	>	painCave.isFatal = 0;
949	>	simError();
950	>	strcpy(ensemble, "NVE");
951	>	ensembleCase = NVE_ENS;
952		}
618	–	strcpy( info->ensemble, ensemble );
953
954	<	// get the mixing rule
954	>	for (i = 0; i < nInfo; i++){
955	>	strcpy(info[i].ensemble, ensemble);
956
957	<	strcpy( info->mixingRule, globals->getMixingRule() );
958	<	info->usePBC = globals->getPBC();
959	<
960	<
957	>	// get the mixing rule
958	>
959	>	strcpy(info[i].mixingRule, globals->getMixingRule());
960	>	info[i].usePBC = globals->getPBC();
961	>	}
962	>
963		// get the components and calculate the tot_nMol and indvidual n_mol
964	<
964	>
965		the_components = globals->getComponents();
966		components_nmol = new int[n_components];
967
968
969	<	if( !globals->haveNMol() ){
969	>	if (!globals->haveNMol()){
970		// we don't have the total number of molecules, so we assume it is
971		// given in each component
972
973		tot_nmol = 0;
974	<	for( i=0; i<n_components; i++ ){
975	<
976	<	if( !the_components[i]->haveNMol() ){
977	<	// we have a problem
978	<	sprintf( painCave.errMsg,
979	<	"SimSetup Error. No global NMol or component NMol"
980	<	" given. Cannot calculate the number of atoms.\n" );
981	<	painCave.isFatal = 1;
645	<	simError();
974	>	for (i = 0; i < n_components; i++){
975	>	if (!the_components[i]->haveNMol()){
976	>	// we have a problem
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup Error. No global NMol or component NMol given.\n"
979	>	"\tCannot calculate the number of atoms.\n");
980	>	painCave.isFatal = 1;
981	>	simError();
982		}
983
984		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 986 | void SimSetup::gatherInfo( void ){
986		}
987		}
988		else{
989	<	sprintf( painCave.errMsg,
990	<	"SimSetup error.\n"
991	<	"\tSorry, the ability to specify total"
992	<	" nMols and then give molfractions in the components\n"
993	<	"\tis not currently supported."
994	<	" Please give nMol in the components.\n" );
989	>	sprintf(painCave.errMsg,
990	>	"SimSetup error.\n"
991	>	"\tSorry, the ability to specify total"
992	>	" nMols and then give molfractions in the components\n"
993	>	"\tis not currently supported."
994	>	" Please give nMol in the components.\n");
995		painCave.isFatal = 1;
996		simError();
997		}
998
999	<	// set the status, sample, and thermal kick times
1000	<
1001	<	if( globals->haveSampleTime() ){
1002	<	info->sampleTime = globals->getSampleTime();
1003	<	info->statusTime = info->sampleTime;
1004	<	info->thermalTime = info->sampleTime;
999	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
1000	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001	>	sprintf(painCave.errMsg,
1002	>	"Sample time is not divisible by dt.\n"
1003	>	"\tThis will result in samples that are not uniformly\n"
1004	>	"\tdistributed in time.  If this is a problem, change\n"
1005	>	"\tyour sampleTime variable.\n");
1006	>	painCave.isFatal = 0;
1007	>	simError();
1008		}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
1009
1010	<	if( globals->haveStatusTime() ){
1011	<	info->statusTime = globals->getStatusTime();
1010	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011	>	sprintf(painCave.errMsg,
1012	>	"Status time is not divisible by dt.\n"
1013	>	"\tThis will result in status reports that are not uniformly\n"
1014	>	"\tdistributed in time.  If this is a problem, change \n"
1015	>	"\tyour statusTime variable.\n");
1016	>	painCave.isFatal = 0;
1017	>	simError();
1018		}
1019
1020	<	if( globals->haveThermalTime() ){
1021	<	info->thermalTime = globals->getThermalTime();
1022	<	}
1020	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1021	>	sprintf(painCave.errMsg,
1022	>	"Thermal time is not divisible by dt.\n"
1023	>	"\tThis will result in thermalizations that are not uniformly\n"
1024	>	"\tdistributed in time.  If this is a problem, change \n"
1025	>	"\tyour thermalTime variable.\n");
1026	>	painCave.isFatal = 0;
1027	>	simError();
1028	>	}
1029
1030	<	// check for the temperature set flag
1030	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1031	>	sprintf(painCave.errMsg,
1032	>	"Reset time is not divisible by dt.\n"
1033	>	"\tThis will result in integrator resets that are not uniformly\n"
1034	>	"\tdistributed in time.  If this is a problem, change\n"
1035	>	"\tyour resetTime variable.\n");
1036	>	painCave.isFatal = 0;
1037	>	simError();
1038	>	}
1039
1040	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
1040	>	// set the status, sample, and thermal kick times
1041
1042	<	// get some of the tricky things that may still be in the globals
1042	>	for (i = 0; i < nInfo; i++){
1043	>	if (globals->haveSampleTime()){
1044	>	info[i].sampleTime = globals->getSampleTime();
1045	>	info[i].statusTime = info[i].sampleTime;
1046	>	}
1047	>	else{
1048	>	info[i].sampleTime = globals->getRunTime();
1049	>	info[i].statusTime = info[i].sampleTime;
1050	>	}
1051
1052	<	double boxVector[3];
1053	<	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();
1052	>	if (globals->haveStatusTime()){
1053	>	info[i].statusTime = globals->getStatusTime();
1054		}
715	–	boxVector[0] = globals->getBoxX();
1055
1056	<	if( !globals->haveBoxY() ){
1057	<	sprintf( painCave.errMsg,
1058	<	"SimSetup error, no periodic BoxY size given.\n" );
1059	<	painCave.isFatal = 1;
721	<	simError();
1056	>	if (globals->haveThermalTime()){
1057	>	info[i].thermalTime = globals->getThermalTime();
1058	>	} else {
1059	>	info[i].thermalTime = globals->getRunTime();
1060		}
723	–	boxVector[1] = globals->getBoxY();
1061
1062	<	if( !globals->haveBoxZ() ){
1063	<	sprintf( painCave.errMsg,
1064	<	"SimSetup error, no periodic BoxZ size given.\n" );
1065	<	painCave.isFatal = 1;
729	<	simError();
1062	>	info[i].resetIntegrator = 0;
1063	>	if( globals->haveResetTime() ){
1064	>	info[i].resetTime = globals->getResetTime();
1065	>	info[i].resetIntegrator = 1;
1066		}
731	–	boxVector[2] = globals->getBoxZ();
1067
1068	<	info->setBox( boxVector );
1068	>	// check for the temperature set flag
1069	>
1070	>	if (globals->haveTempSet())
1071	>	info[i].setTemp = globals->getTempSet();
1072	>
1073	>	// check for the extended State init
1074	>
1075	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1076	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077	>
1078	>	// check for thermodynamic integration
1079	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082	>	info[i].thermIntLambda = globals->getThermIntLambda();
1083	>	info[i].thermIntK = globals->getThermIntK();
1084	>
1085	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086	>	info[i].restraint = myRestraint;
1087	>	}
1088	>	else {
1089	>	sprintf(painCave.errMsg,
1090	>	"SimSetup Error:\n"
1091	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1092	>	"\tthermodynamicIntegrationLambda (and/or\n"
1093	>	"\tthermodynamicIntegrationK) was not specified.\n"
1094	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1095	>	painCave.isFatal = 1;
1096	>	simError();
1097	>	}
1098	>	}
1099	>	else if(globals->getUseLiquidThermInt()) {
1100	>	if (globals->getUseSolidThermInt()) {
1101	>	sprintf( painCave.errMsg,
1102	>	"SimSetup Warning: It appears that you have both solid and\n"
1103	>	"\tliquid thermodynamic integration activated in your .bass\n"
1104	>	"\tfile. To avoid confusion, specify only one technique in\n"
1105	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1106	>	"\twill be assumed for the current simulation. If this is not\n"
1107	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1108	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109	>	painCave.isFatal = 0;
1110	>	simError();
1111	>	}
1112	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114	>	info[i].thermIntLambda = globals->getThermIntLambda();
1115	>	info[i].thermIntK = globals->getThermIntK();
1116	>	}
1117	>	else {
1118	>	sprintf(painCave.errMsg,
1119	>	"SimSetup Error:\n"
1120	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1121	>	"\tthermodynamicIntegrationLambda (and/or\n"
1122	>	"\tthermodynamicIntegrationK) was not specified.\n"
1123	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1124	>	painCave.isFatal = 1;
1125	>	simError();
1126	>	}
1127	>	}
1128	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1129	>	sprintf(painCave.errMsg,
1130	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1131	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132	>	"\t'true' in your .bass file.  These keywords are set to\n"
1133	>	"\t'false' by default, so your lambda and/or k values are\n"
1134	>	"\tbeing ignored.\n");
1135	>	painCave.isFatal = 0;
1136	>	simError();
1137	>	}
1138		}
1139	+
1140	+	//setup seed for random number generator
1141	+	int seedValue;
1142
1143	+	if (globals->haveSeed()){
1144	+	seedValue = globals->getSeed();
1145
1146	+	if(seedValue / 1E9 == 0){
1147	+	sprintf(painCave.errMsg,
1148	+	"Seed for sprng library should contain at least 9 digits\n"
1149	+	"OOPSE will generate a seed for user\n");
1150	+	painCave.isFatal = 0;
1151	+	simError();
1152	+
1153	+	//using seed generated by system instead of invalid seed set by user
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}
1163	+	}//end of if branch of globals->haveSeed()
1164	+	else{
1165
1166	+	#ifndef IS_MPI
1167	+	seedValue = make_sprng_seed();
1168	+	#else
1169	+	if (worldRank == 0){
1170	+	seedValue = make_sprng_seed();
1171	+	}
1172	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1173	+	#endif
1174	+	}//end of globals->haveSeed()
1175	+
1176	+	for (int i = 0; i < nInfo; i++){
1177	+	info[i].setSeed(seedValue);
1178	+	}
1179	+
1180		#ifdef IS_MPI
1181	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1181	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1182		MPIcheckPoint();
1183		#endif // is_mpi
742	–
1184		}
1185
1186
1187	<	void SimSetup::finalInfoCheck( void ){
1187	>	void SimSetup::finalInfoCheck(void){
1188		int index;
1189		int usesDipoles;
1190	<
1190	>	int usesCharges;
1191	>	int i;
1192
1193	<	// check electrostatic parameters
1194	<
1195	<	index = 0;
1196	<	usesDipoles = 0;
1197	<	while( (index < info->n_atoms) && !usesDipoles ){
1198	<	usesDipoles = ((info->atoms)[index])->hasDipole();
1199	<	index++;
1200	<	}
1201	<
1193	>	for (i = 0; i < nInfo; i++){
1194	>	// check electrostatic parameters
1195	>
1196	>	index = 0;
1197	>	usesDipoles = 0;
1198	>	while ((index < info[i].n_atoms) && !usesDipoles){
1199	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1200	>	index++;
1201	>	}
1202	>	index = 0;
1203	>	usesCharges = 0;
1204	>	while ((index < info[i].n_atoms) && !usesCharges){
1205	>	usesCharges= (info[i].atoms[index])->hasCharge();
1206	>	index++;
1207	>	}
1208		#ifdef IS_MPI
1209	<	int myUse = usesDipoles;
1210	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1209	>	int myUse = usesDipoles;
1210	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211		#endif //is_mpi
1212
1213	+	double theRcut, theRsw;
1214
1215	<	if (globals->getUseRF() ) {
1216	<	info->useReactionField = 1;
768	<
769	<	if( !globals->haveECR() ){
770	<	sprintf( painCave.errMsg,
771	<	"SimSetup Warning: using default value of 1/2 the smallest "
772	<	"box length for the electrostaticCutoffRadius.\n"
773	<	"I hope you have a very fast processor!\n");
774	<	painCave.isFatal = 0;
775	<	simError();
776	<	double smallest;
777	<	smallest = info->boxLx;
778	<	if (info->boxLy <= smallest) smallest = info->boxLy;
779	<	if (info->boxLz <= smallest) smallest = info->boxLz;
780	<	info->ecr = 0.5 * smallest;
781	<	} else {
782	<	info->ecr        = globals->getECR();
783	<	}
1215	>	if (globals->haveRcut()) {
1216	>	theRcut = globals->getRcut();
1217
1218	<	if( !globals->haveEST() ){
1219	<	sprintf( painCave.errMsg,
1220	<	"SimSetup Warning: using default value of 0.05 * the "
1221	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1222	<	);
1223	<	painCave.isFatal = 0;
1224	<	simError();
792	<	info->est = 0.05 * info->ecr;
1218	>	if (globals->haveRsw())
1219	>	theRsw = globals->getRsw();
1220	>	else
1221	>	theRsw = theRcut;
1222	>
1223	>	info[i].setDefaultRcut(theRcut, theRsw);
1224	>
1225		} else {
1226	<	info->est        = globals->getEST();
1226	>
1227	>	the_ff->calcRcut();
1228	>	theRcut = info[i].getRcut();
1229	>
1230	>	if (globals->haveRsw())
1231	>	theRsw = globals->getRsw();
1232	>	else
1233	>	theRsw = theRcut;
1234	>
1235	>	info[i].setDefaultRcut(theRcut, theRsw);
1236		}
1237	<
1238	<	if(!globals->haveDielectric() ){
1239	<	sprintf( painCave.errMsg,
799	<	"SimSetup Error: You are trying to use Reaction Field without"
800	<	"setting a dielectric constant!\n"
801	<	);
802	<	painCave.isFatal = 1;
803	<	simError();
804	<	}
805	<	info->dielectric = globals->getDielectric();
806	<	}
807	<	else {
808	<	if (usesDipoles) {
1237	>
1238	>	if (globals->getUseRF()){
1239	>	info[i].useReactionField = 1;
1240
1241	<	if( !globals->haveECR() ){
1242	<	sprintf( painCave.errMsg,
1243	<	"SimSetup Warning: using default value of 1/2 the smallest "
1244	<	"box length for the electrostaticCutoffRadius.\n"
1245	<	"I hope you have a very fast processor!\n");
1241	>	if (!globals->haveRcut()){
1242	>	sprintf(painCave.errMsg,
1243	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1244	>	"\tOOPSE will use a default value of 15.0 angstroms"
1245	>	"\tfor the cutoffRadius.\n");
1246		painCave.isFatal = 0;
1247		simError();
1248	<	double smallest;
818	<	smallest = info->boxLx;
819	<	if (info->boxLy <= smallest) smallest = info->boxLy;
820	<	if (info->boxLz <= smallest) smallest = info->boxLz;
821	<	info->ecr = 0.5 * smallest;
822	<	} else {
823	<	info->ecr        = globals->getECR();
1248	>	theRcut = 15.0;
1249		}
1250	<
1251	<	if( !globals->haveEST() ){
1252	<	sprintf( painCave.errMsg,
1253	<	"SimSetup Warning: using default value of 5%% of the "
1254	<	"electrostaticCutoffRadius for the "
1255	<	"electrostaticSkinThickness\n"
1256	<	);
1250	>	else{
1251	>	theRcut = globals->getRcut();
1252	>	}
1253	>
1254	>	if (!globals->haveRsw()){
1255	>	sprintf(painCave.errMsg,
1256	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1257	>	"\tOOPSE will use a default value of\n"
1258	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1259		painCave.isFatal = 0;
1260		simError();
1261	<	info->est = 0.05 * info->ecr;
1262	<	} else {
1263	<	info->est        = globals->getEST();
1264	<	}
1261	>	theRsw = 0.95 * theRcut;
1262	>	}
1263	>	else{
1264	>	theRsw = globals->getRsw();
1265	>	}
1266	>
1267	>	info[i].setDefaultRcut(theRcut, theRsw);
1268	>
1269	>	if (!globals->haveDielectric()){
1270	>	sprintf(painCave.errMsg,
1271	>	"SimSetup Error: No Dielectric constant was set.\n"
1272	>	"\tYou are trying to use Reaction Field without"
1273	>	"\tsetting a dielectric constant!\n");
1274	>	painCave.isFatal = 1;
1275	>	simError();
1276	>	}
1277	>	info[i].dielectric = globals->getDielectric();
1278		}
1279	<	}
1279	>	else{
1280	>	if (usesDipoles || usesCharges){
1281
1282	+	if (!globals->haveRcut()){
1283	+	sprintf(painCave.errMsg,
1284	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1285	+	"\tOOPSE will use a default value of 15.0 angstroms"
1286	+	"\tfor the cutoffRadius.\n");
1287	+	painCave.isFatal = 0;
1288	+	simError();
1289	+	theRcut = 15.0;
1290	+	}
1291	+	else{
1292	+	theRcut = globals->getRcut();
1293	+	}
1294	+
1295	+	if (!globals->haveRsw()){
1296	+	sprintf(painCave.errMsg,
1297	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1298	+	"\tOOPSE will use a default value of\n"
1299	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1300	+	painCave.isFatal = 0;
1301	+	simError();
1302	+	theRsw = 0.95 * theRcut;
1303	+	}
1304	+	else{
1305	+	theRsw = globals->getRsw();
1306	+	}
1307	+
1308	+	info[i].setDefaultRcut(theRcut, theRsw);
1309	+
1310	+	}
1311	+	}
1312	+	}
1313		#ifdef IS_MPI
1314	<	strcpy( checkPointMsg, "post processing checks out" );
1314	>	strcpy(checkPointMsg, "post processing checks out");
1315		MPIcheckPoint();
1316		#endif // is_mpi
1317
1318	+	// clean up the forcefield
1319	+	the_ff->cleanMe();
1320		}
1321	+
1322	+	void SimSetup::initSystemCoords(void){
1323	+	int i;
1324
1325	<	void SimSetup::initSystemCoords( void ){
1325	>	char* inName;
1326
1327	<	if( globals->haveInitialConfig() ){
1328	<
1329	<	InitializeFromFile* fileInit;
1327	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1328	>
1329	>	for (i = 0; i < info[0].n_atoms; i++)
1330	>	info[0].atoms[i]->setCoords();
1331	>
1332	>	if (globals->haveInitialConfig()){
1333	>	InitializeFromFile* fileInit;
1334		#ifdef IS_MPI // is_mpi
1335	<	if( worldRank == 0 ){
1335	>	if (worldRank == 0){
1336		#endif //is_mpi
1337	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1337	>	inName = globals->getInitialConfig();
1338	>	fileInit = new InitializeFromFile(inName);
1339		#ifdef IS_MPI
1340	<	}else fileInit = new InitializeFromFile( NULL );
1340	>	}
1341	>	else
1342	>	fileInit = new InitializeFromFile(NULL);
1343		#endif
1344	<	fileInit->read_xyz( info ); // default velocities on
1344	>	fileInit->readInit(info); // default velocities on
1345
1346	<	delete fileInit;
1347	<	}
1348	<	else{
1346	>	delete fileInit;
1347	>	}
1348	>	else{
1349	>
1350	>	// no init from bass
1351	>
1352	>	sprintf(painCave.errMsg,
1353	>	"Cannot intialize a simulation without an initial configuration file.\n");
1354	>	painCave.isFatal = 1;;
1355	>	simError();
1356	>
1357	>	}
1358
866	–	#ifdef IS_MPI
867	–
868	–	// no init from bass
869	–
870	–	sprintf( painCave.errMsg,
871	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
872	–	painCave.isFatal;
873	–	simError();
874	–
875	–	#else
876	–
877	–	initFromBass();
878	–
879	–
880	–	#endif
881	–	}
882	–
1359		#ifdef IS_MPI
1360	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1360	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1361		MPIcheckPoint();
1362		#endif // is_mpi
887	–
1363		}
1364
1365
1366	<	void SimSetup::makeOutNames( void ){
1366	>	void SimSetup::makeOutNames(void){
1367	>	int k;
1368
1369	+
1370	+	for (k = 0; k < nInfo; k++){
1371		#ifdef IS_MPI
1372	<	if( worldRank == 0 ){
1372	>	if (worldRank == 0){
1373		#endif // is_mpi
1374	<
1375	<	if( globals->haveFinalConfig() ){
1376	<	strcpy( info->finalName, globals->getFinalConfig() );
1377	<	}
1378	<	else{
1379	<	strcpy( info->finalName, inFileName );
1374	>
1375	>	if (globals->haveFinalConfig()){
1376	>	strcpy(info[k].finalName, globals->getFinalConfig());
1377	>	}
1378	>	else{
1379	>	strcpy(info[k].finalName, inFileName);
1380	>	char* endTest;
1381	>	int nameLength = strlen(info[k].finalName);
1382	>	endTest = &(info[k].finalName[nameLength - 5]);
1383	>	if (!strcmp(endTest, ".bass")){
1384	>	strcpy(endTest, ".eor");
1385	>	}
1386	>	else if (!strcmp(endTest, ".BASS")){
1387	>	strcpy(endTest, ".eor");
1388	>	}
1389	>	else{
1390	>	endTest = &(info[k].finalName[nameLength - 4]);
1391	>	if (!strcmp(endTest, ".bss")){
1392	>	strcpy(endTest, ".eor");
1393	>	}
1394	>	else if (!strcmp(endTest, ".mdl")){
1395	>	strcpy(endTest, ".eor");
1396	>	}
1397	>	else{
1398	>	strcat(info[k].finalName, ".eor");
1399	>	}
1400	>	}
1401	>	}
1402	>
1403	>	// make the sample and status out names
1404	>
1405	>	strcpy(info[k].sampleName, inFileName);
1406		char* endTest;
1407	<	int nameLength = strlen( info->finalName );
1408	<	endTest = &(info->finalName[nameLength - 5]);
1409	<	if( !strcmp( endTest, ".bass" ) ){
1410	<	strcpy( endTest, ".eor" );
1407	>	int nameLength = strlen(info[k].sampleName);
1408	>	endTest = &(info[k].sampleName[nameLength - 5]);
1409	>	if (!strcmp(endTest, ".bass")){
1410	>	strcpy(endTest, ".dump");
1411		}
1412	<	else if( !strcmp( endTest, ".BASS" ) ){
1413	<	strcpy( endTest, ".eor" );
1412	>	else if (!strcmp(endTest, ".BASS")){
1413	>	strcpy(endTest, ".dump");
1414		}
1415		else{
1416	<	endTest = &(info->finalName[nameLength - 4]);
1417	<	if( !strcmp( endTest, ".bss" ) ){
1418	<	strcpy( endTest, ".eor" );
1419	<	}
1420	<	else if( !strcmp( endTest, ".mdl" ) ){
1421	<	strcpy( endTest, ".eor" );
1422	<	}
1423	<	else{
1424	<	strcat( info->finalName, ".eor" );
1425	<	}
1416	>	endTest = &(info[k].sampleName[nameLength - 4]);
1417	>	if (!strcmp(endTest, ".bss")){
1418	>	strcpy(endTest, ".dump");
1419	>	}
1420	>	else if (!strcmp(endTest, ".mdl")){
1421	>	strcpy(endTest, ".dump");
1422	>	}
1423	>	else{
1424	>	strcat(info[k].sampleName, ".dump");
1425	>	}
1426		}
1427	<	}
1428	<
1429	<	// make the sample and status out names
1430	<
1431	<	strcpy( info->sampleName, inFileName );
1432	<	char* endTest;
929	<	int nameLength = strlen( info->sampleName );
930	<	endTest = &(info->sampleName[nameLength - 5]);
931	<	if( !strcmp( endTest, ".bass" ) ){
932	<	strcpy( endTest, ".dump" );
933	<	}
934	<	else if( !strcmp( endTest, ".BASS" ) ){
935	<	strcpy( endTest, ".dump" );
936	<	}
937	<	else{
938	<	endTest = &(info->sampleName[nameLength - 4]);
939	<	if( !strcmp( endTest, ".bss" ) ){
940	<	strcpy( endTest, ".dump" );
1427	>
1428	>	strcpy(info[k].statusName, inFileName);
1429	>	nameLength = strlen(info[k].statusName);
1430	>	endTest = &(info[k].statusName[nameLength - 5]);
1431	>	if (!strcmp(endTest, ".bass")){
1432	>	strcpy(endTest, ".stat");
1433		}
1434	<	else if( !strcmp( endTest, ".mdl" ) ){
1435	<	strcpy( endTest, ".dump" );
1434	>	else if (!strcmp(endTest, ".BASS")){
1435	>	strcpy(endTest, ".stat");
1436		}
1437		else{
1438	<	strcat( info->sampleName, ".dump" );
1438	>	endTest = &(info[k].statusName[nameLength - 4]);
1439	>	if (!strcmp(endTest, ".bss")){
1440	>	strcpy(endTest, ".stat");
1441	>	}
1442	>	else if (!strcmp(endTest, ".mdl")){
1443	>	strcpy(endTest, ".stat");
1444	>	}
1445	>	else{
1446	>	strcat(info[k].statusName, ".stat");
1447	>	}
1448		}
1449	<	}
1450	<
1451	<	strcpy( info->statusName, inFileName );
1452	<	nameLength = strlen( info->statusName );
1453	<	endTest = &(info->statusName[nameLength - 5]);
1454	<	if( !strcmp( endTest, ".bass" ) ){
954	<	strcpy( endTest, ".stat" );
955	<	}
956	<	else if( !strcmp( endTest, ".BASS" ) ){
957	<	strcpy( endTest, ".stat" );
958	<	}
959	<	else{
960	<	endTest = &(info->statusName[nameLength - 4]);
961	<	if( !strcmp( endTest, ".bss" ) ){
962	<	strcpy( endTest, ".stat" );
1449	>
1450	>	strcpy(info[k].rawPotName, inFileName);
1451	>	nameLength = strlen(info[k].rawPotName);
1452	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1453	>	if (!strcmp(endTest, ".bass")){
1454	>	strcpy(endTest, ".raw");
1455		}
1456	<	else if( !strcmp( endTest, ".mdl" ) ){
1457	<	strcpy( endTest, ".stat" );
1456	>	else if (!strcmp(endTest, ".BASS")){
1457	>	strcpy(endTest, ".raw");
1458		}
1459		else{
1460	<	strcat( info->statusName, ".stat" );
1460	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1461	>	if (!strcmp(endTest, ".bss")){
1462	>	strcpy(endTest, ".raw");
1463	>	}
1464	>	else if (!strcmp(endTest, ".mdl")){
1465	>	strcpy(endTest, ".raw");
1466	>	}
1467	>	else{
1468	>	strcat(info[k].rawPotName, ".raw");
1469	>	}
1470		}
1471	<	}
971	<
1471	>
1472		#ifdef IS_MPI
973	–	}
974	–	#endif // is_mpi
1473
1474	+	}
1475	+	#endif // is_mpi
1476	+	}
1477		}
1478
1479
1480	<	void SimSetup::sysObjectsCreation( void ){
1480	>	void SimSetup::sysObjectsCreation(void){
1481	>	int i, k;
1482
981	–	int i;
982	–
1483		// create the forceField
1484
1485		createFF();
#	Line 994 | Line 1494 | void SimSetup::sysObjectsCreation( void ){
1494
1495		#ifdef IS_MPI
1496		// divide the molecules among the processors
1497	<
1497	>
1498		mpiMolDivide();
1499		#endif //is_mpi
1500	<
1500	>
1501		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1502	<
1502	>
1503		makeSysArrays();
1504
1505		// make and initialize the molecules (all but atomic coordinates)
1506	<
1506	>
1507		makeMolecules();
1008	–	info->identArray = new int[info->n_atoms];
1009	–	for(i=0; i<info->n_atoms; i++){
1010	–	info->identArray[i] = the_atoms[i]->getIdent();
1011	–	}
1012	–
1508
1509	<
1509	>	for (k = 0; k < nInfo; k++){
1510	>	info[k].identArray = new int[info[k].n_atoms];
1511	>	for (i = 0; i < info[k].n_atoms; i++){
1512	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1513	>	}
1514	>	}
1515		}
1516
1517
1518	<	void SimSetup::createFF( void ){
1518	>	void SimSetup::createFF(void){
1519	>	switch (ffCase){
1520	>	case FF_DUFF:
1521	>	the_ff = new DUFF();
1522	>	break;
1523
1524	<	switch( ffCase ){
1524	>	case FF_LJ:
1525	>	the_ff = new LJFF();
1526	>	break;
1527
1528	<	case FF_DUFF:
1529	<	the_ff = new DUFF();
1530	<	break;
1528	>	case FF_EAM:
1529	>	if (has_forcefield_variant)
1530	>	the_ff = new EAM_FF(forcefield_variant);
1531	>	else
1532	>	the_ff = new EAM_FF();
1533	>	break;
1534
1535	<	case FF_LJ:
1536	<	the_ff = new LJFF();
1537	<	break;
1535	>	case FF_H2O:
1536	>	the_ff = new WATER();
1537	>	break;
1538
1539	<	default:
1540	<	sprintf( painCave.errMsg,
1541	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1542	<	painCave.isFatal = 1;
1543	<	simError();
1539	>	default:
1540	>	sprintf(painCave.errMsg,
1541	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1542	>	painCave.isFatal = 1;
1543	>	simError();
1544		}
1545
1546	+
1547		#ifdef IS_MPI
1548	<	strcpy( checkPointMsg, "ForceField creation successful" );
1548	>	strcpy(checkPointMsg, "ForceField creation successful");
1549		MPIcheckPoint();
1550		#endif // is_mpi
1041	–
1551		}
1552
1553
1554	<	void SimSetup::compList( void ){
1046	<
1554	>	void SimSetup::compList(void){
1555		int i;
1556	+	char* id;
1557	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1558	+	LinkedMolStamp* currentStamp = NULL;
1559	+	comp_stamps = new MoleculeStamp * [n_components];
1560	+	bool haveCutoffGroups;
1561
1562	<	comp_stamps = new MoleculeStamp*[n_components];
1563	<
1562	>	haveCutoffGroups = false;
1563	>
1564		// make an array of molecule stamps that match the components used.
1565		// also extract the used stamps out into a separate linked list
1566
1567	<	info->nComponents = n_components;
1568	<	info->componentsNmol = components_nmol;
1569	<	info->compStamps = comp_stamps;
1570	<	info->headStamp = new LinkedMolStamp();
1571	<
1572	<	char* id;
1060	<	LinkedMolStamp* headStamp = info->headStamp;
1061	<	LinkedMolStamp* currentStamp = NULL;
1062	<	for( i=0; i<n_components; i++ ){
1567	>	for (i = 0; i < nInfo; i++){
1568	>	info[i].nComponents = n_components;
1569	>	info[i].componentsNmol = components_nmol;
1570	>	info[i].compStamps = comp_stamps;
1571	>	info[i].headStamp = headStamp;
1572	>	}
1573
1574	+
1575	+	for (i = 0; i < n_components; i++){
1576		id = the_components[i]->getType();
1577		comp_stamps[i] = NULL;
1578	<
1578	>
1579		// check to make sure the component isn't already in the list
1580
1581	<	comp_stamps[i] = headStamp->match( id );
1582	<	if( comp_stamps[i] == NULL ){
1071	<
1581	>	comp_stamps[i] = headStamp->match(id);
1582	>	if (comp_stamps[i] == NULL){
1583		// extract the component from the list;
1584	<
1585	<	currentStamp = stamps->extractMolStamp( id );
1586	<	if( currentStamp == NULL ){
1587	<	sprintf( painCave.errMsg,
1588	<	"SimSetup error: Component \"%s\" was not found in the "
1589	<	"list of declared molecules\n",
1590	<	id );
1591	<	painCave.isFatal = 1;
1592	<	simError();
1584	>
1585	>	currentStamp = stamps->extractMolStamp(id);
1586	>	if (currentStamp == NULL){
1587	>	sprintf(painCave.errMsg,
1588	>	"SimSetup error: Component \"%s\" was not found in the "
1589	>	"list of declared molecules\n",
1590	>	id);
1591	>	painCave.isFatal = 1;
1592	>	simError();
1593		}
1594	<
1595	<	headStamp->add( currentStamp );
1596	<	comp_stamps[i] = headStamp->match( id );
1594	>
1595	>	headStamp->add(currentStamp);
1596	>	comp_stamps[i] = headStamp->match(id);
1597		}
1598	+
1599	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1600	+	haveCutoffGroups = true;
1601		}
1602	+
1603	+	for (i = 0; i < nInfo; i++)
1604	+	info[i].haveCutoffGroups = haveCutoffGroups;
1605
1606		#ifdef IS_MPI
1607	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1607	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1608		MPIcheckPoint();
1609		#endif // is_mpi
1093	–
1094	–
1610		}
1611
1612	<	void SimSetup::calcSysValues( void ){
1613	<	int i, j, k;
1612	>	void SimSetup::calcSysValues(void){
1613	>	int i, j;
1614	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1615
1616	+	int* molMembershipArray;
1617	+	CutoffGroupStamp* cg;
1618
1619		tot_atoms = 0;
1620		tot_bonds = 0;
1621		tot_bends = 0;
1622		tot_torsions = 0;
1623	<	for( i=0; i<n_components; i++ ){
1624	<
1625	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1626	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1627	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1623	>	tot_rigid = 0;
1624	>	tot_groups = 0;
1625	>	for (i = 0; i < n_components; i++){
1626	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630	<	}
1630	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631
1632	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633	+	atomsingroups = 0;
1634	+	for (j=0; j < ncutgroups; j++) {
1635	+	cg = comp_stamps[i]->getCutoffGroup(j);
1636	+	atomsingroups += cg->getNMembers();
1637	+	}
1638	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1640	+	}
1641	+
1642		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1643	+	molMembershipArray = new int[tot_atoms];
1644
1645	<	info->n_atoms = tot_atoms;
1646	<	info->n_bonds = tot_bonds;
1647	<	info->n_bends = tot_bends;
1648	<	info->n_torsions = tot_torsions;
1649	<	info->n_SRI = tot_SRI;
1650	<	info->n_mol = tot_nmol;
1651	<
1652	<	info->molMembershipArray = new int[tot_atoms];
1645	>	for (i = 0; i < nInfo; i++){
1646	>	info[i].n_atoms = tot_atoms;
1647	>	info[i].n_bonds = tot_bonds;
1648	>	info[i].n_bends = tot_bends;
1649	>	info[i].n_torsions = tot_torsions;
1650	>	info[i].n_SRI = tot_SRI;
1651	>	info[i].n_mol = tot_nmol;
1652	>	info[i].ngroup = tot_groups;
1653	>	info[i].molMembershipArray = molMembershipArray;
1654	>	}
1655		}
1656
1125	–
1657		#ifdef IS_MPI
1658
1659	<	void SimSetup::mpiMolDivide( void ){
1129	<
1659	>	void SimSetup::mpiMolDivide(void){
1660		int i, j, k;
1661		int localMol, allMol;
1662		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663	+	int local_rigid, local_groups;
1664	+	vector<int> globalMolIndex;
1665	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1666	+	CutoffGroupStamp* cg;
1667
1668	<	mpiSim = new mpiSimulation( info );
1135	<
1136	<	globalIndex = mpiSim->divideLabor();
1668	>	mpiSim = new mpiSimulation(info);
1669
1670	+	mpiSim->divideLabor();
1671	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1674	+
1675		// set up the local variables
1676	<
1676	>
1677		mol2proc = mpiSim->getMolToProcMap();
1678		molCompType = mpiSim->getMolComponentType();
1679	<
1679	>
1680		allMol = 0;
1681		localMol = 0;
1682		local_atoms = 0;
1683		local_bonds = 0;
1684		local_bends = 0;
1685		local_torsions = 0;
1686	<	globalAtomIndex = 0;
1686	>	local_rigid = 0;
1687	>	local_groups = 0;
1688	>	globalAtomCounter = 0;
1689
1690	+	for (i = 0; i < n_components; i++){
1691	+	for (j = 0; j < components_nmol[i]; j++){
1692	+	if (mol2proc[allMol] == worldRank){
1693	+	local_atoms += comp_stamps[i]->getNAtoms();
1694	+	local_bonds += comp_stamps[i]->getNBonds();
1695	+	local_bends += comp_stamps[i]->getNBends();
1696	+	local_torsions += comp_stamps[i]->getNTorsions();
1697	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1698
1699	<	for( i=0; i<n_components; i++ ){
1699	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700	>	atomsingroups = 0;
1701	>	for (k=0; k < ncutgroups; k++) {
1702	>	cg = comp_stamps[i]->getCutoffGroup(k);
1703	>	atomsingroups += cg->getNMembers();
1704	>	}
1705	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706	>	ncutgroups;
1707	>	local_groups += ngroupsinstamp;
1708
1709	<	for( j=0; j<components_nmol[i]; j++ ){
1155	<
1156	<	if( mol2proc[allMol] == worldRank ){
1157	<
1158	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1159	<	local_bonds +=    comp_stamps[i]->getNBonds();
1160	<	local_bends +=    comp_stamps[i]->getNBends();
1161	<	local_torsions += comp_stamps[i]->getNTorsions();
1162	<	localMol++;
1709	>	localMol++;
1710		}
1711	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1712	<	info->molMembershipArray[globalAtomIndex] = allMol;
1713	<	globalAtomIndex++;
1711	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1712	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1713	>	globalAtomCounter++;
1714		}
1715
1716	<	allMol++;
1716	>	allMol++;
1717		}
1718		}
1719		local_SRI = local_bonds + local_bends + local_torsions;
1720	+
1721	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1722
1723	<	info->n_atoms = mpiSim->getMyNlocal();
1724	<
1725	<	if( local_atoms != info->n_atoms ){
1726	<	sprintf( painCave.errMsg,
1727	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1179	<	" localAtom (%d) are not equal.\n",
1180	<	info->n_atoms,
1181	<	local_atoms );
1723	>	if (local_atoms != info[0].n_atoms){
1724	>	sprintf(painCave.errMsg,
1725	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1726	>	"\tlocalAtom (%d) are not equal.\n",
1727	>	info[0].n_atoms, local_atoms);
1728		painCave.isFatal = 1;
1729		simError();
1730		}
1731
1732	<	info->n_bonds = local_bonds;
1733	<	info->n_bends = local_bends;
1734	<	info->n_torsions = local_torsions;
1735	<	info->n_SRI = local_SRI;
1736	<	info->n_mol = localMol;
1732	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1733	>	if (local_groups != info[0].ngroup){
1734	>	sprintf(painCave.errMsg,
1735	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736	>	"\tlocalGroups (%d) are not equal.\n",
1737	>	info[0].ngroup, local_groups);
1738	>	painCave.isFatal = 1;
1739	>	simError();
1740	>	}
1741	>
1742	>	info[0].n_bonds = local_bonds;
1743	>	info[0].n_bends = local_bends;
1744	>	info[0].n_torsions = local_torsions;
1745	>	info[0].n_SRI = local_SRI;
1746	>	info[0].n_mol = localMol;
1747
1748	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1748	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1749		MPIcheckPoint();
1750		}
1751	<
1751	>
1752		#endif // is_mpi
1753
1754
1755	<	void SimSetup::makeSysArrays( void ){
1756	<	int i, j, k;
1755	>	void SimSetup::makeSysArrays(void){
1756	>
1757	>	#ifndef IS_MPI
1758	>	int k, j;
1759	>	#endif // is_mpi
1760	>	int i, l;
1761
1762	+	Atom** the_atoms;
1763	+	Molecule* the_molecules;
1764
1765	<	// create the atom and short range interaction arrays
1765	>	for (l = 0; l < nInfo; l++){
1766	>	// create the atom and short range interaction arrays
1767
1768	<	Atom::createArrays(info->n_atoms);
1769	<	the_atoms = new Atom*[info->n_atoms];
1770	<	the_molecules = new Molecule[info->n_mol];
1208	<	int molIndex;
1768	>	the_atoms = new Atom * [info[l].n_atoms];
1769	>	the_molecules = new Molecule[info[l].n_mol];
1770	>	int molIndex;
1771
1772	<	// initialize the molecule's stampID's
1772	>	// initialize the molecule's stampID's
1773
1774		#ifdef IS_MPI
1213	–
1775
1776	<	molIndex = 0;
1777	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1778	<
1779	<	if(mol2proc[i] == worldRank ){
1780	<	the_molecules[molIndex].setStampID( molCompType[i] );
1781	<	the_molecules[molIndex].setMyIndex( molIndex );
1782	<	the_molecules[molIndex].setGlobalIndex( i );
1783	<	molIndex++;
1776	>
1777	>	molIndex = 0;
1778	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779	>	if (mol2proc[i] == worldRank){
1780	>	the_molecules[molIndex].setStampID(molCompType[i]);
1781	>	the_molecules[molIndex].setMyIndex(molIndex);
1782	>	the_molecules[molIndex].setGlobalIndex(i);
1783	>	molIndex++;
1784	>	}
1785		}
1224	–	}
1786
1787		#else // is_mpi
1788	<
1789	<	molIndex = 0;
1790	<	globalAtomIndex = 0;
1791	<	for(i=0; i<n_components; i++){
1792	<	for(j=0; j<components_nmol[i]; j++ ){
1793	<	the_molecules[molIndex].setStampID( i );
1794	<	the_molecules[molIndex].setMyIndex( molIndex );
1795	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1796	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1797	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1798	<	globalAtomIndex++;
1788	>
1789	>	molIndex = 0;
1790	>	globalAtomCounter = 0;
1791	>	for (i = 0; i < n_components; i++){
1792	>	for (j = 0; j < components_nmol[i]; j++){
1793	>	the_molecules[molIndex].setStampID(i);
1794	>	the_molecules[molIndex].setMyIndex(molIndex);
1795	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1796	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1797	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1798	>	globalAtomCounter++;
1799	>	}
1800	>	molIndex++;
1801		}
1239	–	molIndex++;
1802		}
1241	–	}
1242	–
1803
1804	+
1805		#endif // is_mpi
1806
1807	<
1808	<	if( info->n_SRI ){
1807	>	info[l].globalExcludes = new int;
1808	>	info[l].globalExcludes[0] = 0;
1809
1810	<	Exclude::createArray(info->n_SRI);
1811	<	the_excludes = new Exclude*[info->n_SRI];
1812	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1813	<	info->globalExcludes = new int;
1814	<	info->n_exclude = info->n_SRI;
1254	<	}
1255	<	else{
1810	>	// set the arrays into the SimInfo object
1811	>
1812	>	info[l].atoms = the_atoms;
1813	>	info[l].molecules = the_molecules;
1814	>	info[l].nGlobalExcludes = 0;
1815
1816	<	Exclude::createArray( 1 );
1258	<	the_excludes = new Exclude*;
1259	<	the_excludes[0] = new Exclude(0);
1260	<	the_excludes[0]->setPair( 0,0 );
1261	<	info->globalExcludes = new int;
1262	<	info->globalExcludes[0] = 0;
1263	<	info->n_exclude = 0;
1816	>	the_ff->setSimInfo(info);
1817		}
1818	+	}
1819
1820	<	// set the arrays into the SimInfo object
1820	>	void SimSetup::makeIntegrator(void){
1821	>	int k;
1822
1823	<	info->atoms = the_atoms;
1824	<	info->molecules = the_molecules;
1825	<	info->nGlobalExcludes = 0;
1826	<	info->excludes = the_excludes;
1823	>	NVE<RealIntegrator>* myNVE = NULL;
1824	>	NVT<RealIntegrator>* myNVT = NULL;
1825	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1826	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1827	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1828	>
1829	>	for (k = 0; k < nInfo; k++){
1830	>	switch (ensembleCase){
1831	>	case NVE_ENS:
1832	>	if (globals->haveZconstraints()){
1833	>	setupZConstraint(info[k]);
1834	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1835	>	}
1836	>	else{
1837	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1838	>	}
1839	>
1840	>	info->the_integrator = myNVE;
1841	>	break;
1842
1843	<	the_ff->setSimInfo( info );
1843	>	case NVT_ENS:
1844	>	if (globals->haveZconstraints()){
1845	>	setupZConstraint(info[k]);
1846	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1847	>	}
1848	>	else
1849	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1850
1851	<	}
1851	>	myNVT->setTargetTemp(globals->getTargetTemp());
1852
1853	<	void SimSetup::makeIntegrator( void ){
1853	>	if (globals->haveTauThermostat())
1854	>	myNVT->setTauThermostat(globals->getTauThermostat());
1855	>	else{
1856	>	sprintf(painCave.errMsg,
1857	>	"SimSetup error: If you use the NVT\n"
1858	>	"\tensemble, you must set tauThermostat.\n");
1859	>	painCave.isFatal = 1;
1860	>	simError();
1861	>	}
1862
1863	<	NVT*  myNVT = NULL;
1864	<	NPTi* myNPTi = NULL;
1281	<	NPTf* myNPTf = NULL;
1282	<	NPTim* myNPTim = NULL;
1283	<	NPTfm* myNPTfm = NULL;
1863	>	info->the_integrator = myNVT;
1864	>	break;
1865
1866	<	switch( ensembleCase ){
1866	>	case NPTi_ENS:
1867	>	if (globals->haveZconstraints()){
1868	>	setupZConstraint(info[k]);
1869	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1870	>	}
1871	>	else
1872	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1873
1874	<	case NVE_ENS:
1288	<	new NVE( info, the_ff );
1289	<	break;
1874	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1875
1876	<	case NVT_ENS:
1877	<	myNVT = new NVT( info, the_ff );
1878	<	myNVT->setTargetTemp(globals->getTargetTemp());
1876	>	if (globals->haveTargetPressure())
1877	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1878	>	else{
1879	>	sprintf(painCave.errMsg,
1880	>	"SimSetup error: If you use a constant pressure\n"
1881	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1882	>	painCave.isFatal = 1;
1883	>	simError();
1884	>	}
1885
1886	<	if (globals->haveTauThermostat())
1887	<	myNVT->setTauThermostat(globals->getTauThermostat());
1886	>	if (globals->haveTauThermostat())
1887	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1888	>	else{
1889	>	sprintf(painCave.errMsg,
1890	>	"SimSetup error: If you use an NPT\n"
1891	>	"\tensemble, you must set tauThermostat.\n");
1892	>	painCave.isFatal = 1;
1893	>	simError();
1894	>	}
1895
1896	<	else {
1897	<	sprintf( painCave.errMsg,
1898	<	"SimSetup error: If you use the NVT\n"
1899	<	"    ensemble, you must set tauThermostat.\n");
1900	<	painCave.isFatal = 1;
1901	<	simError();
1902	<	}
1903	<	break;
1896	>	if (globals->haveTauBarostat())
1897	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1898	>	else{
1899	>	sprintf(painCave.errMsg,
1900	>	"SimSetup error: If you use an NPT\n"
1901	>	"\tensemble, you must set tauBarostat.\n");
1902	>	painCave.isFatal = 1;
1903	>	simError();
1904	>	}
1905
1906	<	case NPTi_ENS:
1907	<	myNPTi = new NPTi( info, the_ff );
1309	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1906	>	info->the_integrator = myNPTi;
1907	>	break;
1908
1909	<	if (globals->haveTargetPressure())
1910	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1911	<	else {
1912	<	sprintf( painCave.errMsg,
1913	<	"SimSetup error: If you use a constant pressure\n"
1914	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1915	<	painCave.isFatal = 1;
1318	<	simError();
1319	<	}
1320	<
1321	<	if( globals->haveTauThermostat() )
1322	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1323	<	else{
1324	<	sprintf( painCave.errMsg,
1325	<	"SimSetup error: If you use an NPT\n"
1326	<	"    ensemble, you must set tauThermostat.\n");
1327	<	painCave.isFatal = 1;
1328	<	simError();
1329	<	}
1909	>	case NPTf_ENS:
1910	>	if (globals->haveZconstraints()){
1911	>	setupZConstraint(info[k]);
1912	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1913	>	}
1914	>	else
1915	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1916
1917	<	if( globals->haveTauBarostat() )
1332	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1333	<	else{
1334	<	sprintf( painCave.errMsg,
1335	<	"SimSetup error: If you use an NPT\n"
1336	<	"    ensemble, you must set tauBarostat.\n");
1337	<	painCave.isFatal = 1;
1338	<	simError();
1339	<	}
1340	<	break;
1917	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1918
1919	<	case NPTf_ENS:
1920	<	myNPTf = new NPTf( info, the_ff );
1921	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1922	<
1923	<	if (globals->haveTargetPressure())
1924	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1925	<	else {
1926	<	sprintf( painCave.errMsg,
1927	<	"SimSetup error: If you use a constant pressure\n"
1351	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1352	<	painCave.isFatal = 1;
1353	<	simError();
1354	<	}
1919	>	if (globals->haveTargetPressure())
1920	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1921	>	else{
1922	>	sprintf(painCave.errMsg,
1923	>	"SimSetup error: If you use a constant pressure\n"
1924	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1925	>	painCave.isFatal = 1;
1926	>	simError();
1927	>	}
1928
1929	<	if( globals->haveTauThermostat() )
1930	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1358	<	else{
1359	<	sprintf( painCave.errMsg,
1360	<	"SimSetup error: If you use an NPT\n"
1361	<	"    ensemble, you must set tauThermostat.\n");
1362	<	painCave.isFatal = 1;
1363	<	simError();
1364	<	}
1929	>	if (globals->haveTauThermostat())
1930	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1931
1932	<	if( globals->haveTauBarostat() )
1933	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1934	<	else{
1935	<	sprintf( painCave.errMsg,
1936	<	"SimSetup error: If you use an NPT\n"
1937	<	"    ensemble, you must set tauBarostat.\n");
1938	<	painCave.isFatal = 1;
1373	<	simError();
1374	<	}
1375	<	break;
1376	<
1377	<	case NPTim_ENS:
1378	<	myNPTim = new NPTim( info, the_ff );
1379	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1932	>	else{
1933	>	sprintf(painCave.errMsg,
1934	>	"SimSetup error: If you use an NPT\n"
1935	>	"\tensemble, you must set tauThermostat.\n");
1936	>	painCave.isFatal = 1;
1937	>	simError();
1938	>	}
1939
1940	<	if (globals->haveTargetPressure())
1941	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1383	<	else {
1384	<	sprintf( painCave.errMsg,
1385	<	"SimSetup error: If you use a constant pressure\n"
1386	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1387	<	painCave.isFatal = 1;
1388	<	simError();
1389	<	}
1390	<
1391	<	if( globals->haveTauThermostat() )
1392	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1393	<	else{
1394	<	sprintf( painCave.errMsg,
1395	<	"SimSetup error: If you use an NPT\n"
1396	<	"    ensemble, you must set tauThermostat.\n");
1397	<	painCave.isFatal = 1;
1398	<	simError();
1399	<	}
1940	>	if (globals->haveTauBarostat())
1941	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1942
1943	<	if( globals->haveTauBarostat() )
1944	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1945	<	else{
1946	<	sprintf( painCave.errMsg,
1947	<	"SimSetup error: If you use an NPT\n"
1948	<	"    ensemble, you must set tauBarostat.\n");
1949	<	painCave.isFatal = 1;
1408	<	simError();
1409	<	}
1410	<	break;
1943	>	else{
1944	>	sprintf(painCave.errMsg,
1945	>	"SimSetup error: If you use an NPT\n"
1946	>	"\tensemble, you must set tauBarostat.\n");
1947	>	painCave.isFatal = 1;
1948	>	simError();
1949	>	}
1950
1951	<	case NPTfm_ENS:
1952	<	myNPTfm = new NPTfm( info, the_ff );
1414	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1951	>	info->the_integrator = myNPTf;
1952	>	break;
1953
1954	<	if (globals->haveTargetPressure())
1955	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1956	<	else {
1957	<	sprintf( painCave.errMsg,
1958	<	"SimSetup error: If you use a constant pressure\n"
1959	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1960	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauThermostat() )
1427	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauThermostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1954	>	case NPTxyz_ENS:
1955	>	if (globals->haveZconstraints()){
1956	>	setupZConstraint(info[k]);
1957	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1958	>	}
1959	>	else
1960	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1961
1962	<	if( globals->haveTauBarostat() )
1437	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1438	<	else{
1439	<	sprintf( painCave.errMsg,
1440	<	"SimSetup error: If you use an NPT\n"
1441	<	"    ensemble, you must set tauBarostat.\n");
1442	<	painCave.isFatal = 1;
1443	<	simError();
1444	<	}
1445	<	break;
1962	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1963
1964	<	default:
1965	<	sprintf( painCave.errMsg,
1966	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1967	<	painCave.isFatal = 1;
1968	<	simError();
1969	<	}
1964	>	if (globals->haveTargetPressure())
1965	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1966	>	else{
1967	>	sprintf(painCave.errMsg,
1968	>	"SimSetup error: If you use a constant pressure\n"
1969	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1970	>	painCave.isFatal = 1;
1971	>	simError();
1972	>	}
1973
1974	+	if (globals->haveTauThermostat())
1975	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1976	+	else{
1977	+	sprintf(painCave.errMsg,
1978	+	"SimSetup error: If you use an NPT\n"
1979	+	"\tensemble, you must set tauThermostat.\n");
1980	+	painCave.isFatal = 1;
1981	+	simError();
1982	+	}
1983	+
1984	+	if (globals->haveTauBarostat())
1985	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1986	+	else{
1987	+	sprintf(painCave.errMsg,
1988	+	"SimSetup error: If you use an NPT\n"
1989	+	"\tensemble, you must set tauBarostat.\n");
1990	+	painCave.isFatal = 1;
1991	+	simError();
1992	+	}
1993	+
1994	+	info->the_integrator = myNPTxyz;
1995	+	break;
1996	+
1997	+	default:
1998	+	sprintf(painCave.errMsg,
1999	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
2000	+	painCave.isFatal = 1;
2001	+	simError();
2002	+	}
2003	+	}
2004		}
2005
2006	<	void SimSetup::initFortran( void ){
2006	>	void SimSetup::initFortran(void){
2007	>	info[0].refreshSim();
2008
2009	<	info->refreshSim();
2010	<
1460	<	if( !strcmp( info->mixingRule, "standard") ){
1461	<	the_ff->initForceField( LB_MIXING_RULE );
2009	>	if (!strcmp(info[0].mixingRule, "standard")){
2010	>	the_ff->initForceField(LB_MIXING_RULE);
2011		}
2012	<	else if( !strcmp( info->mixingRule, "explicit") ){
2013	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
2012	>	else if (!strcmp(info[0].mixingRule, "explicit")){
2013	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
2014		}
2015		else{
2016	<	sprintf( painCave.errMsg,
2017	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1469	<	info->mixingRule );
2016	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2017	>	info[0].mixingRule);
2018		painCave.isFatal = 1;
2019		simError();
2020		}
2021
2022
2023		#ifdef IS_MPI
2024	<	strcpy( checkPointMsg,
1477	<	"Successfully intialized the mixingRule for Fortran." );
2024	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2025		MPIcheckPoint();
2026		#endif // is_mpi
2027	+	}
2028
2029	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2030	+	int nZConstraints;
2031	+	ZconStamp** zconStamp;
2032	+
2033	+	if (globals->haveZconstraintTime()){
2034	+	//add sample time of z-constraint  into SimInfo's property list
2035	+	DoubleData* zconsTimeProp = new DoubleData();
2036	+	zconsTimeProp->setID(ZCONSTIME_ID);
2037	+	zconsTimeProp->setData(globals->getZconsTime());
2038	+	theInfo.addProperty(zconsTimeProp);
2039	+	}
2040	+	else{
2041	+	sprintf(painCave.errMsg,
2042	+	"ZConstraint error: If you use a ZConstraint,\n"
2043	+	"\tyou must set zconsTime.\n");
2044	+	painCave.isFatal = 1;
2045	+	simError();
2046	+	}
2047	+
2048	+	//push zconsTol into siminfo, if user does not specify
2049	+	//value for zconsTol, a default value will be used
2050	+	DoubleData* zconsTol = new DoubleData();
2051	+	zconsTol->setID(ZCONSTOL_ID);
2052	+	if (globals->haveZconsTol()){
2053	+	zconsTol->setData(globals->getZconsTol());
2054	+	}
2055	+	else{
2056	+	double defaultZConsTol = 0.01;
2057	+	sprintf(painCave.errMsg,
2058	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2059	+	"\tOOPSE will use a default value of %f.\n"
2060	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2061	+	defaultZConsTol);
2062	+	painCave.isFatal = 0;
2063	+	simError();
2064	+
2065	+	zconsTol->setData(defaultZConsTol);
2066	+	}
2067	+	theInfo.addProperty(zconsTol);
2068	+
2069	+	//set Force Subtraction Policy
2070	+	StringData* zconsForcePolicy = new StringData();
2071	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2072	+
2073	+	if (globals->haveZconsForcePolicy()){
2074	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2075	+	}
2076	+	else{
2077	+	sprintf(painCave.errMsg,
2078	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2079	+	"\tOOPSE will use PolicyByMass.\n"
2080	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2081	+	painCave.isFatal = 0;
2082	+	simError();
2083	+	zconsForcePolicy->setData("BYMASS");
2084	+	}
2085	+
2086	+	theInfo.addProperty(zconsForcePolicy);
2087	+
2088	+	//set zcons gap
2089	+	DoubleData* zconsGap = new DoubleData();
2090	+	zconsGap->setID(ZCONSGAP_ID);
2091	+
2092	+	if (globals->haveZConsGap()){
2093	+	zconsGap->setData(globals->getZconsGap());
2094	+	theInfo.addProperty(zconsGap);
2095	+	}
2096	+
2097	+	//set zcons fixtime
2098	+	DoubleData* zconsFixtime = new DoubleData();
2099	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2100	+
2101	+	if (globals->haveZConsFixTime()){
2102	+	zconsFixtime->setData(globals->getZconsFixtime());
2103	+	theInfo.addProperty(zconsFixtime);
2104	+	}
2105	+
2106	+	//set zconsUsingSMD
2107	+	IntData* zconsUsingSMD = new IntData();
2108	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2109	+
2110	+	if (globals->haveZConsUsingSMD()){
2111	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2112	+	theInfo.addProperty(zconsUsingSMD);
2113	+	}
2114	+
2115	+	//Determine the name of ouput file and add it into SimInfo's property list
2116	+	//Be careful, do not use inFileName, since it is a pointer which
2117	+	//point to a string at master node, and slave nodes do not contain that string
2118	+
2119	+	string zconsOutput(theInfo.finalName);
2120	+
2121	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2122	+
2123	+	StringData* zconsFilename = new StringData();
2124	+	zconsFilename->setID(ZCONSFILENAME_ID);
2125	+	zconsFilename->setData(zconsOutput);
2126	+
2127	+	theInfo.addProperty(zconsFilename);
2128	+
2129	+	//setup index, pos and other parameters of z-constraint molecules
2130	+	nZConstraints = globals->getNzConstraints();
2131	+	theInfo.nZconstraints = nZConstraints;
2132	+
2133	+	zconStamp = globals->getZconStamp();
2134	+	ZConsParaItem tempParaItem;
2135	+
2136	+	ZConsParaData* zconsParaData = new ZConsParaData();
2137	+	zconsParaData->setID(ZCONSPARADATA_ID);
2138	+
2139	+	for (int i = 0; i < nZConstraints; i++){
2140	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2141	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2142	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2143	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2144	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2145	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2146	+	zconsParaData->addItem(tempParaItem);
2147	+	}
2148	+
2149	+	//check the uniqueness of index
2150	+	if(!zconsParaData->isIndexUnique()){
2151	+	sprintf(painCave.errMsg,
2152	+	"ZConstraint Error: molIndex is not unique!\n");
2153	+	painCave.isFatal = 1;
2154	+	simError();
2155	+	}
2156	+
2157	+	//sort the parameters by index of molecules
2158	+	zconsParaData->sortByIndex();
2159	+
2160	+	//push data into siminfo, therefore, we can retrieve later
2161	+	theInfo.addProperty(zconsParaData);
2162		}
2163	+
2164	+	void SimSetup::makeMinimizer(){
2165	+
2166	+	OOPSEMinimizer* myOOPSEMinimizer;
2167	+	MinimizerParameterSet* param;
2168	+	char minimizerName[100];
2169	+
2170	+	for (int i = 0; i < nInfo; i++){
2171	+
2172	+	//prepare parameter set for minimizer
2173	+	param = new MinimizerParameterSet();
2174	+	param->setDefaultParameter();
2175	+
2176	+	if (globals->haveMinimizer()){
2177	+	param->setFTol(globals->getMinFTol());
2178	+	}
2179	+
2180	+	if (globals->haveMinGTol()){
2181	+	param->setGTol(globals->getMinGTol());
2182	+	}
2183	+
2184	+	if (globals->haveMinMaxIter()){
2185	+	param->setMaxIteration(globals->getMinMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinWriteFrq()){
2189	+	param->setMaxIteration(globals->getMinMaxIter());
2190	+	}
2191	+
2192	+	if (globals->haveMinWriteFrq()){
2193	+	param->setWriteFrq(globals->getMinWriteFrq());
2194	+	}
2195	+
2196	+	if (globals->haveMinStepSize()){
2197	+	param->setStepSize(globals->getMinStepSize());
2198	+	}
2199	+
2200	+	if (globals->haveMinLSMaxIter()){
2201	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2202	+	}
2203	+
2204	+	if (globals->haveMinLSTol()){
2205	+	param->setLineSearchTol(globals->getMinLSTol());
2206	+	}
2207	+
2208	+	strcpy(minimizerName, globals->getMinimizer());
2209	+
2210	+	if (!strcasecmp(minimizerName, "CG")){
2211	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2212	+	}
2213	+	else if (!strcasecmp(minimizerName, "SD")){
2214	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2215	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2216	+	}
2217	+	else{
2218	+	sprintf(painCave.errMsg,
2219	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2220	+	painCave.isFatal = 0;
2221	+	simError();
2222	+
2223	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2224	+	}
2225	+	info[i].the_integrator = myOOPSEMinimizer;
2226	+
2227	+	//store the minimizer into simInfo
2228	+	info[i].the_minimizer = myOOPSEMinimizer;
2229	+	info[i].has_minimizer = true;
2230	+	}
2231	+
2232	+	}

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