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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1104 by gezelter, Tue Apr 13 16:26:03 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 "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 41 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
81	–	int i, j, k, globalAtomIndex;
82	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 89 | Line 132 | void SimSetup::createSim( void ){
132		sysObjectsCreation();
133
134		// check on the post processing info
135	<
135	>
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	initSystemCoords();
141	<
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
150	<
151	<	// make the integrator
150	>
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157
106	–	makeIntegrator();
107	–
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
#	Line 112 | Line 162 | void SimSetup::createSim( void ){
162		// initialize the Fortran
163
164		initFortran();
115	–
116	–
117	–
165		}
166
167
168	<	void SimSetup::makeMolecules( void ){
169	<
170	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174		molInit molInfo;
175		DirectionalAtom* dAtom;
176	+	RigidBody* myRB;
177	+	StuntDouble* mySD;
178		LinkedAssign* extras;
179		LinkedAssign* current_extra;
180		AtomStamp* currentAtom;
181		BondStamp* currentBond;
182		BendStamp* currentBend;
183		TorsionStamp* currentTorsion;
184	+	RigidBodyStamp* currentRigidBody;
185
186		bond_pair* theBonds;
187		bend_set* theBends;
188		torsion_set* theTorsions;
189
190	<
190	>	set<int> skipList;
191	>
192	>	double phi, theta, psi;
193	>
194		//init the forceField paramters
195
196		the_ff->readParams();
197
142	–
198		// init the atoms
199
200	<	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();
200	>	int nMembers, nNew, rb1, rb2;
201
202	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
203	<	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;
202	>	for (k = 0; k < nInfo; k++){
203	>	the_ff->setSimInfo(&(info[k]));
204
205	<	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];
205	>	atomOffset = 0;
206
207	<	theBonds = new bond_pair[molInfo.nBonds];
208	<	theBends = new bend_set[molInfo.nBends];
209	<	theTorsions = new torsion_set[molInfo.nTorsions];
210	<
211	<	// make the Atoms
212	<
213	<	for(j=0; j<molInfo.nAtoms; j++){
207	>	for (i = 0; i < info[k].n_mol; i++){
208	>	stampID = info[k].molecules[i].getStampID();
209	>
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215
216	<	currentAtom = comp_stamps[stampID]->getAtom( j );
174	<	if( currentAtom->haveOrientation() ){
175	<
176	<	dAtom = new DirectionalAtom(j + atomOffset);
177	<	info->n_oriented++;
178	<	molInfo.myAtoms[j] = dAtom;
179	<
180	<	ux = currentAtom->getOrntX();
181	<	uy = currentAtom->getOrntY();
182	<	uz = currentAtom->getOrntZ();
183	<
184	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
185	<
186	<	u = sqrt( uSqr );
187	<	ux = ux / u;
188	<	uy = uy / u;
189	<	uz = uz / u;
190	<
191	<	dAtom->setSUx( ux );
192	<	dAtom->setSUy( uy );
193	<	dAtom->setSUz( uz );
194	<	}
195	<	else{
196	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197	<	}
198	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
199	<
200	<	#ifdef IS_MPI
201	<
202	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
203	<
204	<	#endif // is_mpi
205	<	}
206	<
207	<	// make the bonds
208	<	for(j=0; j<molInfo.nBonds; j++){
209	<
210	<	currentBond = comp_stamps[stampID]->getBond( j );
211	<	theBonds[j].a = currentBond->getA() + atomOffset;
212	<	theBonds[j].b = currentBond->getB() + atomOffset;
216	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
217
218	<	exI = theBonds[j].a;
219	<	exJ = theBonds[j].b;
218	>	if (molInfo.nBonds > 0)
219	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	>	else
221	>	molInfo.myBonds = NULL;
222
223	<	// exclude_I must always be the smaller of the pair
224	<	if( exI > exJ ){
225	<	tempEx = exI;
226	<	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
223	>	if (molInfo.nBends > 0)
224	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	>	else
226	>	molInfo.myBends = NULL;
227
228	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
229	<	#endif  //is_mpi
230	<	}
231	<	excludeOffset += molInfo.nBonds;
228	>	if (molInfo.nTorsions > 0)
229	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	>	else
231	>	molInfo.myTorsions = NULL;
232
233	<	//make the bends
234	<	for(j=0; j<molInfo.nBends; j++){
233	>	theBonds = new bond_pair[molInfo.nBonds];
234	>	theBends = new bend_set[molInfo.nBends];
235	>	theTorsions = new torsion_set[molInfo.nTorsions];
236
237	<	currentBend = comp_stamps[stampID]->getBend( j );
238	<	theBends[j].a = currentBend->getA() + atomOffset;
239	<	theBends[j].b = currentBend->getB() + atomOffset;
240	<	theBends[j].c = currentBend->getC() + atomOffset;
241	<
242	<	if( currentBend->haveExtras() ){
243	<
244	<	extras = currentBend->getExtras();
245	<	current_extra = extras;
246	<
247	<	while( current_extra != NULL ){
248	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
249	<
250	<	switch( current_extra->getType() ){
251	<
252	<	case 0:
253	<	theBends[j].ghost =
254	<	current_extra->getInt() + atomOffset;
255	<	theBends[j].isGhost = 1;
256	<	break;
257	<
258	<	case 1:
259	<	theBends[j].ghost =
260	<	(int)current_extra->getDouble() + atomOffset;
261	<	theBends[j].isGhost = 1;
262	<	break;
263	<
264	<	default:
265	<	sprintf( painCave.errMsg,
266	<	"SimSetup Error: ghostVectorSource was neither a "
267	<	"double nor an int.\n"
268	<	"-->Bend[%d] in %s\n",
269	<	j, comp_stamps[stampID]->getID() );
270	<	painCave.isFatal = 1;
271	<	simError();
272	<	}
273	<	}
274	<
275	<	else{
276	<
277	<	sprintf( painCave.errMsg,
278	<	"SimSetup Error: unhandled bend assignment:\n"
279	<	"    -->%s in Bend[%d] in %s\n",
280	<	current_extra->getlhs(),
281	<	j, comp_stamps[stampID]->getID() );
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<
286	<	current_extra = current_extra->getNext();
287	<	}
237	>	// make the Atoms
238	>
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241	>
242	>	if (currentAtom->haveOrientation()){
243	>	dAtom = new DirectionalAtom((j + atomOffset),
244	>	info[k].getConfiguration());
245	>	info[k].n_oriented++;
246	>	molInfo.myAtoms[j] = dAtom;
247	>
248	>	// Directional Atoms have standard unit vectors which are oriented
249	>	// in space using the three Euler angles.  We assume the standard
250	>	// unit vector was originally along the z axis below.
251	>
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255	>
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260	>
261	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	>	}
263	>
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265	>
266	>	#ifdef IS_MPI
267	>
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269	>
270	>	#endif // is_mpi
271	>	}
272	>
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278	>
279	>	tempI = theBonds[j].a;
280	>	tempJ = theBonds[j].b;
281	>
282	>	#ifdef IS_MPI
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289	>
290	>	info[k].excludes->addPair(exI, exJ);
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	<	}
303	<
304	<	// exclude_I must always be the smaller of the pair
305	<	if( exI > exJ ){
306	<	tempEx = exI;
307	<	exI = exJ;
308	<	exJ = tempEx;
309	<	}
292	>
293	>	//make the bends
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299	>
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303	>
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311	>
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317	>
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336	>
337	>	current_extra = current_extra->getNext();
338	>	}
339	>	}
340	>
341	>	if (theBends[j].isGhost) {
342	>
343	>	tempI = theBends[j].a;
344	>	tempJ = theBends[j].b;
345	>
346		#ifdef IS_MPI
347	<	tempEx = exI;
348	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
349	<	tempEx = exJ;
350	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	<
352	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
353	<	#else  // isn't MPI
318	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319	<	#endif  //is_mpi
320	<	}
321	<	excludeOffset += molInfo.nBends;
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354
355	<	for(j=0; j<molInfo.nTorsions; j++){
324	<
325	<	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;
330	<
331	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
355	>	} else {
356
357	<	// exclude_I must always be the smaller of the pair
358	<	if( exI > exJ ){
359	<	tempEx = exI;
360	<	exI = exJ;
361	<	exJ = tempEx;
357	>	tempI = theBends[j].a;
358	>	tempJ = theBends[j].b;
359	>	tempK = theBends[j].c;
360	>
361	>	#ifdef IS_MPI
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375		}
376	+
377	+	for (j = 0; j < molInfo.nTorsions; j++){
378	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383	+
384	+	tempI = theTorsions[j].a;
385	+	tempJ = theTorsions[j].b;
386	+	tempK = theTorsions[j].c;
387	+	tempL = theTorsions[j].d;
388	+
389		#ifdef IS_MPI
390	<	tempEx = exI;
391	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
392	<	tempEx = exJ;
393	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
394	<
395	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
396	<	#else  // isn't MPI
397	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
398	<	#endif  //is_mpi
399	<	}
351	<	excludeOffset += molInfo.nTorsions;
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399	>	#endif
400
401	<
402	<	// send the arrays off to the forceField for init.
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407	>	}
408
409	<	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 );
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410
411	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	+	nMembers = currentRigidBody->getNMembers();
413
414	<	the_molecules[i].initialize( molInfo );
414	>	// Create the Rigid Body:
415
416	+	myRB = new RigidBody();
417	+
418	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
419
420	<	atomOffset += molInfo.nAtoms;
421	<	delete[] theBonds;
422	<	delete[] theBends;
423	<	delete[] theTorsions;
420	>	// molI is atom numbering inside this molecule
421	>	molI = currentRigidBody->getMember(rb1);
422	>
423	>	// tempI is atom numbering on local processor
424	>	tempI = molI + atomOffset;
425	>
426	>	// currentAtom is the AtomStamp (which we need for
427	>	// rigid body reference positions)
428	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
429	>
430	>	// When we add to the rigid body, add the atom itself and
431	>	// the stamp info:
432	>
433	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	>
435	>	// Add this atom to the Skip List for the integrators
436	>	#ifdef IS_MPI
437	>	slI = info[k].atoms[tempI]->getGlobalIndex();
438	>	#else
439	>	slI = tempI;
440	>	#endif
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468	>
469	>	molInfo.myRigidBodies.push_back(myRB);
470	>	info[k].rigidBodies.push_back(myRB);
471	>	}
472	>
473	>
474	>	// After this is all set up, scan through the atoms to
475	>	// see if they can be added to the integrableObjects:
476	>
477	>	for (j = 0; j < molInfo.nAtoms; j++){
478	>
479	>	#ifdef IS_MPI
480	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
481	>	#else
482	>	slJ = j+atomOffset;
483	>	#endif
484	>
485	>	// if they aren't on the skip list, then they can be integrated
486	>
487	>	if (skipList.find(slJ) == skipList.end()) {
488	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
489	>	info[k].integrableObjects.push_back(mySD);
490	>	molInfo.myIntegrableObjects.push_back(mySD);
491	>	}
492	>	}
493	>
494	>	// all rigid bodies are integrated:
495	>
496	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
497	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
498	>	info[k].integrableObjects.push_back(mySD);
499	>	molInfo.myIntegrableObjects.push_back(mySD);
500	>	}
501	>
502	>
503	>	// send the arrays off to the forceField for init.
504	>
505	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
506	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
507	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
508	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
509	>	theTorsions);
510	>
511	>	info[k].molecules[i].initialize(molInfo);
512	>
513	>
514	>	atomOffset += molInfo.nAtoms;
515	>	delete[] theBonds;
516	>	delete[] theBends;
517	>	delete[] theTorsions;
518	>	}
519		}
520
521		#ifdef IS_MPI
522	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
522	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
523		MPIcheckPoint();
524		#endif // is_mpi
525
526		// clean up the forcefield
377	–	the_ff->calcRcut();
378	–	the_ff->cleanMe();
527
528	<	}
528	>	if (!globals->haveLJrcut()){
529
530	<	void SimSetup::initFromBass( void ){
530	>	the_ff->calcRcut();
531
532	+	} else {
533	+
534	+	the_ff->setRcut( globals->getLJrcut() );
535	+	}
536	+
537	+	the_ff->cleanMe();
538	+	}
539	+
540	+	void SimSetup::initFromBass(void){
541		int i, j, k;
542		int n_cells;
543		double cellx, celly, cellz;
#	Line 389 | Line 546 | void SimSetup::initFromBass( void ){
546		int n_extra;
547		int have_extra, done;
548
549	<	temp1 = (double)tot_nmol / 4.0;
550	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
551	<	temp3 = ceil( temp2 );
549	>	double vel[3];
550	>	vel[0] = 0.0;
551	>	vel[1] = 0.0;
552	>	vel[2] = 0.0;
553
554	<	have_extra =0;
555	<	if( temp2 < temp3 ){ // we have a non-complete lattice
556	<	have_extra =1;
554	>	temp1 = (double) tot_nmol / 4.0;
555	>	temp2 = pow(temp1, (1.0 / 3.0));
556	>	temp3 = ceil(temp2);
557
558	<	n_cells = (int)temp3 - 1;
559	<	cellx = info->boxL[0] / temp3;
560	<	celly = info->boxL[1] / temp3;
561	<	cellz = info->boxL[2] / temp3;
404	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406	<	n_per_extra = (int)ceil( temp1 );
558	>	have_extra = 0;
559	>	if (temp2 < temp3){
560	>	// we have a non-complete lattice
561	>	have_extra = 1;
562
563	<	if( n_per_extra > 4){
564	<	sprintf( painCave.errMsg,
565	<	"SimSetup error. There has been an error in constructing"
566	<	" the non-complete lattice.\n" );
563	>	n_cells = (int) temp3 - 1;
564	>	cellx = info[0].boxL[0] / temp3;
565	>	celly = info[0].boxL[1] / temp3;
566	>	cellz = info[0].boxL[2] / temp3;
567	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
568	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
569	>	n_per_extra = (int) ceil(temp1);
570	>
571	>	if (n_per_extra > 4){
572	>	sprintf(painCave.errMsg,
573	>	"SimSetup error. There has been an error in constructing"
574	>	" the non-complete lattice.\n");
575		painCave.isFatal = 1;
576		simError();
577		}
578		}
579		else{
580	<	n_cells = (int)temp3;
581	<	cellx = info->boxL[0] / temp3;
582	<	celly = info->boxL[1] / temp3;
583	<	cellz = info->boxL[2] / temp3;
580	>	n_cells = (int) temp3;
581	>	cellx = info[0].boxL[0] / temp3;
582	>	celly = info[0].boxL[1] / temp3;
583	>	cellz = info[0].boxL[2] / temp3;
584		}
585
586		current_mol = 0;
#	Line 425 | Line 588 | void SimSetup::initFromBass( void ){
588		current_comp = 0;
589		current_atom_ndx = 0;
590
591	<	for( i=0; i < n_cells ; i++ ){
592	<	for( j=0; j < n_cells; j++ ){
593	<	for( k=0; k < n_cells; k++ ){
591	>	for (i = 0; i < n_cells ; i++){
592	>	for (j = 0; j < n_cells; j++){
593	>	for (k = 0; k < n_cells; k++){
594	>	makeElement(i * cellx, j * celly, k * cellz);
595
596	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
596	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
597
598	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
598	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
599
600	<	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 );
600	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
601		}
602		}
603		}
604
605	<	if( have_extra ){
605	>	if (have_extra){
606		done = 0;
607
608		int start_ndx;
609	<	for( i=0; i < (n_cells+1) && !done; i++ ){
610	<	for( j=0; j < (n_cells+1) && !done; j++ ){
609	>	for (i = 0; i < (n_cells + 1) && !done; i++){
610	>	for (j = 0; j < (n_cells + 1) && !done; j++){
611	>	if (i < n_cells){
612	>	if (j < n_cells){
613	>	start_ndx = n_cells;
614	>	}
615	>	else
616	>	start_ndx = 0;
617	>	}
618	>	else
619	>	start_ndx = 0;
620
621	<	if( i < n_cells ){
621	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
622	>	makeElement(i * cellx, j * celly, k * cellz);
623	>	done = (current_mol >= tot_nmol);
624
625	<	if( j < n_cells ){
626	<	start_ndx = n_cells;
627	<	}
628	<	else start_ndx = 0;
629	<	}
465	<	else start_ndx = 0;
625	>	if (!done && n_per_extra > 1){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
627	>	k * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630
631	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
631	>	if (!done && n_per_extra > 2){
632	>	makeElement(i * cellx, j * celly + 0.5 * celly,
633	>	k * cellz + 0.5 * cellz);
634	>	done = (current_mol >= tot_nmol);
635	>	}
636
637	<	makeElement( i * cellx,
638	<	j * celly,
639	<	k * cellz );
640	<	done = ( current_mol >= tot_nmol );
641	<
642	<	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	<	}
637	>	if (!done && n_per_extra > 3){
638	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642	>	}
643		}
644		}
645		}
646
647	<
648	<	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 );
647	>	for (i = 0; i < info[0].n_atoms; i++){
648	>	info[0].atoms[i]->setVel(vel);
649		}
650		}
651
652	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
652	>	void SimSetup::makeElement(double x, double y, double z){
653		int k;
654		AtomStamp* current_atom;
655		DirectionalAtom* dAtom;
656		double rotMat[3][3];
657	+	double pos[3];
658
659	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
660	<
661	<	current_atom = comp_stamps[current_comp]->getAtom( k );
662	<	if( !current_atom->havePosition() ){
663	<	sprintf( painCave.errMsg,
664	<	"SimSetup:initFromBass error.\n"
665	<	"\tComponent %s, atom %s does not have a position specified.\n"
666	<	"\tThe initialization routine is unable to give a start"
667	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
659	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
660	>	current_atom = comp_stamps[current_comp]->getAtom(k);
661	>	if (!current_atom->havePosition()){
662	>	sprintf(painCave.errMsg,
663	>	"SimSetup:initFromBass error.\n"
664	>	"\tComponent %s, atom %s does not have a position specified.\n"
665	>	"\tThe initialization routine is unable to give a start"
666	>	" position.\n",
667	>	comp_stamps[current_comp]->getID(), current_atom->getType());
668		painCave.isFatal = 1;
669		simError();
670		}
671
672	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
673	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
674	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
672	>	pos[0] = x + current_atom->getPosX();
673	>	pos[1] = y + current_atom->getPosY();
674	>	pos[2] = z + current_atom->getPosZ();
675
676	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
676	>	info[0].atoms[current_atom_ndx]->setPos(pos);
677
678	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
678	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
679	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
680
681		rotMat[0][0] = 1.0;
682		rotMat[0][1] = 0.0;
#	Line 546 | Line 690 | void SimSetup::makeElement( double x, double y, double
690		rotMat[2][1] = 0.0;
691		rotMat[2][2] = 1.0;
692
693	<	dAtom->setA( rotMat );
693	>	dAtom->setA(rotMat);
694		}
695
696		current_atom_ndx++;
#	Line 555 | Line 699 | void SimSetup::makeElement( double x, double y, double
699		current_mol++;
700		current_comp_mol++;
701
702	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
702	>	if (current_comp_mol >= components_nmol[current_comp]){
703		current_comp_mol = 0;
704		current_comp++;
705		}
706		}
707
708
709	<	void SimSetup::gatherInfo( void ){
710	<	int i,j,k;
709	>	void SimSetup::gatherInfo(void){
710	>	int i;
711
712		ensembleCase = -1;
713		ffCase = -1;
714
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
715		// set the easy ones first
716	<	info->target_temp = globals->getTargetTemp();
717	<	info->dt = globals->getDt();
718	<	info->run_time = globals->getRunTime();
716	>
717	>	for (i = 0; i < nInfo; i++){
718	>	info[i].target_temp = globals->getTargetTemp();
719	>	info[i].dt = globals->getDt();
720	>	info[i].run_time = globals->getRunTime();
721	>	}
722		n_components = globals->getNComponents();
723
724
725		// get the forceField
726
727	<	strcpy( force_field, globals->getForceField() );
727	>	strcpy(force_field, globals->getForceField());
728
729	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
730	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
729	>	if (!strcasecmp(force_field, "DUFF")){
730	>	ffCase = FF_DUFF;
731	>	}
732	>	else if (!strcasecmp(force_field, "LJ")){
733	>	ffCase = FF_LJ;
734	>	}
735	>	else if (!strcasecmp(force_field, "EAM")){
736	>	ffCase = FF_EAM;
737	>	}
738	>	else if (!strcasecmp(force_field, "WATER")){
739	>	ffCase = FF_H2O;
740	>	}
741		else{
742	<	sprintf( painCave.errMsg,
743	<	"SimSetup Error. Unrecognized force field -> %s\n",
744	<	force_field );
745	<	painCave.isFatal = 1;
594	<	simError();
742	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
743	>	force_field);
744	>	painCave.isFatal = 1;
745	>	simError();
746		}
747
748	<	// get the ensemble
748	>	// get the ensemble
749
750	<	strcpy( ensemble, globals->getEnsemble() );
750	>	strcpy(ensemble, globals->getEnsemble());
751
752	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
753	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
754	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
752	>	if (!strcasecmp(ensemble, "NVE")){
753	>	ensembleCase = NVE_ENS;
754	>	}
755	>	else if (!strcasecmp(ensemble, "NVT")){
756	>	ensembleCase = NVT_ENS;
757	>	}
758	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
759		ensembleCase = NPTi_ENS;
760	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
761	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
762	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
760	>	}
761	>	else if (!strcasecmp(ensemble, "NPTf")){
762	>	ensembleCase = NPTf_ENS;
763	>	}
764	>	else if (!strcasecmp(ensemble, "NPTxyz")){
765	>	ensembleCase = NPTxyz_ENS;
766	>	}
767		else{
768	<	sprintf( painCave.errMsg,
769	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
770	<	"reverting to NVE for this simulation.\n",
771	<	ensemble );
772	<	painCave.isFatal = 0;
773	<	simError();
774	<	strcpy( ensemble, "NVE" );
775	<	ensembleCase = NVE_ENS;
768	>	sprintf(painCave.errMsg,
769	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
770	>	"\treverting to NVE for this simulation.\n",
771	>	ensemble);
772	>	painCave.isFatal = 0;
773	>	simError();
774	>	strcpy(ensemble, "NVE");
775	>	ensembleCase = NVE_ENS;
776		}
618	–	strcpy( info->ensemble, ensemble );
777
778	<	// get the mixing rule
778	>	for (i = 0; i < nInfo; i++){
779	>	strcpy(info[i].ensemble, ensemble);
780
781	<	strcpy( info->mixingRule, globals->getMixingRule() );
782	<	info->usePBC = globals->getPBC();
783	<
784	<
781	>	// get the mixing rule
782	>
783	>	strcpy(info[i].mixingRule, globals->getMixingRule());
784	>	info[i].usePBC = globals->getPBC();
785	>	}
786	>
787		// get the components and calculate the tot_nMol and indvidual n_mol
788	<
788	>
789		the_components = globals->getComponents();
790		components_nmol = new int[n_components];
791
792
793	<	if( !globals->haveNMol() ){
793	>	if (!globals->haveNMol()){
794		// we don't have the total number of molecules, so we assume it is
795		// given in each component
796
797		tot_nmol = 0;
798	<	for( i=0; i<n_components; i++ ){
799	<
800	<	if( !the_components[i]->haveNMol() ){
801	<	// we have a problem
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Error. No global NMol or component NMol"
804	<	" given. Cannot calculate the number of atoms.\n" );
805	<	painCave.isFatal = 1;
645	<	simError();
798	>	for (i = 0; i < n_components; i++){
799	>	if (!the_components[i]->haveNMol()){
800	>	// we have a problem
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup Error. No global NMol or component NMol given.\n"
803	>	"\tCannot calculate the number of atoms.\n");
804	>	painCave.isFatal = 1;
805	>	simError();
806		}
807
808		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 810 | void SimSetup::gatherInfo( void ){
810		}
811		}
812		else{
813	<	sprintf( painCave.errMsg,
814	<	"SimSetup error.\n"
815	<	"\tSorry, the ability to specify total"
816	<	" nMols and then give molfractions in the components\n"
817	<	"\tis not currently supported."
818	<	" Please give nMol in the components.\n" );
813	>	sprintf(painCave.errMsg,
814	>	"SimSetup error.\n"
815	>	"\tSorry, the ability to specify total"
816	>	" nMols and then give molfractions in the components\n"
817	>	"\tis not currently supported."
818	>	" Please give nMol in the components.\n");
819		painCave.isFatal = 1;
820		simError();
821		}
822
823	<	// set the status, sample, and thermal kick times
824	<
825	<	if( globals->haveSampleTime() ){
826	<	info->sampleTime = globals->getSampleTime();
827	<	info->statusTime = info->sampleTime;
828	<	info->thermalTime = info->sampleTime;
823	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
824	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
825	>	sprintf(painCave.errMsg,
826	>	"Sample time is not divisible by dt.\n"
827	>	"\tThis will result in samples that are not uniformly\n"
828	>	"\tdistributed in time.  If this is a problem, change\n"
829	>	"\tyour sampleTime variable.\n");
830	>	painCave.isFatal = 0;
831	>	simError();
832		}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
833
834	<	if( globals->haveStatusTime() ){
835	<	info->statusTime = globals->getStatusTime();
834	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
835	>	sprintf(painCave.errMsg,
836	>	"Status time is not divisible by dt.\n"
837	>	"\tThis will result in status reports that are not uniformly\n"
838	>	"\tdistributed in time.  If this is a problem, change \n"
839	>	"\tyour statusTime variable.\n");
840	>	painCave.isFatal = 0;
841	>	simError();
842		}
843
844	<	if( globals->haveThermalTime() ){
845	<	info->thermalTime = globals->getThermalTime();
846	<	}
844	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
845	>	sprintf(painCave.errMsg,
846	>	"Thermal time is not divisible by dt.\n"
847	>	"\tThis will result in thermalizations that are not uniformly\n"
848	>	"\tdistributed in time.  If this is a problem, change \n"
849	>	"\tyour thermalTime variable.\n");
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	}
853
854	<	// check for the temperature set flag
854	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
855	>	sprintf(painCave.errMsg,
856	>	"Reset time is not divisible by dt.\n"
857	>	"\tThis will result in integrator resets that are not uniformly\n"
858	>	"\tdistributed in time.  If this is a problem, change\n"
859	>	"\tyour resetTime variable.\n");
860	>	painCave.isFatal = 0;
861	>	simError();
862	>	}
863
864	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
864	>	// set the status, sample, and thermal kick times
865
866	<	// get some of the tricky things that may still be in the globals
866	>	for (i = 0; i < nInfo; i++){
867	>	if (globals->haveSampleTime()){
868	>	info[i].sampleTime = globals->getSampleTime();
869	>	info[i].statusTime = info[i].sampleTime;
870	>	info[i].thermalTime = info[i].sampleTime;
871	>	}
872	>	else{
873	>	info[i].sampleTime = globals->getRunTime();
874	>	info[i].statusTime = info[i].sampleTime;
875	>	info[i].thermalTime = info[i].sampleTime;
876	>	}
877
878	<	double boxVector[3];
879	<	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();
878	>	if (globals->haveStatusTime()){
879	>	info[i].statusTime = globals->getStatusTime();
880		}
715	–	boxVector[0] = globals->getBoxX();
881
882	<	if( !globals->haveBoxY() ){
883	<	sprintf( painCave.errMsg,
719	<	"SimSetup error, no periodic BoxY size given.\n" );
720	<	painCave.isFatal = 1;
721	<	simError();
882	>	if (globals->haveThermalTime()){
883	>	info[i].thermalTime = globals->getThermalTime();
884		}
723	–	boxVector[1] = globals->getBoxY();
885
886	<	if( !globals->haveBoxZ() ){
887	<	sprintf( painCave.errMsg,
888	<	"SimSetup error, no periodic BoxZ size given.\n" );
889	<	painCave.isFatal = 1;
729	<	simError();
886	>	info[i].resetIntegrator = 0;
887	>	if( globals->haveResetTime() ){
888	>	info[i].resetTime = globals->getResetTime();
889	>	info[i].resetIntegrator = 1;
890		}
731	–	boxVector[2] = globals->getBoxZ();
891
892	<	info->setBox( boxVector );
892	>	// check for the temperature set flag
893	>
894	>	if (globals->haveTempSet())
895	>	info[i].setTemp = globals->getTempSet();
896	>
897	>	// check for the extended State init
898	>
899	>	info[i].useInitXSstate = globals->getUseInitXSstate();
900	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
901	>
902		}
903	+
904	+	//setup seed for random number generator
905	+	int seedValue;
906
907	+	if (globals->haveSeed()){
908	+	seedValue = globals->getSeed();
909
910	+	if(seedValue / 1E9 == 0){
911	+	sprintf(painCave.errMsg,
912	+	"Seed for sprng library should contain at least 9 digits\n"
913	+	"OOPSE will generate a seed for user\n");
914	+	painCave.isFatal = 0;
915	+	simError();
916	+
917	+	//using seed generated by system instead of invalid seed set by user
918	+	#ifndef IS_MPI
919	+	seedValue = make_sprng_seed();
920	+	#else
921	+	if (worldRank == 0){
922	+	seedValue = make_sprng_seed();
923	+	}
924	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	+	#endif
926	+	}
927	+	}//end of if branch of globals->haveSeed()
928	+	else{
929
930	+	#ifndef IS_MPI
931	+	seedValue = make_sprng_seed();
932	+	#else
933	+	if (worldRank == 0){
934	+	seedValue = make_sprng_seed();
935	+	}
936	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
937	+	#endif
938	+	}//end of globals->haveSeed()
939	+
940	+	for (int i = 0; i < nInfo; i++){
941	+	info[i].setSeed(seedValue);
942	+	}
943	+
944		#ifdef IS_MPI
945	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
945	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
946		MPIcheckPoint();
947		#endif // is_mpi
742	–
948		}
949
950
951	<	void SimSetup::finalInfoCheck( void ){
951	>	void SimSetup::finalInfoCheck(void){
952		int index;
953		int usesDipoles;
954	<
954	>	int i;
955
956	<	// check electrostatic parameters
957	<
958	<	index = 0;
959	<	usesDipoles = 0;
960	<	while( (index < info->n_atoms) && !usesDipoles ){
961	<	usesDipoles = ((info->atoms)[index])->hasDipole();
962	<	index++;
963	<	}
964	<
956	>	for (i = 0; i < nInfo; i++){
957	>	// check electrostatic parameters
958	>
959	>	index = 0;
960	>	usesDipoles = 0;
961	>	while ((index < info[i].n_atoms) && !usesDipoles){
962	>	usesDipoles = (info[i].atoms[index])->hasDipole();
963	>	index++;
964	>	}
965	>
966		#ifdef IS_MPI
967	<	int myUse = usesDipoles;
968	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
967	>	int myUse = usesDipoles;
968	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
969		#endif //is_mpi
970
971	<	double theEcr, theEst;
971	>	double theEcr, theEst;
972
973	<	if (globals->getUseRF() ) {
974	<	info->useReactionField = 1;
769	<
770	<	if( !globals->haveECR() ){
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup Warning: using default value of 1/2 the smallest "
773	<	"box length for the electrostaticCutoffRadius.\n"
774	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
784	<	}
973	>	if (globals->getUseRF()){
974	>	info[i].useReactionField = 1;
975
976	<	if( !globals->haveEST() ){
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Warning: using default value of 0.05 * the "
979	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
980	<	);
981	<	painCave.isFatal = 0;
982	<	simError();
983	<	theEst = 0.05 * theEcr;
984	<	} else {
985	<	theEst= globals->getEST();
986	<	}
976	>	if (!globals->haveECR()){
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
979	>	"\tOOPSE will use a default value of 15.0 angstroms"
980	>	"\tfor the electrostaticCutoffRadius.\n");
981	>	painCave.isFatal = 0;
982	>	simError();
983	>	theEcr = 15.0;
984	>	}
985	>	else{
986	>	theEcr = globals->getECR();
987	>	}
988
989	<	info->setEcr( theEcr, theEst );
990	<
991	<	if(!globals->haveDielectric() ){
992	<	sprintf( painCave.errMsg,
993	<	"SimSetup Error: You are trying to use Reaction Field without"
994	<	"setting a dielectric constant!\n"
995	<	);
996	<	painCave.isFatal = 1;
997	<	simError();
807	<	}
808	<	info->dielectric = globals->getDielectric();
809	<	}
810	<	else {
811	<	if (usesDipoles) {
812	<
813	<	if( !globals->haveECR() ){
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Warning: using default value of 1/2 the smallest "
816	<	"box length for the electrostaticCutoffRadius.\n"
817	<	"I hope you have a very fast processor!\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	double smallest;
821	<	smallest = info->boxL[0];
822	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
989	>	if (!globals->haveEST()){
990	>	sprintf(painCave.errMsg,
991	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
992	>	"\tOOPSE will use a default value of\n"
993	>	"\t0.05 * electrostaticCutoffRadius\n"
994	>	"\tfor the electrostaticSkinThickness\n");
995	>	painCave.isFatal = 0;
996	>	simError();
997	>	theEst = 0.05 * theEcr;
998		}
999	<
1000	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the "
833	<	"electrostaticSkinThickness\n"
834	<	);
835	<	painCave.isFatal = 0;
836	<	simError();
837	<	theEst = 0.05 * theEcr;
838	<	} else {
839	<	theEst= globals->getEST();
999	>	else{
1000	>	theEst = globals->getEST();
1001		}
1002
1003	<	info->setEcr( theEcr, theEst );
843	<	}
844	<	}
1003	>	info[i].setDefaultEcr(theEcr, theEst);
1004
1005	+	if (!globals->haveDielectric()){
1006	+	sprintf(painCave.errMsg,
1007	+	"SimSetup Error: No Dielectric constant was set.\n"
1008	+	"\tYou are trying to use Reaction Field without"
1009	+	"\tsetting a dielectric constant!\n");
1010	+	painCave.isFatal = 1;
1011	+	simError();
1012	+	}
1013	+	info[i].dielectric = globals->getDielectric();
1014	+	}
1015	+	else{
1016	+	if (usesDipoles){
1017	+	if (!globals->haveECR()){
1018	+	sprintf(painCave.errMsg,
1019	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1020	+	"\tOOPSE will use a default value of 15.0 angstroms"
1021	+	"\tfor the electrostaticCutoffRadius.\n");
1022	+	painCave.isFatal = 0;
1023	+	simError();
1024	+	theEcr = 15.0;
1025	+	}
1026	+	else{
1027	+	theEcr = globals->getECR();
1028	+	}
1029	+
1030	+	if (!globals->haveEST()){
1031	+	sprintf(painCave.errMsg,
1032	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1033	+	"\tOOPSE will use a default value of\n"
1034	+	"\t0.05 * electrostaticCutoffRadius\n"
1035	+	"\tfor the electrostaticSkinThickness\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	theEst = 0.05 * theEcr;
1039	+	}
1040	+	else{
1041	+	theEst = globals->getEST();
1042	+	}
1043	+
1044	+	info[i].setDefaultEcr(theEcr, theEst);
1045	+	}
1046	+	}
1047	+	}
1048		#ifdef IS_MPI
1049	<	strcpy( checkPointMsg, "post processing checks out" );
1049	>	strcpy(checkPointMsg, "post processing checks out");
1050		MPIcheckPoint();
1051		#endif // is_mpi
850	–
1052		}
1053	+
1054	+	void SimSetup::initSystemCoords(void){
1055	+	int i;
1056
1057	<	void SimSetup::initSystemCoords( void ){
1057	>	char* inName;
1058
1059	<	if( globals->haveInitialConfig() ){
1060	<
1061	<	InitializeFromFile* fileInit;
1059	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1060	>
1061	>	for (i = 0; i < info[0].n_atoms; i++)
1062	>	info[0].atoms[i]->setCoords();
1063	>
1064	>	if (globals->haveInitialConfig()){
1065	>	InitializeFromFile* fileInit;
1066		#ifdef IS_MPI // is_mpi
1067	<	if( worldRank == 0 ){
1067	>	if (worldRank == 0){
1068		#endif //is_mpi
1069	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1069	>	inName = globals->getInitialConfig();
1070	>	fileInit = new InitializeFromFile(inName);
1071		#ifdef IS_MPI
1072	<	}else fileInit = new InitializeFromFile( NULL );
1072	>	}
1073	>	else
1074	>	fileInit = new InitializeFromFile(NULL);
1075		#endif
1076	<	fileInit->read_xyz( info ); // default velocities on
1076	>	fileInit->readInit(info); // default velocities on
1077
1078	<	delete fileInit;
1079	<	}
1080	<	else{
1078	>	delete fileInit;
1079	>	}
1080	>	else{
1081	>
1082	>	// no init from bass
1083	>
1084	>	sprintf(painCave.errMsg,
1085	>	"Cannot intialize a simulation without an initial configuration file.\n");
1086	>	painCave.isFatal = 1;;
1087	>	simError();
1088	>
1089	>	}
1090
871	–	#ifdef IS_MPI
872	–
873	–	// no init from bass
874	–
875	–	sprintf( painCave.errMsg,
876	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	–	painCave.isFatal;
878	–	simError();
879	–
880	–	#else
881	–
882	–	initFromBass();
883	–
884	–
885	–	#endif
886	–	}
887	–
1091		#ifdef IS_MPI
1092	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1092	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1093		MPIcheckPoint();
1094		#endif // is_mpi
892	–
1095		}
1096
1097
1098	<	void SimSetup::makeOutNames( void ){
1098	>	void SimSetup::makeOutNames(void){
1099	>	int k;
1100
1101	+
1102	+	for (k = 0; k < nInfo; k++){
1103		#ifdef IS_MPI
1104	<	if( worldRank == 0 ){
1104	>	if (worldRank == 0){
1105		#endif // is_mpi
1106	<
1107	<	if( globals->haveFinalConfig() ){
1108	<	strcpy( info->finalName, globals->getFinalConfig() );
904	<	}
905	<	else{
906	<	strcpy( info->finalName, inFileName );
907	<	char* endTest;
908	<	int nameLength = strlen( info->finalName );
909	<	endTest = &(info->finalName[nameLength - 5]);
910	<	if( !strcmp( endTest, ".bass" ) ){
911	<	strcpy( endTest, ".eor" );
1106	>
1107	>	if (globals->haveFinalConfig()){
1108	>	strcpy(info[k].finalName, globals->getFinalConfig());
1109		}
913	–	else if( !strcmp( endTest, ".BASS" ) ){
914	–	strcpy( endTest, ".eor" );
915	–	}
1110		else{
1111	<	endTest = &(info->finalName[nameLength - 4]);
1112	<	if( !strcmp( endTest, ".bss" ) ){
1113	<	strcpy( endTest, ".eor" );
1114	<	}
1115	<	else if( !strcmp( endTest, ".mdl" ) ){
1116	<	strcpy( endTest, ".eor" );
1117	<	}
1118	<	else{
1119	<	strcat( info->finalName, ".eor" );
1120	<	}
1111	>	strcpy(info[k].finalName, inFileName);
1112	>	char* endTest;
1113	>	int nameLength = strlen(info[k].finalName);
1114	>	endTest = &(info[k].finalName[nameLength - 5]);
1115	>	if (!strcmp(endTest, ".bass")){
1116	>	strcpy(endTest, ".eor");
1117	>	}
1118	>	else if (!strcmp(endTest, ".BASS")){
1119	>	strcpy(endTest, ".eor");
1120	>	}
1121	>	else{
1122	>	endTest = &(info[k].finalName[nameLength - 4]);
1123	>	if (!strcmp(endTest, ".bss")){
1124	>	strcpy(endTest, ".eor");
1125	>	}
1126	>	else if (!strcmp(endTest, ".mdl")){
1127	>	strcpy(endTest, ".eor");
1128	>	}
1129	>	else{
1130	>	strcat(info[k].finalName, ".eor");
1131	>	}
1132	>	}
1133		}
1134	<	}
1135	<
1136	<	// make the sample and status out names
1137	<
1138	<	strcpy( info->sampleName, inFileName );
1139	<	char* endTest;
1140	<	int nameLength = strlen( info->sampleName );
1141	<	endTest = &(info->sampleName[nameLength - 5]);
1142	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
945	<	strcpy( endTest, ".dump" );
1134	>
1135	>	// make the sample and status out names
1136	>
1137	>	strcpy(info[k].sampleName, inFileName);
1138	>	char* endTest;
1139	>	int nameLength = strlen(info[k].sampleName);
1140	>	endTest = &(info[k].sampleName[nameLength - 5]);
1141	>	if (!strcmp(endTest, ".bass")){
1142	>	strcpy(endTest, ".dump");
1143		}
1144	<	else if( !strcmp( endTest, ".mdl" ) ){
1145	<	strcpy( endTest, ".dump" );
1144	>	else if (!strcmp(endTest, ".BASS")){
1145	>	strcpy(endTest, ".dump");
1146		}
1147		else{
1148	<	strcat( info->sampleName, ".dump" );
1148	>	endTest = &(info[k].sampleName[nameLength - 4]);
1149	>	if (!strcmp(endTest, ".bss")){
1150	>	strcpy(endTest, ".dump");
1151	>	}
1152	>	else if (!strcmp(endTest, ".mdl")){
1153	>	strcpy(endTest, ".dump");
1154	>	}
1155	>	else{
1156	>	strcat(info[k].sampleName, ".dump");
1157	>	}
1158		}
1159	<	}
1160	<
1161	<	strcpy( info->statusName, inFileName );
1162	<	nameLength = strlen( info->statusName );
1163	<	endTest = &(info->statusName[nameLength - 5]);
1164	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".stat" );
1159	>
1160	>	strcpy(info[k].statusName, inFileName);
1161	>	nameLength = strlen(info[k].statusName);
1162	>	endTest = &(info[k].statusName[nameLength - 5]);
1163	>	if (!strcmp(endTest, ".bass")){
1164	>	strcpy(endTest, ".stat");
1165		}
1166	<	else if( !strcmp( endTest, ".mdl" ) ){
1167	<	strcpy( endTest, ".stat" );
1166	>	else if (!strcmp(endTest, ".BASS")){
1167	>	strcpy(endTest, ".stat");
1168		}
1169		else{
1170	<	strcat( info->statusName, ".stat" );
1170	>	endTest = &(info[k].statusName[nameLength - 4]);
1171	>	if (!strcmp(endTest, ".bss")){
1172	>	strcpy(endTest, ".stat");
1173	>	}
1174	>	else if (!strcmp(endTest, ".mdl")){
1175	>	strcpy(endTest, ".stat");
1176	>	}
1177	>	else{
1178	>	strcat(info[k].statusName, ".stat");
1179	>	}
1180		}
1181	<	}
976	<
1181	>
1182		#ifdef IS_MPI
978	–	}
979	–	#endif // is_mpi
1183
1184	+	}
1185	+	#endif // is_mpi
1186	+	}
1187		}
1188
1189
1190	<	void SimSetup::sysObjectsCreation( void ){
1190	>	void SimSetup::sysObjectsCreation(void){
1191	>	int i, k;
1192
986	–	int i;
987	–
1193		// create the forceField
1194
1195		createFF();
#	Line 999 | Line 1204 | void SimSetup::sysObjectsCreation( void ){
1204
1205		#ifdef IS_MPI
1206		// divide the molecules among the processors
1207	<
1207	>
1208		mpiMolDivide();
1209		#endif //is_mpi
1210	<
1210	>
1211		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1212	<
1212	>
1213		makeSysArrays();
1214
1215		// make and initialize the molecules (all but atomic coordinates)
1216	<
1216	>
1217		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1017	–
1218
1219	<
1219	>	for (k = 0; k < nInfo; k++){
1220	>	info[k].identArray = new int[info[k].n_atoms];
1221	>	for (i = 0; i < info[k].n_atoms; i++){
1222	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1223	>	}
1224	>	}
1225		}
1226
1227
1228	<	void SimSetup::createFF( void ){
1228	>	void SimSetup::createFF(void){
1229	>	switch (ffCase){
1230	>	case FF_DUFF:
1231	>	the_ff = new DUFF();
1232	>	break;
1233
1234	<	switch( ffCase ){
1234	>	case FF_LJ:
1235	>	the_ff = new LJFF();
1236	>	break;
1237
1238	<	case FF_DUFF:
1239	<	the_ff = new DUFF();
1240	<	break;
1238	>	case FF_EAM:
1239	>	the_ff = new EAM_FF();
1240	>	break;
1241
1242	<	case FF_LJ:
1243	<	the_ff = new LJFF();
1244	<	break;
1242	>	case FF_H2O:
1243	>	the_ff = new WATER();
1244	>	break;
1245
1246	<	default:
1247	<	sprintf( painCave.errMsg,
1248	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1249	<	painCave.isFatal = 1;
1250	<	simError();
1246	>	default:
1247	>	sprintf(painCave.errMsg,
1248	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1249	>	painCave.isFatal = 1;
1250	>	simError();
1251		}
1252
1253		#ifdef IS_MPI
1254	<	strcpy( checkPointMsg, "ForceField creation successful" );
1254	>	strcpy(checkPointMsg, "ForceField creation successful");
1255		MPIcheckPoint();
1256		#endif // is_mpi
1046	–
1257		}
1258
1259
1260	<	void SimSetup::compList( void ){
1051	<
1260	>	void SimSetup::compList(void){
1261		int i;
1262	<
1263	<	comp_stamps = new MoleculeStamp*[n_components];
1262	>	char* id;
1263	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1264	>	LinkedMolStamp* currentStamp = NULL;
1265	>	comp_stamps = new MoleculeStamp * [n_components];
1266
1267		// make an array of molecule stamps that match the components used.
1268		// also extract the used stamps out into a separate linked list
1269
1270	<	info->nComponents = n_components;
1271	<	info->componentsNmol = components_nmol;
1272	<	info->compStamps = comp_stamps;
1273	<	info->headStamp = new LinkedMolStamp();
1274	<
1275	<	char* id;
1065	<	LinkedMolStamp* headStamp = info->headStamp;
1066	<	LinkedMolStamp* currentStamp = NULL;
1067	<	for( i=0; i<n_components; i++ ){
1270	>	for (i = 0; i < nInfo; i++){
1271	>	info[i].nComponents = n_components;
1272	>	info[i].componentsNmol = components_nmol;
1273	>	info[i].compStamps = comp_stamps;
1274	>	info[i].headStamp = headStamp;
1275	>	}
1276
1277	+
1278	+	for (i = 0; i < n_components; i++){
1279		id = the_components[i]->getType();
1280		comp_stamps[i] = NULL;
1281	<
1281	>
1282		// check to make sure the component isn't already in the list
1283
1284	<	comp_stamps[i] = headStamp->match( id );
1285	<	if( comp_stamps[i] == NULL ){
1076	<
1284	>	comp_stamps[i] = headStamp->match(id);
1285	>	if (comp_stamps[i] == NULL){
1286		// extract the component from the list;
1287	<
1288	<	currentStamp = stamps->extractMolStamp( id );
1289	<	if( currentStamp == NULL ){
1290	<	sprintf( painCave.errMsg,
1291	<	"SimSetup error: Component \"%s\" was not found in the "
1292	<	"list of declared molecules\n",
1293	<	id );
1294	<	painCave.isFatal = 1;
1295	<	simError();
1287	>
1288	>	currentStamp = stamps->extractMolStamp(id);
1289	>	if (currentStamp == NULL){
1290	>	sprintf(painCave.errMsg,
1291	>	"SimSetup error: Component \"%s\" was not found in the "
1292	>	"list of declared molecules\n",
1293	>	id);
1294	>	painCave.isFatal = 1;
1295	>	simError();
1296		}
1297	<
1298	<	headStamp->add( currentStamp );
1299	<	comp_stamps[i] = headStamp->match( id );
1297	>
1298	>	headStamp->add(currentStamp);
1299	>	comp_stamps[i] = headStamp->match(id);
1300		}
1301		}
1302
1303		#ifdef IS_MPI
1304	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1304	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1305		MPIcheckPoint();
1306		#endif // is_mpi
1098	–
1099	–
1307		}
1308
1309	<	void SimSetup::calcSysValues( void ){
1310	<	int i, j, k;
1309	>	void SimSetup::calcSysValues(void){
1310	>	int i;
1311
1312	+	int* molMembershipArray;
1313
1314		tot_atoms = 0;
1315		tot_bonds = 0;
1316		tot_bends = 0;
1317		tot_torsions = 0;
1318	<	for( i=0; i<n_components; i++ ){
1319	<
1320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1318	>	tot_rigid = 0;
1319	>	for (i = 0; i < n_components; i++){
1320	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1321	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1322	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1323		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1324	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1325		}
1326	<
1326	>
1327		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1328	+	molMembershipArray = new int[tot_atoms];
1329
1330	<	info->n_atoms = tot_atoms;
1331	<	info->n_bonds = tot_bonds;
1332	<	info->n_bends = tot_bends;
1333	<	info->n_torsions = tot_torsions;
1334	<	info->n_SRI = tot_SRI;
1335	<	info->n_mol = tot_nmol;
1336	<
1337	<	info->molMembershipArray = new int[tot_atoms];
1330	>	for (i = 0; i < nInfo; i++){
1331	>	info[i].n_atoms = tot_atoms;
1332	>	info[i].n_bonds = tot_bonds;
1333	>	info[i].n_bends = tot_bends;
1334	>	info[i].n_torsions = tot_torsions;
1335	>	info[i].n_SRI = tot_SRI;
1336	>	info[i].n_mol = tot_nmol;
1337	>
1338	>	info[i].molMembershipArray = molMembershipArray;
1339	>	}
1340		}
1341
1130	–
1342		#ifdef IS_MPI
1343
1344	<	void SimSetup::mpiMolDivide( void ){
1134	<
1344	>	void SimSetup::mpiMolDivide(void){
1345		int i, j, k;
1346		int localMol, allMol;
1347		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1348	+	int local_rigid;
1349
1350	<	mpiSim = new mpiSimulation( info );
1351	<
1350	>	mpiSim = new mpiSimulation(info);
1351	>
1352		globalIndex = mpiSim->divideLabor();
1353
1354		// set up the local variables
1355	<
1355	>
1356		mol2proc = mpiSim->getMolToProcMap();
1357		molCompType = mpiSim->getMolComponentType();
1358	<
1358	>
1359		allMol = 0;
1360		localMol = 0;
1361		local_atoms = 0;
1362		local_bonds = 0;
1363		local_bends = 0;
1364		local_torsions = 0;
1365	+	local_rigid = 0;
1366		globalAtomIndex = 0;
1367
1368	<
1369	<	for( i=0; i<n_components; i++ ){
1370	<
1371	<	for( j=0; j<components_nmol[i]; j++ ){
1372	<
1373	<	if( mol2proc[allMol] == worldRank ){
1374	<
1375	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1376	<	local_bonds +=    comp_stamps[i]->getNBonds();
1165	<	local_bends +=    comp_stamps[i]->getNBends();
1166	<	local_torsions += comp_stamps[i]->getNTorsions();
1167	<	localMol++;
1368	>	for (i = 0; i < n_components; i++){
1369	>	for (j = 0; j < components_nmol[i]; j++){
1370	>	if (mol2proc[allMol] == worldRank){
1371	>	local_atoms += comp_stamps[i]->getNAtoms();
1372	>	local_bonds += comp_stamps[i]->getNBonds();
1373	>	local_bends += comp_stamps[i]->getNBends();
1374	>	local_torsions += comp_stamps[i]->getNTorsions();
1375	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1376	>	localMol++;
1377		}
1378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1379	<	info->molMembershipArray[globalAtomIndex] = allMol;
1378	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1379	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1380		globalAtomIndex++;
1381		}
1382
1383	<	allMol++;
1383	>	allMol++;
1384		}
1385		}
1386		local_SRI = local_bonds + local_bends + local_torsions;
1387	+
1388	+	info[0].n_atoms = mpiSim->getMyNlocal();
1389
1390	<	info->n_atoms = mpiSim->getMyNlocal();
1391	<
1392	<	if( local_atoms != info->n_atoms ){
1393	<	sprintf( painCave.errMsg,
1394	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1395	<	" localAtom (%d) are not equal.\n",
1185	<	info->n_atoms,
1186	<	local_atoms );
1390	>
1391	>	if (local_atoms != info[0].n_atoms){
1392	>	sprintf(painCave.errMsg,
1393	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1394	>	"\tlocalAtom (%d) are not equal.\n",
1395	>	info[0].n_atoms, local_atoms);
1396		painCave.isFatal = 1;
1397		simError();
1398		}
1399
1400	<	info->n_bonds = local_bonds;
1401	<	info->n_bends = local_bends;
1402	<	info->n_torsions = local_torsions;
1403	<	info->n_SRI = local_SRI;
1404	<	info->n_mol = localMol;
1400	>	info[0].n_bonds = local_bonds;
1401	>	info[0].n_bends = local_bends;
1402	>	info[0].n_torsions = local_torsions;
1403	>	info[0].n_SRI = local_SRI;
1404	>	info[0].n_mol = localMol;
1405
1406	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1406	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1407		MPIcheckPoint();
1408		}
1409	<
1409	>
1410		#endif // is_mpi
1411
1412
1413	<	void SimSetup::makeSysArrays( void ){
1414	<	int i, j, k;
1413	>	void SimSetup::makeSysArrays(void){
1414	>
1415	>	#ifndef IS_MPI
1416	>	int k, j;
1417	>	#endif // is_mpi
1418	>	int i, l;
1419
1420	+	Atom** the_atoms;
1421	+	Molecule* the_molecules;
1422
1423	<	// create the atom and short range interaction arrays
1423	>	for (l = 0; l < nInfo; l++){
1424	>	// create the atom and short range interaction arrays
1425
1426	<	Atom::createArrays(info->n_atoms);
1427	<	the_atoms = new Atom*[info->n_atoms];
1428	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1426	>	the_atoms = new Atom * [info[l].n_atoms];
1427	>	the_molecules = new Molecule[info[l].n_mol];
1428	>	int molIndex;
1429
1430	<	// initialize the molecule's stampID's
1430	>	// initialize the molecule's stampID's
1431
1432		#ifdef IS_MPI
1218	–
1433
1434	<	molIndex = 0;
1435	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1436	<
1437	<	if(mol2proc[i] == worldRank ){
1438	<	the_molecules[molIndex].setStampID( molCompType[i] );
1439	<	the_molecules[molIndex].setMyIndex( molIndex );
1440	<	the_molecules[molIndex].setGlobalIndex( i );
1441	<	molIndex++;
1434	>
1435	>	molIndex = 0;
1436	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1437	>	if (mol2proc[i] == worldRank){
1438	>	the_molecules[molIndex].setStampID(molCompType[i]);
1439	>	the_molecules[molIndex].setMyIndex(molIndex);
1440	>	the_molecules[molIndex].setGlobalIndex(i);
1441	>	molIndex++;
1442	>	}
1443		}
1229	–	}
1444
1445		#else // is_mpi
1446	<
1447	<	molIndex = 0;
1448	<	globalAtomIndex = 0;
1449	<	for(i=0; i<n_components; i++){
1450	<	for(j=0; j<components_nmol[i]; j++ ){
1451	<	the_molecules[molIndex].setStampID( i );
1452	<	the_molecules[molIndex].setMyIndex( molIndex );
1453	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1454	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1455	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1456	<	globalAtomIndex++;
1446	>
1447	>	molIndex = 0;
1448	>	globalAtomIndex = 0;
1449	>	for (i = 0; i < n_components; i++){
1450	>	for (j = 0; j < components_nmol[i]; j++){
1451	>	the_molecules[molIndex].setStampID(i);
1452	>	the_molecules[molIndex].setMyIndex(molIndex);
1453	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1454	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1455	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1456	>	globalAtomIndex++;
1457	>	}
1458	>	molIndex++;
1459		}
1244	–	molIndex++;
1460		}
1246	–	}
1247	–
1461
1462	+
1463		#endif // is_mpi
1464
1465	<
1466	<	if( info->n_SRI ){
1465	>	info[l].globalExcludes = new int;
1466	>	info[l].globalExcludes[0] = 0;
1467
1468	<	Exclude::createArray(info->n_SRI);
1255	<	the_excludes = new Exclude*[info->n_SRI];
1256	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1257	<	info->globalExcludes = new int;
1258	<	info->n_exclude = info->n_SRI;
1259	<	}
1260	<	else{
1261	<
1262	<	Exclude::createArray( 1 );
1263	<	the_excludes = new Exclude*;
1264	<	the_excludes[0] = new Exclude(0);
1265	<	the_excludes[0]->setPair( 0,0 );
1266	<	info->globalExcludes = new int;
1267	<	info->globalExcludes[0] = 0;
1268	<	info->n_exclude = 0;
1269	<	}
1468	>	// set the arrays into the SimInfo object
1469
1470	<	// set the arrays into the SimInfo object
1470	>	info[l].atoms = the_atoms;
1471	>	info[l].molecules = the_molecules;
1472	>	info[l].nGlobalExcludes = 0;
1473
1474	<	info->atoms = the_atoms;
1475	<	info->molecules = the_molecules;
1275	<	info->nGlobalExcludes = 0;
1276	<	info->excludes = the_excludes;
1277	<
1278	<	the_ff->setSimInfo( info );
1279	<
1474	>	the_ff->setSimInfo(info);
1475	>	}
1476		}
1477
1478	<	void SimSetup::makeIntegrator( void ){
1478	>	void SimSetup::makeIntegrator(void){
1479	>	int k;
1480
1481	<	NVT*  myNVT = NULL;
1482	<	NPTi* myNPTi = NULL;
1483	<	NPTf* myNPTf = NULL;
1484	<	NPTim* myNPTim = NULL;
1485	<	NPTfm* myNPTfm = NULL;
1481	>	NVE<RealIntegrator>* myNVE = NULL;
1482	>	NVT<RealIntegrator>* myNVT = NULL;
1483	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1484	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1485	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1486	>
1487	>	for (k = 0; k < nInfo; k++){
1488	>	switch (ensembleCase){
1489	>	case NVE_ENS:
1490	>	if (globals->haveZconstraints()){
1491	>	setupZConstraint(info[k]);
1492	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1493	>	}
1494	>	else{
1495	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1496	>	}
1497	>
1498	>	info->the_integrator = myNVE;
1499	>	break;
1500
1501	<	switch( ensembleCase ){
1501	>	case NVT_ENS:
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1505	>	}
1506	>	else
1507	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1508
1509	<	case NVE_ENS:
1293	<	new NVE( info, the_ff );
1294	<	break;
1509	>	myNVT->setTargetTemp(globals->getTargetTemp());
1510
1511	<	case NVT_ENS:
1512	<	myNVT = new NVT( info, the_ff );
1513	<	myNVT->setTargetTemp(globals->getTargetTemp());
1511	>	if (globals->haveTauThermostat())
1512	>	myNVT->setTauThermostat(globals->getTauThermostat());
1513	>	else{
1514	>	sprintf(painCave.errMsg,
1515	>	"SimSetup error: If you use the NVT\n"
1516	>	"\tensemble, you must set tauThermostat.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520
1521	<	if (globals->haveTauThermostat())
1522	<	myNVT->setTauThermostat(globals->getTauThermostat());
1521	>	info->the_integrator = myNVT;
1522	>	break;
1523
1524	<	else {
1525	<	sprintf( painCave.errMsg,
1526	<	"SimSetup error: If you use the NVT\n"
1527	<	"    ensemble, you must set tauThermostat.\n");
1528	<	painCave.isFatal = 1;
1529	<	simError();
1530	<	}
1310	<	break;
1524	>	case NPTi_ENS:
1525	>	if (globals->haveZconstraints()){
1526	>	setupZConstraint(info[k]);
1527	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1528	>	}
1529	>	else
1530	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1531
1532	<	case NPTi_ENS:
1313	<	myNPTi = new NPTi( info, the_ff );
1314	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1532	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1533
1534	<	if (globals->haveTargetPressure())
1535	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1536	<	else {
1537	<	sprintf( painCave.errMsg,
1538	<	"SimSetup error: If you use a constant pressure\n"
1539	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1540	<	painCave.isFatal = 1;
1541	<	simError();
1542	<	}
1325	<
1326	<	if( globals->haveTauThermostat() )
1327	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	<	else{
1329	<	sprintf( painCave.errMsg,
1330	<	"SimSetup error: If you use an NPT\n"
1331	<	"    ensemble, you must set tauThermostat.\n");
1332	<	painCave.isFatal = 1;
1333	<	simError();
1334	<	}
1534	>	if (globals->haveTargetPressure())
1535	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1536	>	else{
1537	>	sprintf(painCave.errMsg,
1538	>	"SimSetup error: If you use a constant pressure\n"
1539	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1540	>	painCave.isFatal = 1;
1541	>	simError();
1542	>	}
1543
1544	<	if( globals->haveTauBarostat() )
1545	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1546	<	else{
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use an NPT\n"
1549	<	"    ensemble, you must set tauBarostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1345	<	break;
1544	>	if (globals->haveTauThermostat())
1545	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1546	>	else{
1547	>	sprintf(painCave.errMsg,
1548	>	"SimSetup error: If you use an NPT\n"
1549	>	"\tensemble, you must set tauThermostat.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553
1554	<	case NPTf_ENS:
1555	<	myNPTf = new NPTf( info, the_ff );
1556	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1554	>	if (globals->haveTauBarostat())
1555	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1556	>	else{
1557	>	sprintf(painCave.errMsg,
1558	>	"SimSetup error: If you use an NPT\n"
1559	>	"\tensemble, you must set tauBarostat.\n");
1560	>	painCave.isFatal = 1;
1561	>	simError();
1562	>	}
1563
1564	<	if (globals->haveTargetPressure())
1565	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	<	else {
1354	<	sprintf( painCave.errMsg,
1355	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	<	painCave.isFatal = 1;
1358	<	simError();
1359	<	}
1564	>	info->the_integrator = myNPTi;
1565	>	break;
1566
1567	<	if( globals->haveTauThermostat() )
1568	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1569	<	else{
1570	<	sprintf( painCave.errMsg,
1571	<	"SimSetup error: If you use an NPT\n"
1572	<	"    ensemble, you must set tauThermostat.\n");
1573	<	painCave.isFatal = 1;
1368	<	simError();
1369	<	}
1567	>	case NPTf_ENS:
1568	>	if (globals->haveZconstraints()){
1569	>	setupZConstraint(info[k]);
1570	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1571	>	}
1572	>	else
1573	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1574
1575	<	if( globals->haveTauBarostat() )
1372	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	<	else{
1374	<	sprintf( painCave.errMsg,
1375	<	"SimSetup error: If you use an NPT\n"
1376	<	"    ensemble, you must set tauBarostat.\n");
1377	<	painCave.isFatal = 1;
1378	<	simError();
1379	<	}
1380	<	break;
1381	<
1382	<	case NPTim_ENS:
1383	<	myNPTim = new NPTim( info, the_ff );
1384	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1575	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1576
1577	<	if (globals->haveTargetPressure())
1578	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1579	<	else {
1580	<	sprintf( painCave.errMsg,
1581	<	"SimSetup error: If you use a constant pressure\n"
1582	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1583	<	painCave.isFatal = 1;
1584	<	simError();
1585	<	}
1395	<
1396	<	if( globals->haveTauThermostat() )
1397	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	<	else{
1399	<	sprintf( painCave.errMsg,
1400	<	"SimSetup error: If you use an NPT\n"
1401	<	"    ensemble, you must set tauThermostat.\n");
1402	<	painCave.isFatal = 1;
1403	<	simError();
1404	<	}
1577	>	if (globals->haveTargetPressure())
1578	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1579	>	else{
1580	>	sprintf(painCave.errMsg,
1581	>	"SimSetup error: If you use a constant pressure\n"
1582	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585	>	}
1586
1587	<	if( globals->haveTauBarostat() )
1588	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	<	else{
1409	<	sprintf( painCave.errMsg,
1410	<	"SimSetup error: If you use an NPT\n"
1411	<	"    ensemble, you must set tauBarostat.\n");
1412	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<	break;
1587	>	if (globals->haveTauThermostat())
1588	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1589
1590	<	case NPTfm_ENS:
1591	<	myNPTfm = new NPTfm( info, the_ff );
1592	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1590	>	else{
1591	>	sprintf(painCave.errMsg,
1592	>	"SimSetup error: If you use an NPT\n"
1593	>	"\tensemble, you must set tauThermostat.\n");
1594	>	painCave.isFatal = 1;
1595	>	simError();
1596	>	}
1597
1598	<	if (globals->haveTargetPressure())
1599	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	<	else {
1424	<	sprintf( painCave.errMsg,
1425	<	"SimSetup error: If you use a constant pressure\n"
1426	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1430	<
1431	<	if( globals->haveTauThermostat() )
1432	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	<	else{
1434	<	sprintf( painCave.errMsg,
1435	<	"SimSetup error: If you use an NPT\n"
1436	<	"    ensemble, you must set tauThermostat.\n");
1437	<	painCave.isFatal = 1;
1438	<	simError();
1439	<	}
1598	>	if (globals->haveTauBarostat())
1599	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1600
1601	<	if( globals->haveTauBarostat() )
1602	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1603	<	else{
1604	<	sprintf( painCave.errMsg,
1605	<	"SimSetup error: If you use an NPT\n"
1606	<	"    ensemble, you must set tauBarostat.\n");
1607	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1450	<	break;
1601	>	else{
1602	>	sprintf(painCave.errMsg,
1603	>	"SimSetup error: If you use an NPT\n"
1604	>	"\tensemble, you must set tauBarostat.\n");
1605	>	painCave.isFatal = 1;
1606	>	simError();
1607	>	}
1608
1609	<	default:
1610	<	sprintf( painCave.errMsg,
1454	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1609	>	info->the_integrator = myNPTf;
1610	>	break;
1611
1612	+	case NPTxyz_ENS:
1613	+	if (globals->haveZconstraints()){
1614	+	setupZConstraint(info[k]);
1615	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1616	+	}
1617	+	else
1618	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1619	+
1620	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1621	+
1622	+	if (globals->haveTargetPressure())
1623	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1624	+	else{
1625	+	sprintf(painCave.errMsg,
1626	+	"SimSetup error: If you use a constant pressure\n"
1627	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1628	+	painCave.isFatal = 1;
1629	+	simError();
1630	+	}
1631	+
1632	+	if (globals->haveTauThermostat())
1633	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1634	+	else{
1635	+	sprintf(painCave.errMsg,
1636	+	"SimSetup error: If you use an NPT\n"
1637	+	"\tensemble, you must set tauThermostat.\n");
1638	+	painCave.isFatal = 1;
1639	+	simError();
1640	+	}
1641	+
1642	+	if (globals->haveTauBarostat())
1643	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1644	+	else{
1645	+	sprintf(painCave.errMsg,
1646	+	"SimSetup error: If you use an NPT\n"
1647	+	"\tensemble, you must set tauBarostat.\n");
1648	+	painCave.isFatal = 1;
1649	+	simError();
1650	+	}
1651	+
1652	+	info->the_integrator = myNPTxyz;
1653	+	break;
1654	+
1655	+	default:
1656	+	sprintf(painCave.errMsg,
1657	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1658	+	painCave.isFatal = 1;
1659	+	simError();
1660	+	}
1661	+	}
1662		}
1663
1664	<	void SimSetup::initFortran( void ){
1664	>	void SimSetup::initFortran(void){
1665	>	info[0].refreshSim();
1666
1667	<	info->refreshSim();
1668	<
1465	<	if( !strcmp( info->mixingRule, "standard") ){
1466	<	the_ff->initForceField( LB_MIXING_RULE );
1667	>	if (!strcmp(info[0].mixingRule, "standard")){
1668	>	the_ff->initForceField(LB_MIXING_RULE);
1669		}
1670	<	else if( !strcmp( info->mixingRule, "explicit") ){
1671	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1670	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1671	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1672		}
1673		else{
1674	<	sprintf( painCave.errMsg,
1675	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	<	info->mixingRule );
1674	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1675	>	info[0].mixingRule);
1676		painCave.isFatal = 1;
1677		simError();
1678		}
1679
1680
1681		#ifdef IS_MPI
1682	<	strcpy( checkPointMsg,
1482	<	"Successfully intialized the mixingRule for Fortran." );
1682	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1683		MPIcheckPoint();
1684		#endif // is_mpi
1685	+	}
1686
1687	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1688	+	int nZConstraints;
1689	+	ZconStamp** zconStamp;
1690	+
1691	+	if (globals->haveZconstraintTime()){
1692	+	//add sample time of z-constraint  into SimInfo's property list
1693	+	DoubleData* zconsTimeProp = new DoubleData();
1694	+	zconsTimeProp->setID(ZCONSTIME_ID);
1695	+	zconsTimeProp->setData(globals->getZconsTime());
1696	+	theInfo.addProperty(zconsTimeProp);
1697	+	}
1698	+	else{
1699	+	sprintf(painCave.errMsg,
1700	+	"ZConstraint error: If you use a ZConstraint,\n"
1701	+	"\tyou must set zconsTime.\n");
1702	+	painCave.isFatal = 1;
1703	+	simError();
1704	+	}
1705	+
1706	+	//push zconsTol into siminfo, if user does not specify
1707	+	//value for zconsTol, a default value will be used
1708	+	DoubleData* zconsTol = new DoubleData();
1709	+	zconsTol->setID(ZCONSTOL_ID);
1710	+	if (globals->haveZconsTol()){
1711	+	zconsTol->setData(globals->getZconsTol());
1712	+	}
1713	+	else{
1714	+	double defaultZConsTol = 0.01;
1715	+	sprintf(painCave.errMsg,
1716	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1717	+	"\tOOPSE will use a default value of %f.\n"
1718	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1719	+	defaultZConsTol);
1720	+	painCave.isFatal = 0;
1721	+	simError();
1722	+
1723	+	zconsTol->setData(defaultZConsTol);
1724	+	}
1725	+	theInfo.addProperty(zconsTol);
1726	+
1727	+	//set Force Subtraction Policy
1728	+	StringData* zconsForcePolicy = new StringData();
1729	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1730	+
1731	+	if (globals->haveZconsForcePolicy()){
1732	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1733	+	}
1734	+	else{
1735	+	sprintf(painCave.errMsg,
1736	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1737	+	"\tOOPSE will use PolicyByMass.\n"
1738	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1739	+	painCave.isFatal = 0;
1740	+	simError();
1741	+	zconsForcePolicy->setData("BYMASS");
1742	+	}
1743	+
1744	+	theInfo.addProperty(zconsForcePolicy);
1745	+
1746	+	//set zcons gap
1747	+	DoubleData* zconsGap = new DoubleData();
1748	+	zconsGap->setID(ZCONSGAP_ID);
1749	+
1750	+	if (globals->haveZConsGap()){
1751	+	zconsGap->setData(globals->getZconsGap());
1752	+	theInfo.addProperty(zconsGap);
1753	+	}
1754	+
1755	+	//set zcons fixtime
1756	+	DoubleData* zconsFixtime = new DoubleData();
1757	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1758	+
1759	+	if (globals->haveZConsFixTime()){
1760	+	zconsFixtime->setData(globals->getZconsFixtime());
1761	+	theInfo.addProperty(zconsFixtime);
1762	+	}
1763	+
1764	+	//set zconsUsingSMD
1765	+	IntData* zconsUsingSMD = new IntData();
1766	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1767	+
1768	+	if (globals->haveZConsUsingSMD()){
1769	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1770	+	theInfo.addProperty(zconsUsingSMD);
1771	+	}
1772	+
1773	+	//Determine the name of ouput file and add it into SimInfo's property list
1774	+	//Be careful, do not use inFileName, since it is a pointer which
1775	+	//point to a string at master node, and slave nodes do not contain that string
1776	+
1777	+	string zconsOutput(theInfo.finalName);
1778	+
1779	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1780	+
1781	+	StringData* zconsFilename = new StringData();
1782	+	zconsFilename->setID(ZCONSFILENAME_ID);
1783	+	zconsFilename->setData(zconsOutput);
1784	+
1785	+	theInfo.addProperty(zconsFilename);
1786	+
1787	+	//setup index, pos and other parameters of z-constraint molecules
1788	+	nZConstraints = globals->getNzConstraints();
1789	+	theInfo.nZconstraints = nZConstraints;
1790	+
1791	+	zconStamp = globals->getZconStamp();
1792	+	ZConsParaItem tempParaItem;
1793	+
1794	+	ZConsParaData* zconsParaData = new ZConsParaData();
1795	+	zconsParaData->setID(ZCONSPARADATA_ID);
1796	+
1797	+	for (int i = 0; i < nZConstraints; i++){
1798	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1799	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1800	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1801	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1802	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1803	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1804	+	zconsParaData->addItem(tempParaItem);
1805	+	}
1806	+
1807	+	//check the uniqueness of index
1808	+	if(!zconsParaData->isIndexUnique()){
1809	+	sprintf(painCave.errMsg,
1810	+	"ZConstraint Error: molIndex is not unique!\n");
1811	+	painCave.isFatal = 1;
1812	+	simError();
1813	+	}
1814	+
1815	+	//sort the parameters by index of molecules
1816	+	zconsParaData->sortByIndex();
1817	+
1818	+	//push data into siminfo, therefore, we can retrieve later
1819	+	theInfo.addProperty(zconsParaData);
1820		}
1821	+
1822	+	void SimSetup::makeMinimizer(){
1823	+
1824	+	OOPSEMinimizer* myOOPSEMinimizer;
1825	+	MinimizerParameterSet* param;
1826	+	char minimizerName[100];
1827	+
1828	+	for (int i = 0; i < nInfo; i++){
1829	+
1830	+	//prepare parameter set for minimizer
1831	+	param = new MinimizerParameterSet();
1832	+	param->setDefaultParameter();
1833	+
1834	+	if (globals->haveMinimizer()){
1835	+	param->setFTol(globals->getMinFTol());
1836	+	}
1837	+
1838	+	if (globals->haveMinGTol()){
1839	+	param->setGTol(globals->getMinGTol());
1840	+	}
1841	+
1842	+	if (globals->haveMinMaxIter()){
1843	+	param->setMaxIteration(globals->getMinMaxIter());
1844	+	}
1845	+
1846	+	if (globals->haveMinWriteFrq()){
1847	+	param->setMaxIteration(globals->getMinMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinWriteFrq()){
1851	+	param->setWriteFrq(globals->getMinWriteFrq());
1852	+	}
1853	+
1854	+	if (globals->haveMinStepSize()){
1855	+	param->setStepSize(globals->getMinStepSize());
1856	+	}
1857	+
1858	+	if (globals->haveMinLSMaxIter()){
1859	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1860	+	}
1861	+
1862	+	if (globals->haveMinLSTol()){
1863	+	param->setLineSearchTol(globals->getMinLSTol());
1864	+	}
1865	+
1866	+	strcpy(minimizerName, globals->getMinimizer());
1867	+
1868	+	if (!strcasecmp(minimizerName, "CG")){
1869	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870	+	}
1871	+	else if (!strcasecmp(minimizerName, "SD")){
1872	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1873	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1874	+	}
1875	+	else{
1876	+	sprintf(painCave.errMsg,
1877	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1878	+	painCave.isFatal = 0;
1879	+	simError();
1880	+
1881	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1882	+	}
1883	+	info[i].the_integrator = myOOPSEMinimizer;
1884	+
1885	+	//store the minimizer into simInfo
1886	+	info[i].the_minimizer = myOOPSEMinimizer;
1887	+	info[i].has_minimizer = true;
1888	+	}
1889	+
1890	+	}

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