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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 653 by chuckv, Fri Jul 25 20:00:17 2003 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 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
32	<	#define FF_EAM  2
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();
103	–
104	–	// make the integrator
150
106	–	makeIntegrator();
107	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 113 | Line 156 | void SimSetup::createSim( void ){
156
157		initFortran();
158
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165
117	–
166		}
167
168
169	<	void SimSetup::makeMolecules( void ){
170	<
171	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186
187		bond_pair* theBonds;
188		bend_set* theBends;
189		torsion_set* theTorsions;
190
191	<
191	>	set<int> skipList;
192	>
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196	>
197		//init the forceField paramters
198
199		the_ff->readParams();
200
142	–
201		// init the atoms
202
203	<	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();
203	>	int nMembers, nNew, rb1, rb2;
204
205	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
206	<	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;
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207
208	<	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];
208	>	atomOffset = 0;
209
210	<	theBonds = new bond_pair[molInfo.nBonds];
211	<	theBends = new bend_set[molInfo.nBends];
212	<	theTorsions = new torsion_set[molInfo.nTorsions];
213	<
214	<	// make the Atoms
215	<
216	<	for(j=0; j<molInfo.nAtoms; j++){
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213	>
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219
220	<	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;
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221
222	<	exI = theBonds[j].a;
223	<	exJ = theBonds[j].b;
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226
227	<	// exclude_I must always be the smaller of the pair
228	<	if( exI > exJ ){
229	<	tempEx = exI;
230	<	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
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231
232	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
233	<	#endif  //is_mpi
234	<	}
235	<	excludeOffset += molInfo.nBonds;
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236
237	<	//make the bends
238	<	for(j=0; j<molInfo.nBends; j++){
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	currentBend = comp_stamps[stampID]->getBend( j );
242	<	theBends[j].a = currentBend->getA() + atomOffset;
243	<	theBends[j].b = currentBend->getB() + atomOffset;
244	<	theBends[j].c = currentBend->getC() + atomOffset;
245	<
246	<	if( currentBend->haveExtras() ){
247	<
248	<	extras = currentBend->getExtras();
249	<	current_extra = extras;
250	<
251	<	while( current_extra != NULL ){
252	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
253	<
254	<	switch( current_extra->getType() ){
255	<
256	<	case 0:
257	<	theBends[j].ghost =
258	<	current_extra->getInt() + atomOffset;
259	<	theBends[j].isGhost = 1;
260	<	break;
261	<
262	<	case 1:
263	<	theBends[j].ghost =
264	<	(int)current_extra->getDouble() + atomOffset;
265	<	theBends[j].isGhost = 1;
266	<	break;
267	<
268	<	default:
269	<	sprintf( painCave.errMsg,
270	<	"SimSetup Error: ghostVectorSource was neither a "
271	<	"double nor an int.\n"
272	<	"-->Bend[%d] in %s\n",
273	<	j, comp_stamps[stampID]->getID() );
274	<	painCave.isFatal = 1;
275	<	simError();
276	<	}
277	<	}
278	<
279	<	else{
280	<
281	<	sprintf( painCave.errMsg,
282	<	"SimSetup Error: unhandled bend assignment:\n"
283	<	"    -->%s in Bend[%d] in %s\n",
284	<	current_extra->getlhs(),
285	<	j, comp_stamps[stampID]->getID() );
286	<	painCave.isFatal = 1;
287	<	simError();
288	<	}
289	<
290	<	current_extra = current_extra->getNext();
291	<	}
241	>	// make the Atoms
242	>
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245	>
246	>	if (currentAtom->haveOrientation()){
247	>	dAtom = new DirectionalAtom((j + atomOffset),
248	>	info[k].getConfiguration());
249	>	info[k].n_oriented++;
250	>	molInfo.myAtoms[j] = dAtom;
251	>
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255	>
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259	>
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264	>
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266	>
267	>	}
268	>
269	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
270	>	#ifdef IS_MPI
271	>
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273	>
274	>	#endif // is_mpi
275	>	}
276	>
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282	>
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285	>
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293	>
294	>	info[k].excludes->addPair(exI, exJ);
295		}
296	<
297	<	if( !theBends[j].isGhost ){
298	<
299	<	exI = theBends[j].a;
300	<	exJ = theBends[j].c;
301	<	}
302	<	else{
303	<
304	<	exI = theBends[j].a;
305	<	exJ = theBends[j].b;
306	<	}
307	<
308	<	// exclude_I must always be the smaller of the pair
309	<	if( exI > exJ ){
310	<	tempEx = exI;
311	<	exI = exJ;
312	<	exJ = tempEx;
313	<	}
296	>
297	>	//make the bends
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303	>
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307	>
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315	>
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321	>
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>
341	>	current_extra = current_extra->getNext();
342	>	}
343	>	}
344	>
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350		#ifdef IS_MPI
351	<	tempEx = exI;
352	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
353	<	tempEx = exJ;
354	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
355	<
356	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
357	<	#else  // isn't MPI
318	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319	<	#endif  //is_mpi
320	<	}
321	<	excludeOffset += molInfo.nBends;
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	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;
359	>	} else {
360
361	<	// exclude_I must always be the smaller of the pair
362	<	if( exI > exJ ){
363	<	tempEx = exI;
364	<	exI = exJ;
365	<	exJ = tempEx;
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
380	+
381	+	for (j = 0; j < molInfo.nTorsions; j++){
382	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387	+
388	+	tempI = theTorsions[j].a;
389	+	tempJ = theTorsions[j].b;
390	+	tempK = theTorsions[j].c;
391	+	tempL = theTorsions[j].d;
392	+
393		#ifdef IS_MPI
394	<	tempEx = exI;
395	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
396	<	tempEx = exJ;
397	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
398	<
399	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
400	<	#else  // isn't MPI
401	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
402	<	#endif  //is_mpi
403	<	}
351	<	excludeOffset += molInfo.nTorsions;
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	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404
405	<
406	<	// send the arrays off to the forceField for init.
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
414	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
415	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
416	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	+	nMembers = currentRigidBody->getNMembers();
420
421	<	the_molecules[i].initialize( molInfo );
421	>	// Create the Rigid Body:
422
423	+	myRB = new RigidBody();
424
425	<	atomOffset += molInfo.nAtoms;
426	<	delete[] theBonds;
427	<	delete[] theBends;
428	<	delete[] theTorsions;
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	>
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432	>
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435	>
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	>
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478	>
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481	>	}
482	>
483	>
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486	>
487	>	molInfo.myIntegrableObjects.clear();
488	>
489	>
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491	>
492	>	#ifdef IS_MPI
493	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	>	#else
495	>	slJ = j+atomOffset;
496	>	#endif
497	>
498	>	// if they aren't on the skip list, then they can be integrated
499	>
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505	>	}
506	>
507	>	// all rigid bodies are integrated:
508	>
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513	>	}
514	>
515	>
516	>	// send the arrays off to the forceField for init.
517	>
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523	>
524	>	info[k].molecules[i].initialize(molInfo);
525	>
526	>
527	>	atomOffset += molInfo.nAtoms;
528	>	delete[] theBonds;
529	>	delete[] theBends;
530	>	delete[] theTorsions;
531	>	}
532		}
533
534		#ifdef IS_MPI
535	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
538
539		// clean up the forcefield
377	–	the_ff->calcRcut();
378	–	the_ff->cleanMe();
540
541	<	}
541	>	if (!globals->haveRcut()){
542
543	<	void SimSetup::initFromBass( void ){
543	>	the_ff->calcRcut();
544
545	+	} else {
546	+
547	+	the_ff->setRcut( globals->getRcut() );
548	+	}
549	+
550	+	the_ff->cleanMe();
551	+	}
552	+
553	+	void SimSetup::initFromBass(void){
554		int i, j, k;
555		int n_cells;
556		double cellx, celly, cellz;
#	Line 389 | Line 559 | void SimSetup::initFromBass( void ){
559		int n_extra;
560		int have_extra, done;
561
562	<	temp1 = (double)tot_nmol / 4.0;
563	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
564	<	temp3 = ceil( temp2 );
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	have_extra =0;
568	<	if( temp2 < temp3 ){ // we have a non-complete lattice
569	<	have_extra =1;
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	<	n_cells = (int)temp3 - 1;
572	<	cellx = info->boxL[0] / temp3;
573	<	celly = info->boxL[1] / temp3;
574	<	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 );
571	>	have_extra = 0;
572	>	if (temp2 < temp3){
573	>	// we have a non-complete lattice
574	>	have_extra = 1;
575
576	<	if( n_per_extra > 4){
577	<	sprintf( painCave.errMsg,
578	<	"SimSetup error. There has been an error in constructing"
579	<	" the non-complete lattice.\n" );
576	>	n_cells = (int) temp3 - 1;
577	>	cellx = info[0].boxL[0] / temp3;
578	>	celly = info[0].boxL[1] / temp3;
579	>	cellz = info[0].boxL[2] / temp3;
580	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	>	n_per_extra = (int) ceil(temp1);
583	>
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588		painCave.isFatal = 1;
589		simError();
590		}
591		}
592		else{
593	<	n_cells = (int)temp3;
594	<	cellx = info->boxL[0] / temp3;
595	<	celly = info->boxL[1] / temp3;
596	<	cellz = info->boxL[2] / temp3;
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597		}
598
599		current_mol = 0;
#	Line 425 | Line 601 | void SimSetup::initFromBass( void ){
601		current_comp = 0;
602		current_atom_ndx = 0;
603
604	<	for( i=0; i < n_cells ; i++ ){
605	<	for( j=0; j < n_cells; j++ ){
606	<	for( k=0; k < n_cells; k++ ){
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	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 );
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
615		}
616		}
617
618	<	if( have_extra ){
618	>	if (have_extra){
619		done = 0;
620
621		int start_ndx;
622	<	for( i=0; i < (n_cells+1) && !done; i++ ){
623	<	for( j=0; j < (n_cells+1) && !done; j++ ){
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	if( i < n_cells ){
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( j < n_cells ){
639	<	start_ndx = n_cells;
640	<	}
641	<	else start_ndx = 0;
642	<	}
465	<	else start_ndx = 0;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	makeElement( i * cellx,
651	<	j * celly,
652	<	k * cellz );
653	<	done = ( current_mol >= tot_nmol );
654	<
655	<	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	<	}
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657		}
658		}
659
660	<
661	<	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 );
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662		}
663		}
664
665	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
665	>	void SimSetup::makeElement(double x, double y, double z){
666		int k;
667		AtomStamp* current_atom;
668		DirectionalAtom* dAtom;
669		double rotMat[3][3];
670	+	double pos[3];
671
672	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
673	<
674	<	current_atom = comp_stamps[current_comp]->getAtom( k );
675	<	if( !current_atom->havePosition() ){
676	<	sprintf( painCave.errMsg,
677	<	"SimSetup:initFromBass error.\n"
678	<	"\tComponent %s, atom %s does not have a position specified.\n"
679	<	"\tThe initialization routine is unable to give a start"
680	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
684
685	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
686	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
687	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694		rotMat[0][0] = 1.0;
695		rotMat[0][1] = 0.0;
#	Line 546 | Line 703 | void SimSetup::makeElement( double x, double y, double
703		rotMat[2][1] = 0.0;
704		rotMat[2][2] = 1.0;
705
706	<	dAtom->setA( rotMat );
706	>	dAtom->setA(rotMat);
707		}
708
709		current_atom_ndx++;
#	Line 555 | Line 712 | void SimSetup::makeElement( double x, double y, double
712		current_mol++;
713		current_comp_mol++;
714
715	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716		current_comp_mol = 0;
717		current_comp++;
718		}
719		}
720
721
722	<	void SimSetup::gatherInfo( void ){
723	<	int i,j,k;
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725		ensembleCase = -1;
726		ffCase = -1;
727
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
728		// set the easy ones first
729	<	info->target_temp = globals->getTargetTemp();
730	<	info->dt = globals->getDt();
731	<	info->run_time = globals->getRunTime();
729	>
730	>	for (i = 0; i < nInfo; i++){
731	>	info[i].target_temp = globals->getTargetTemp();
732	>	info[i].dt = globals->getDt();
733	>	info[i].run_time = globals->getRunTime();
734	>	}
735		n_components = globals->getNComponents();
736
737
738		// get the forceField
739
740	<	strcpy( force_field, globals->getForceField() );
740	>	strcpy(force_field, globals->getForceField());
741
742	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
743	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
744	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
742	>	if (!strcasecmp(force_field, "DUFF")){
743	>	ffCase = FF_DUFF;
744	>	}
745	>	else if (!strcasecmp(force_field, "LJ")){
746	>	ffCase = FF_LJ;
747	>	}
748	>	else if (!strcasecmp(force_field, "EAM")){
749	>	ffCase = FF_EAM;
750	>	}
751	>	else if (!strcasecmp(force_field, "WATER")){
752	>	ffCase = FF_H2O;
753	>	}
754		else{
755	<	sprintf( painCave.errMsg,
756	<	"SimSetup Error. Unrecognized force field -> %s\n",
757	<	force_field );
758	<	painCave.isFatal = 1;
595	<	simError();
755	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	>	force_field);
757	>	painCave.isFatal = 1;
758	>	simError();
759		}
760
761	<	// get the ensemble
761	>	// get the ensemble
762
763	<	strcpy( ensemble, globals->getEnsemble() );
763	>	strcpy(ensemble, globals->getEnsemble());
764
765	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
766	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
767	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
765	>	if (!strcasecmp(ensemble, "NVE")){
766	>	ensembleCase = NVE_ENS;
767	>	}
768	>	else if (!strcasecmp(ensemble, "NVT")){
769	>	ensembleCase = NVT_ENS;
770	>	}
771	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772		ensembleCase = NPTi_ENS;
773	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
774	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
775	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
773	>	}
774	>	else if (!strcasecmp(ensemble, "NPTf")){
775	>	ensembleCase = NPTf_ENS;
776	>	}
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779	>	}
780		else{
781	<	sprintf( painCave.errMsg,
782	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
783	<	"reverting to NVE for this simulation.\n",
784	<	ensemble );
785	<	painCave.isFatal = 0;
786	<	simError();
787	<	strcpy( ensemble, "NVE" );
788	<	ensembleCase = NVE_ENS;
781	>	sprintf(painCave.errMsg,
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784	>	ensemble);
785	>	painCave.isFatal = 0;
786	>	simError();
787	>	strcpy(ensemble, "NVE");
788	>	ensembleCase = NVE_ENS;
789		}
619	–	strcpy( info->ensemble, ensemble );
790
791	<	// get the mixing rule
791	>	for (i = 0; i < nInfo; i++){
792	>	strcpy(info[i].ensemble, ensemble);
793
794	<	strcpy( info->mixingRule, globals->getMixingRule() );
795	<	info->usePBC = globals->getPBC();
796	<
797	<
794	>	// get the mixing rule
795	>
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797	>	info[i].usePBC = globals->getPBC();
798	>	}
799	>
800		// get the components and calculate the tot_nMol and indvidual n_mol
801	<
801	>
802		the_components = globals->getComponents();
803		components_nmol = new int[n_components];
804
805
806	<	if( !globals->haveNMol() ){
806	>	if (!globals->haveNMol()){
807		// we don't have the total number of molecules, so we assume it is
808		// given in each component
809
810		tot_nmol = 0;
811	<	for( i=0; i<n_components; i++ ){
812	<
813	<	if( !the_components[i]->haveNMol() ){
814	<	// we have a problem
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup Error. No global NMol or component NMol"
817	<	" given. Cannot calculate the number of atoms.\n" );
818	<	painCave.isFatal = 1;
646	<	simError();
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819		}
820
821		tot_nmol += the_components[i]->getNMol();
#	Line 651 | Line 823 | void SimSetup::gatherInfo( void ){
823		}
824		}
825		else{
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup error.\n"
828	<	"\tSorry, the ability to specify total"
829	<	" nMols and then give molfractions in the components\n"
830	<	"\tis not currently supported."
831	<	" Please give nMol in the components.\n" );
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup error.\n"
828	>	"\tSorry, the ability to specify total"
829	>	" nMols and then give molfractions in the components\n"
830	>	"\tis not currently supported."
831	>	" Please give nMol in the components.\n");
832		painCave.isFatal = 1;
833		simError();
834		}
835
836	<	// set the status, sample, and thermal kick times
837	<
838	<	if( globals->haveSampleTime() ){
839	<	info->sampleTime = globals->getSampleTime();
840	<	info->statusTime = info->sampleTime;
841	<	info->thermalTime = info->sampleTime;
836	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	>	sprintf(painCave.errMsg,
839	>	"Sample time is not divisible by dt.\n"
840	>	"\tThis will result in samples that are not uniformly\n"
841	>	"\tdistributed in time.  If this is a problem, change\n"
842	>	"\tyour sampleTime variable.\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845		}
671	–	else{
672	–	info->sampleTime = globals->getRunTime();
673	–	info->statusTime = info->sampleTime;
674	–	info->thermalTime = info->sampleTime;
675	–	}
846
847	<	if( globals->haveStatusTime() ){
848	<	info->statusTime = globals->getStatusTime();
847	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	>	sprintf(painCave.errMsg,
849	>	"Status time is not divisible by dt.\n"
850	>	"\tThis will result in status reports that are not uniformly\n"
851	>	"\tdistributed in time.  If this is a problem, change \n"
852	>	"\tyour statusTime variable.\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855		}
856
857	<	if( globals->haveThermalTime() ){
858	<	info->thermalTime = globals->getThermalTime();
859	<	}
857	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	>	sprintf(painCave.errMsg,
859	>	"Thermal time is not divisible by dt.\n"
860	>	"\tThis will result in thermalizations that are not uniformly\n"
861	>	"\tdistributed in time.  If this is a problem, change \n"
862	>	"\tyour thermalTime variable.\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	}
866
867	<	// check for the temperature set flag
868	<
869	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
870	<
871	<	// get some of the tricky things that may still be in the globals
867	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	>	sprintf(painCave.errMsg,
869	>	"Reset time is not divisible by dt.\n"
870	>	"\tThis will result in integrator resets that are not uniformly\n"
871	>	"\tdistributed in time.  If this is a problem, change\n"
872	>	"\tyour resetTime variable.\n");
873	>	painCave.isFatal = 0;
874	>	simError();
875	>	}
876
877	<	double boxVector[3];
692	<	if( globals->haveBox() ){
693	<	boxVector[0] = globals->getBox();
694	<	boxVector[1] = globals->getBox();
695	<	boxVector[2] = globals->getBox();
696	<
697	<	info->setBox( boxVector );
698	<	}
699	<	else if( globals->haveDensity() ){
877	>	// set the status, sample, and thermal kick times
878
879	<	double vol;
880	<	vol = (double)tot_nmol / globals->getDensity();
881	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
882	<	boxVector[1] = boxVector[0];
883	<	boxVector[2] = boxVector[0];
879	>	for (i = 0; i < nInfo; i++){
880	>	if (globals->haveSampleTime()){
881	>	info[i].sampleTime = globals->getSampleTime();
882	>	info[i].statusTime = info[i].sampleTime;
883	>	}
884	>	else{
885	>	info[i].sampleTime = globals->getRunTime();
886	>	info[i].statusTime = info[i].sampleTime;
887	>	}
888
889	<	info->setBox( boxVector );
890	<	}
709	<	else{
710	<	if( !globals->haveBoxX() ){
711	<	sprintf( painCave.errMsg,
712	<	"SimSetup error, no periodic BoxX size given.\n" );
713	<	painCave.isFatal = 1;
714	<	simError();
889	>	if (globals->haveStatusTime()){
890	>	info[i].statusTime = globals->getStatusTime();
891		}
716	–	boxVector[0] = globals->getBoxX();
892
893	<	if( !globals->haveBoxY() ){
894	<	sprintf( painCave.errMsg,
895	<	"SimSetup error, no periodic BoxY size given.\n" );
896	<	painCave.isFatal = 1;
722	<	simError();
893	>	if (globals->haveThermalTime()){
894	>	info[i].thermalTime = globals->getThermalTime();
895	>	} else {
896	>	info[i].thermalTime = globals->getRunTime();
897		}
724	–	boxVector[1] = globals->getBoxY();
898
899	<	if( !globals->haveBoxZ() ){
900	<	sprintf( painCave.errMsg,
901	<	"SimSetup error, no periodic BoxZ size given.\n" );
902	<	painCave.isFatal = 1;
730	<	simError();
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903		}
732	–	boxVector[2] = globals->getBoxZ();
904
905	<	info->setBox( boxVector );
905	>	// check for the temperature set flag
906	>
907	>	if (globals->haveTempSet())
908	>	info[i].setTemp = globals->getTempSet();
909	>
910	>	// check for the extended State init
911	>
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	>
915		}
916	+
917	+	//setup seed for random number generator
918	+	int seedValue;
919
920	+	if (globals->haveSeed()){
921	+	seedValue = globals->getSeed();
922
923	+	if(seedValue / 1E9 == 0){
924	+	sprintf(painCave.errMsg,
925	+	"Seed for sprng library should contain at least 9 digits\n"
926	+	"OOPSE will generate a seed for user\n");
927	+	painCave.isFatal = 0;
928	+	simError();
929	+
930	+	//using seed generated by system instead of invalid seed set by user
931	+	#ifndef IS_MPI
932	+	seedValue = make_sprng_seed();
933	+	#else
934	+	if (worldRank == 0){
935	+	seedValue = make_sprng_seed();
936	+	}
937	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
938	+	#endif
939	+	}
940	+	}//end of if branch of globals->haveSeed()
941	+	else{
942
943	+	#ifndef IS_MPI
944	+	seedValue = make_sprng_seed();
945	+	#else
946	+	if (worldRank == 0){
947	+	seedValue = make_sprng_seed();
948	+	}
949	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
950	+	#endif
951	+	}//end of globals->haveSeed()
952	+
953	+	for (int i = 0; i < nInfo; i++){
954	+	info[i].setSeed(seedValue);
955	+	}
956	+
957		#ifdef IS_MPI
958	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
958	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959		MPIcheckPoint();
960		#endif // is_mpi
743	–
961		}
962
963
964	<	void SimSetup::finalInfoCheck( void ){
964	>	void SimSetup::finalInfoCheck(void){
965		int index;
966		int usesDipoles;
967	<
967	>	int usesCharges;
968	>	int i;
969
970	<	// check electrostatic parameters
971	<
972	<	index = 0;
973	<	usesDipoles = 0;
974	<	while( (index < info->n_atoms) && !usesDipoles ){
975	<	usesDipoles = ((info->atoms)[index])->hasDipole();
976	<	index++;
977	<	}
978	<
970	>	for (i = 0; i < nInfo; i++){
971	>	// check electrostatic parameters
972	>
973	>	index = 0;
974	>	usesDipoles = 0;
975	>	while ((index < info[i].n_atoms) && !usesDipoles){
976	>	usesDipoles = (info[i].atoms[index])->hasDipole();
977	>	index++;
978	>	}
979	>	index = 0;
980	>	usesCharges = 0;
981	>	while ((index < info[i].n_atoms) && !usesCharges){
982	>	usesCharges= (info[i].atoms[index])->hasCharge();
983	>	index++;
984	>	}
985		#ifdef IS_MPI
986	<	int myUse = usesDipoles;
987	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
986	>	int myUse = usesDipoles;
987	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988		#endif //is_mpi
989
990	<	double theEcr, theEst;
990	>	double theRcut, theRsw;
991
992	<	if (globals->getUseRF() ) {
993	<	info->useReactionField = 1;
770	<
771	<	if( !globals->haveECR() ){
772	<	sprintf( painCave.errMsg,
773	<	"SimSetup Warning: using default value of 1/2 the smallest "
774	<	"box length for the electrostaticCutoffRadius.\n"
775	<	"I hope you have a very fast processor!\n");
776	<	painCave.isFatal = 0;
777	<	simError();
778	<	double smallest;
779	<	smallest = info->boxL[0];
780	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
781	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
782	<	theEcr = 0.5 * smallest;
783	<	} else {
784	<	theEcr = globals->getECR();
785	<	}
992	>	if (globals->getUseRF()){
993	>	info[i].useReactionField = 1;
994
995	<	if( !globals->haveEST() ){
996	<	sprintf( painCave.errMsg,
997	<	"SimSetup Warning: using default value of 0.05 * the "
998	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
999	<	);
1000	<	painCave.isFatal = 0;
1001	<	simError();
1002	<	theEst = 0.05 * theEcr;
1003	<	} else {
1004	<	theEst= globals->getEST();
1005	<	}
995	>	if (!globals->haveRcut()){
996	>	sprintf(painCave.errMsg,
997	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
998	>	"\tOOPSE will use a default value of 15.0 angstroms"
999	>	"\tfor the cutoffRadius.\n");
1000	>	painCave.isFatal = 0;
1001	>	simError();
1002	>	theRcut = 15.0;
1003	>	}
1004	>	else{
1005	>	theRcut = globals->getRcut();
1006	>	}
1007
1008	<	info->setEcr( theEcr, theEst );
1009	<
1010	<	if(!globals->haveDielectric() ){
1011	<	sprintf( painCave.errMsg,
1012	<	"SimSetup Error: You are trying to use Reaction Field without"
1013	<	"setting a dielectric constant!\n"
1014	<	);
1015	<	painCave.isFatal = 1;
807	<	simError();
808	<	}
809	<	info->dielectric = globals->getDielectric();
810	<	}
811	<	else {
812	<	if (usesDipoles) {
813	<
814	<	if( !globals->haveECR() ){
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup Warning: using default value of 1/2 the smallest "
817	<	"box length for the electrostaticCutoffRadius.\n"
818	<	"I hope you have a very fast processor!\n");
819	<	painCave.isFatal = 0;
820	<	simError();
821	<	double smallest;
822	<	smallest = info->boxL[0];
823	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
824	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
825	<	theEcr = 0.5 * smallest;
826	<	} else {
827	<	theEcr = globals->getECR();
1008	>	if (!globals->haveRsw()){
1009	>	sprintf(painCave.errMsg,
1010	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	theRsw = 0.95 * theRcut;
1016		}
1017	<
1018	<	if( !globals->haveEST() ){
831	<	sprintf( painCave.errMsg,
832	<	"SimSetup Warning: using default value of 0.05 * the "
833	<	"electrostaticCutoffRadius for the "
834	<	"electrostaticSkinThickness\n"
835	<	);
836	<	painCave.isFatal = 0;
837	<	simError();
838	<	theEst = 0.05 * theEcr;
839	<	} else {
840	<	theEst= globals->getEST();
1017	>	else{
1018	>	theRsw = globals->getRsw();
1019		}
1020
1021	<	info->setEcr( theEcr, theEst );
1021	>	info[i].setDefaultRcut(theRcut, theRsw);
1022	>
1023	>	if (!globals->haveDielectric()){
1024	>	sprintf(painCave.errMsg,
1025	>	"SimSetup Error: No Dielectric constant was set.\n"
1026	>	"\tYou are trying to use Reaction Field without"
1027	>	"\tsetting a dielectric constant!\n");
1028	>	painCave.isFatal = 1;
1029	>	simError();
1030	>	}
1031	>	info[i].dielectric = globals->getDielectric();
1032		}
1033	<	}
1033	>	else{
1034	>	if (usesDipoles || usesCharges){
1035
1036	+	if (!globals->haveRcut()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1039	+	"\tOOPSE will use a default value of 15.0 angstroms"
1040	+	"\tfor the cutoffRadius.\n");
1041	+	painCave.isFatal = 0;
1042	+	simError();
1043	+	theRcut = 15.0;
1044	+	}
1045	+	else{
1046	+	theRcut = globals->getRcut();
1047	+	}
1048	+
1049	+	if (!globals->haveRsw()){
1050	+	sprintf(painCave.errMsg,
1051	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1052	+	"\tOOPSE will use a default value of\n"
1053	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1054	+	painCave.isFatal = 0;
1055	+	simError();
1056	+	theRsw = 0.95 * theRcut;
1057	+	}
1058	+	else{
1059	+	theRsw = globals->getRsw();
1060	+	}
1061	+
1062	+	info[i].setDefaultRcut(theRcut, theRsw);
1063	+
1064	+	}
1065	+	}
1066	+	}
1067		#ifdef IS_MPI
1068	<	strcpy( checkPointMsg, "post processing checks out" );
1068	>	strcpy(checkPointMsg, "post processing checks out");
1069		MPIcheckPoint();
1070		#endif // is_mpi
851	–
1071		}
1072	+
1073	+	void SimSetup::initSystemCoords(void){
1074	+	int i;
1075
1076	<	void SimSetup::initSystemCoords( void ){
1076	>	char* inName;
1077
1078	<	if( globals->haveInitialConfig() ){
1079	<
1080	<	InitializeFromFile* fileInit;
1078	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079	>
1080	>	for (i = 0; i < info[0].n_atoms; i++)
1081	>	info[0].atoms[i]->setCoords();
1082	>
1083	>	if (globals->haveInitialConfig()){
1084	>	InitializeFromFile* fileInit;
1085		#ifdef IS_MPI // is_mpi
1086	<	if( worldRank == 0 ){
1086	>	if (worldRank == 0){
1087		#endif //is_mpi
1088	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1088	>	inName = globals->getInitialConfig();
1089	>	fileInit = new InitializeFromFile(inName);
1090		#ifdef IS_MPI
1091	<	}else fileInit = new InitializeFromFile( NULL );
1091	>	}
1092	>	else
1093	>	fileInit = new InitializeFromFile(NULL);
1094		#endif
1095	<	fileInit->readInit( info ); // default velocities on
1095	>	fileInit->readInit(info); // default velocities on
1096
1097	<	delete fileInit;
1098	<	}
1099	<	else{
1097	>	delete fileInit;
1098	>	}
1099	>	else{
1100	>
1101	>	// no init from bass
1102	>
1103	>	sprintf(painCave.errMsg,
1104	>	"Cannot intialize a simulation without an initial configuration file.\n");
1105	>	painCave.isFatal = 1;;
1106	>	simError();
1107	>
1108	>	}
1109
872	–	#ifdef IS_MPI
873	–
874	–	// no init from bass
875	–
876	–	sprintf( painCave.errMsg,
877	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
878	–	painCave.isFatal;
879	–	simError();
880	–
881	–	#else
882	–
883	–	initFromBass();
884	–
885	–
886	–	#endif
887	–	}
888	–
1110		#ifdef IS_MPI
1111	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1111	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112		MPIcheckPoint();
1113		#endif // is_mpi
893	–
1114		}
1115
1116
1117	<	void SimSetup::makeOutNames( void ){
1117	>	void SimSetup::makeOutNames(void){
1118	>	int k;
1119
1120	+
1121	+	for (k = 0; k < nInfo; k++){
1122		#ifdef IS_MPI
1123	<	if( worldRank == 0 ){
1123	>	if (worldRank == 0){
1124		#endif // is_mpi
1125	<
1126	<	if( globals->haveFinalConfig() ){
1127	<	strcpy( info->finalName, globals->getFinalConfig() );
905	<	}
906	<	else{
907	<	strcpy( info->finalName, inFileName );
908	<	char* endTest;
909	<	int nameLength = strlen( info->finalName );
910	<	endTest = &(info->finalName[nameLength - 5]);
911	<	if( !strcmp( endTest, ".bass" ) ){
912	<	strcpy( endTest, ".eor" );
1125	>
1126	>	if (globals->haveFinalConfig()){
1127	>	strcpy(info[k].finalName, globals->getFinalConfig());
1128		}
1129	<	else if( !strcmp( endTest, ".BASS" ) ){
1130	<	strcpy( endTest, ".eor" );
1129	>	else{
1130	>	strcpy(info[k].finalName, inFileName);
1131	>	char* endTest;
1132	>	int nameLength = strlen(info[k].finalName);
1133	>	endTest = &(info[k].finalName[nameLength - 5]);
1134	>	if (!strcmp(endTest, ".bass")){
1135	>	strcpy(endTest, ".eor");
1136	>	}
1137	>	else if (!strcmp(endTest, ".BASS")){
1138	>	strcpy(endTest, ".eor");
1139	>	}
1140	>	else{
1141	>	endTest = &(info[k].finalName[nameLength - 4]);
1142	>	if (!strcmp(endTest, ".bss")){
1143	>	strcpy(endTest, ".eor");
1144	>	}
1145	>	else if (!strcmp(endTest, ".mdl")){
1146	>	strcpy(endTest, ".eor");
1147	>	}
1148	>	else{
1149	>	strcat(info[k].finalName, ".eor");
1150	>	}
1151	>	}
1152		}
1153	<	else{
1154	<	endTest = &(info->finalName[nameLength - 4]);
1155	<	if( !strcmp( endTest, ".bss" ) ){
1156	<	strcpy( endTest, ".eor" );
1157	<	}
1158	<	else if( !strcmp( endTest, ".mdl" ) ){
1159	<	strcpy( endTest, ".eor" );
1160	<	}
1161	<	else{
926	<	strcat( info->finalName, ".eor" );
927	<	}
1153	>
1154	>	// make the sample and status out names
1155	>
1156	>	strcpy(info[k].sampleName, inFileName);
1157	>	char* endTest;
1158	>	int nameLength = strlen(info[k].sampleName);
1159	>	endTest = &(info[k].sampleName[nameLength - 5]);
1160	>	if (!strcmp(endTest, ".bass")){
1161	>	strcpy(endTest, ".dump");
1162		}
1163	<	}
1164	<
931	<	// make the sample and status out names
932	<
933	<	strcpy( info->sampleName, inFileName );
934	<	char* endTest;
935	<	int nameLength = strlen( info->sampleName );
936	<	endTest = &(info->sampleName[nameLength - 5]);
937	<	if( !strcmp( endTest, ".bass" ) ){
938	<	strcpy( endTest, ".dump" );
939	<	}
940	<	else if( !strcmp( endTest, ".BASS" ) ){
941	<	strcpy( endTest, ".dump" );
942	<	}
943	<	else{
944	<	endTest = &(info->sampleName[nameLength - 4]);
945	<	if( !strcmp( endTest, ".bss" ) ){
946	<	strcpy( endTest, ".dump" );
1163	>	else if (!strcmp(endTest, ".BASS")){
1164	>	strcpy(endTest, ".dump");
1165		}
948	–	else if( !strcmp( endTest, ".mdl" ) ){
949	–	strcpy( endTest, ".dump" );
950	–	}
1166		else{
1167	<	strcat( info->sampleName, ".dump" );
1167	>	endTest = &(info[k].sampleName[nameLength - 4]);
1168	>	if (!strcmp(endTest, ".bss")){
1169	>	strcpy(endTest, ".dump");
1170	>	}
1171	>	else if (!strcmp(endTest, ".mdl")){
1172	>	strcpy(endTest, ".dump");
1173	>	}
1174	>	else{
1175	>	strcat(info[k].sampleName, ".dump");
1176	>	}
1177		}
1178	<	}
1179	<
1180	<	strcpy( info->statusName, inFileName );
1181	<	nameLength = strlen( info->statusName );
1182	<	endTest = &(info->statusName[nameLength - 5]);
1183	<	if( !strcmp( endTest, ".bass" ) ){
960	<	strcpy( endTest, ".stat" );
961	<	}
962	<	else if( !strcmp( endTest, ".BASS" ) ){
963	<	strcpy( endTest, ".stat" );
964	<	}
965	<	else{
966	<	endTest = &(info->statusName[nameLength - 4]);
967	<	if( !strcmp( endTest, ".bss" ) ){
968	<	strcpy( endTest, ".stat" );
1178	>
1179	>	strcpy(info[k].statusName, inFileName);
1180	>	nameLength = strlen(info[k].statusName);
1181	>	endTest = &(info[k].statusName[nameLength - 5]);
1182	>	if (!strcmp(endTest, ".bass")){
1183	>	strcpy(endTest, ".stat");
1184		}
1185	<	else if( !strcmp( endTest, ".mdl" ) ){
1186	<	strcpy( endTest, ".stat" );
1185	>	else if (!strcmp(endTest, ".BASS")){
1186	>	strcpy(endTest, ".stat");
1187		}
1188		else{
1189	<	strcat( info->statusName, ".stat" );
1189	>	endTest = &(info[k].statusName[nameLength - 4]);
1190	>	if (!strcmp(endTest, ".bss")){
1191	>	strcpy(endTest, ".stat");
1192	>	}
1193	>	else if (!strcmp(endTest, ".mdl")){
1194	>	strcpy(endTest, ".stat");
1195	>	}
1196	>	else{
1197	>	strcat(info[k].statusName, ".stat");
1198	>	}
1199		}
1200	<	}
977	<
1200	>
1201		#ifdef IS_MPI
979	–	}
980	–	#endif // is_mpi
1202
1203	+	}
1204	+	#endif // is_mpi
1205	+	}
1206		}
1207
1208
1209	<	void SimSetup::sysObjectsCreation( void ){
1209	>	void SimSetup::sysObjectsCreation(void){
1210	>	int i, k;
1211
987	–	int i;
988	–
1212		// create the forceField
1213
1214		createFF();
#	Line 1000 | Line 1223 | void SimSetup::sysObjectsCreation( void ){
1223
1224		#ifdef IS_MPI
1225		// divide the molecules among the processors
1226	<
1226	>
1227		mpiMolDivide();
1228		#endif //is_mpi
1229	<
1229	>
1230		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231	<
1231	>
1232		makeSysArrays();
1233
1234		// make and initialize the molecules (all but atomic coordinates)
1235	<
1235	>
1236		makeMolecules();
1014	–	info->identArray = new int[info->n_atoms];
1015	–	for(i=0; i<info->n_atoms; i++){
1016	–	info->identArray[i] = the_atoms[i]->getIdent();
1017	–	}
1018	–
1237
1238	<
1238	>	for (k = 0; k < nInfo; k++){
1239	>	info[k].identArray = new int[info[k].n_atoms];
1240	>	for (i = 0; i < info[k].n_atoms; i++){
1241	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1242	>	}
1243	>	}
1244		}
1245
1246
1247	<	void SimSetup::createFF( void ){
1247	>	void SimSetup::createFF(void){
1248	>	switch (ffCase){
1249	>	case FF_DUFF:
1250	>	the_ff = new DUFF();
1251	>	break;
1252
1253	<	switch( ffCase ){
1253	>	case FF_LJ:
1254	>	the_ff = new LJFF();
1255	>	break;
1256
1257	<	case FF_DUFF:
1258	<	the_ff = new DUFF();
1259	<	break;
1257	>	case FF_EAM:
1258	>	the_ff = new EAM_FF();
1259	>	break;
1260
1261	<	case FF_LJ:
1262	<	the_ff = new LJFF();
1263	<	break;
1261	>	case FF_H2O:
1262	>	the_ff = new WATER();
1263	>	break;
1264
1265	<	case FF_EAM:
1266	<	the_ff = new EAM_FF();
1267	<	break;
1268	<
1269	<	default:
1041	<	sprintf( painCave.errMsg,
1042	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1043	<	painCave.isFatal = 1;
1044	<	simError();
1265	>	default:
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1268	>	painCave.isFatal = 1;
1269	>	simError();
1270		}
1271
1272		#ifdef IS_MPI
1273	<	strcpy( checkPointMsg, "ForceField creation successful" );
1273	>	strcpy(checkPointMsg, "ForceField creation successful");
1274		MPIcheckPoint();
1275		#endif // is_mpi
1051	–
1276		}
1277
1278
1279	<	void SimSetup::compList( void ){
1056	<
1279	>	void SimSetup::compList(void){
1280		int i;
1281	<
1282	<	comp_stamps = new MoleculeStamp*[n_components];
1281	>	char* id;
1282	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1283	>	LinkedMolStamp* currentStamp = NULL;
1284	>	comp_stamps = new MoleculeStamp * [n_components];
1285
1286		// make an array of molecule stamps that match the components used.
1287		// also extract the used stamps out into a separate linked list
1288
1289	<	info->nComponents = n_components;
1290	<	info->componentsNmol = components_nmol;
1291	<	info->compStamps = comp_stamps;
1292	<	info->headStamp = new LinkedMolStamp();
1293	<
1294	<	char* id;
1070	<	LinkedMolStamp* headStamp = info->headStamp;
1071	<	LinkedMolStamp* currentStamp = NULL;
1072	<	for( i=0; i<n_components; i++ ){
1289	>	for (i = 0; i < nInfo; i++){
1290	>	info[i].nComponents = n_components;
1291	>	info[i].componentsNmol = components_nmol;
1292	>	info[i].compStamps = comp_stamps;
1293	>	info[i].headStamp = headStamp;
1294	>	}
1295
1296	+
1297	+	for (i = 0; i < n_components; i++){
1298		id = the_components[i]->getType();
1299		comp_stamps[i] = NULL;
1300	<
1300	>
1301		// check to make sure the component isn't already in the list
1302
1303	<	comp_stamps[i] = headStamp->match( id );
1304	<	if( comp_stamps[i] == NULL ){
1081	<
1303	>	comp_stamps[i] = headStamp->match(id);
1304	>	if (comp_stamps[i] == NULL){
1305		// extract the component from the list;
1306	<
1307	<	currentStamp = stamps->extractMolStamp( id );
1308	<	if( currentStamp == NULL ){
1309	<	sprintf( painCave.errMsg,
1310	<	"SimSetup error: Component \"%s\" was not found in the "
1311	<	"list of declared molecules\n",
1312	<	id );
1313	<	painCave.isFatal = 1;
1314	<	simError();
1306	>
1307	>	currentStamp = stamps->extractMolStamp(id);
1308	>	if (currentStamp == NULL){
1309	>	sprintf(painCave.errMsg,
1310	>	"SimSetup error: Component \"%s\" was not found in the "
1311	>	"list of declared molecules\n",
1312	>	id);
1313	>	painCave.isFatal = 1;
1314	>	simError();
1315		}
1316	<
1317	<	headStamp->add( currentStamp );
1318	<	comp_stamps[i] = headStamp->match( id );
1316	>
1317	>	headStamp->add(currentStamp);
1318	>	comp_stamps[i] = headStamp->match(id);
1319		}
1320		}
1321
1322		#ifdef IS_MPI
1323	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1323	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1324		MPIcheckPoint();
1325		#endif // is_mpi
1103	–
1104	–
1326		}
1327
1328	<	void SimSetup::calcSysValues( void ){
1329	<	int i, j, k;
1328	>	void SimSetup::calcSysValues(void){
1329	>	int i;
1330
1331	+	int* molMembershipArray;
1332
1333		tot_atoms = 0;
1334		tot_bonds = 0;
1335		tot_bends = 0;
1336		tot_torsions = 0;
1337	<	for( i=0; i<n_components; i++ ){
1338	<
1339	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1341	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1337	>	tot_rigid = 0;
1338	>	for (i = 0; i < n_components; i++){
1339	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344		}
1345	<
1345	>
1346		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347	+	molMembershipArray = new int[tot_atoms];
1348
1349	<	info->n_atoms = tot_atoms;
1350	<	info->n_bonds = tot_bonds;
1351	<	info->n_bends = tot_bends;
1352	<	info->n_torsions = tot_torsions;
1353	<	info->n_SRI = tot_SRI;
1354	<	info->n_mol = tot_nmol;
1355	<
1356	<	info->molMembershipArray = new int[tot_atoms];
1349	>	for (i = 0; i < nInfo; i++){
1350	>	info[i].n_atoms = tot_atoms;
1351	>	info[i].n_bonds = tot_bonds;
1352	>	info[i].n_bends = tot_bends;
1353	>	info[i].n_torsions = tot_torsions;
1354	>	info[i].n_SRI = tot_SRI;
1355	>	info[i].n_mol = tot_nmol;
1356	>
1357	>	info[i].molMembershipArray = molMembershipArray;
1358	>	}
1359		}
1360
1135	–
1361		#ifdef IS_MPI
1362
1363	<	void SimSetup::mpiMolDivide( void ){
1139	<
1363	>	void SimSetup::mpiMolDivide(void){
1364		int i, j, k;
1365		int localMol, allMol;
1366		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	+	int local_rigid;
1368	+	vector<int> globalMolIndex;
1369
1370	<	mpiSim = new mpiSimulation( info );
1145	<
1146	<	globalIndex = mpiSim->divideLabor();
1370	>	mpiSim = new mpiSimulation(info);
1371
1372	+	mpiSim->divideLabor();
1373	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1374	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1375	+
1376		// set up the local variables
1377	<
1377	>
1378		mol2proc = mpiSim->getMolToProcMap();
1379		molCompType = mpiSim->getMolComponentType();
1380	<
1380	>
1381		allMol = 0;
1382		localMol = 0;
1383		local_atoms = 0;
1384		local_bonds = 0;
1385		local_bends = 0;
1386		local_torsions = 0;
1387	<	globalAtomIndex = 0;
1387	>	local_rigid = 0;
1388	>	globalAtomCounter = 0;
1389
1390	<
1391	<	for( i=0; i<n_components; i++ ){
1392	<
1393	<	for( j=0; j<components_nmol[i]; j++ ){
1394	<
1395	<	if( mol2proc[allMol] == worldRank ){
1396	<
1397	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1398	<	local_bonds +=    comp_stamps[i]->getNBonds();
1170	<	local_bends +=    comp_stamps[i]->getNBends();
1171	<	local_torsions += comp_stamps[i]->getNTorsions();
1172	<	localMol++;
1390	>	for (i = 0; i < n_components; i++){
1391	>	for (j = 0; j < components_nmol[i]; j++){
1392	>	if (mol2proc[allMol] == worldRank){
1393	>	local_atoms += comp_stamps[i]->getNAtoms();
1394	>	local_bonds += comp_stamps[i]->getNBonds();
1395	>	local_bends += comp_stamps[i]->getNBends();
1396	>	local_torsions += comp_stamps[i]->getNTorsions();
1397	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1398	>	localMol++;
1399		}
1400	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1401	<	info->molMembershipArray[globalAtomIndex] = allMol;
1402	<	globalAtomIndex++;
1400	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1401	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1402	>	globalAtomCounter++;
1403		}
1404
1405	<	allMol++;
1405	>	allMol++;
1406		}
1407		}
1408		local_SRI = local_bonds + local_bends + local_torsions;
1409	+
1410	+	info[0].n_atoms = mpiSim->getMyNlocal();
1411
1412	<	info->n_atoms = mpiSim->getMyNlocal();
1413	<
1414	<	if( local_atoms != info->n_atoms ){
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1417	<	" localAtom (%d) are not equal.\n",
1190	<	info->n_atoms,
1191	<	local_atoms );
1412	>
1413	>	if (local_atoms != info[0].n_atoms){
1414	>	sprintf(painCave.errMsg,
1415	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1416	>	"\tlocalAtom (%d) are not equal.\n",
1417	>	info[0].n_atoms, local_atoms);
1418		painCave.isFatal = 1;
1419		simError();
1420		}
1421
1422	<	info->n_bonds = local_bonds;
1423	<	info->n_bends = local_bends;
1424	<	info->n_torsions = local_torsions;
1425	<	info->n_SRI = local_SRI;
1426	<	info->n_mol = localMol;
1422	>	info[0].n_bonds = local_bonds;
1423	>	info[0].n_bends = local_bends;
1424	>	info[0].n_torsions = local_torsions;
1425	>	info[0].n_SRI = local_SRI;
1426	>	info[0].n_mol = localMol;
1427
1428	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1428	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1429		MPIcheckPoint();
1430		}
1431	<
1431	>
1432		#endif // is_mpi
1433
1434
1435	<	void SimSetup::makeSysArrays( void ){
1436	<	int i, j, k;
1435	>	void SimSetup::makeSysArrays(void){
1436	>
1437	>	#ifndef IS_MPI
1438	>	int k, j;
1439	>	#endif // is_mpi
1440	>	int i, l;
1441
1442	+	Atom** the_atoms;
1443	+	Molecule* the_molecules;
1444
1445	<	// create the atom and short range interaction arrays
1445	>	for (l = 0; l < nInfo; l++){
1446	>	// create the atom and short range interaction arrays
1447
1448	<	Atom::createArrays(info->n_atoms);
1449	<	the_atoms = new Atom*[info->n_atoms];
1450	<	the_molecules = new Molecule[info->n_mol];
1218	<	int molIndex;
1448	>	the_atoms = new Atom * [info[l].n_atoms];
1449	>	the_molecules = new Molecule[info[l].n_mol];
1450	>	int molIndex;
1451
1452	<	// initialize the molecule's stampID's
1452	>	// initialize the molecule's stampID's
1453
1454		#ifdef IS_MPI
1223	–
1455
1456	<	molIndex = 0;
1457	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1458	<
1459	<	if(mol2proc[i] == worldRank ){
1460	<	the_molecules[molIndex].setStampID( molCompType[i] );
1461	<	the_molecules[molIndex].setMyIndex( molIndex );
1462	<	the_molecules[molIndex].setGlobalIndex( i );
1463	<	molIndex++;
1456	>
1457	>	molIndex = 0;
1458	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1459	>	if (mol2proc[i] == worldRank){
1460	>	the_molecules[molIndex].setStampID(molCompType[i]);
1461	>	the_molecules[molIndex].setMyIndex(molIndex);
1462	>	the_molecules[molIndex].setGlobalIndex(i);
1463	>	molIndex++;
1464	>	}
1465		}
1234	–	}
1466
1467		#else // is_mpi
1468	<
1469	<	molIndex = 0;
1470	<	globalAtomIndex = 0;
1471	<	for(i=0; i<n_components; i++){
1472	<	for(j=0; j<components_nmol[i]; j++ ){
1473	<	the_molecules[molIndex].setStampID( i );
1474	<	the_molecules[molIndex].setMyIndex( molIndex );
1475	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1476	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1477	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1478	<	globalAtomIndex++;
1468	>
1469	>	molIndex = 0;
1470	>	globalAtomCounter = 0;
1471	>	for (i = 0; i < n_components; i++){
1472	>	for (j = 0; j < components_nmol[i]; j++){
1473	>	the_molecules[molIndex].setStampID(i);
1474	>	the_molecules[molIndex].setMyIndex(molIndex);
1475	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1476	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1477	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1478	>	globalAtomCounter++;
1479	>	}
1480	>	molIndex++;
1481		}
1249	–	molIndex++;
1482		}
1251	–	}
1252	–
1483
1484	+
1485		#endif // is_mpi
1486
1487	<
1488	<	if( info->n_SRI ){
1487	>	info[l].globalExcludes = new int;
1488	>	info[l].globalExcludes[0] = 0;
1489
1490	<	Exclude::createArray(info->n_SRI);
1260	<	the_excludes = new Exclude*[info->n_SRI];
1261	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1262	<	info->globalExcludes = new int;
1263	<	info->n_exclude = info->n_SRI;
1264	<	}
1265	<	else{
1266	<
1267	<	Exclude::createArray( 1 );
1268	<	the_excludes = new Exclude*;
1269	<	the_excludes[0] = new Exclude(0);
1270	<	the_excludes[0]->setPair( 0,0 );
1271	<	info->globalExcludes = new int;
1272	<	info->globalExcludes[0] = 0;
1273	<	info->n_exclude = 0;
1274	<	}
1490	>	// set the arrays into the SimInfo object
1491
1492	<	// set the arrays into the SimInfo object
1492	>	info[l].atoms = the_atoms;
1493	>	info[l].molecules = the_molecules;
1494	>	info[l].nGlobalExcludes = 0;
1495
1496	<	info->atoms = the_atoms;
1497	<	info->molecules = the_molecules;
1280	<	info->nGlobalExcludes = 0;
1281	<	info->excludes = the_excludes;
1282	<
1283	<	the_ff->setSimInfo( info );
1284	<
1496	>	the_ff->setSimInfo(info);
1497	>	}
1498		}
1499
1500	<	void SimSetup::makeIntegrator( void ){
1500	>	void SimSetup::makeIntegrator(void){
1501	>	int k;
1502
1503	<	NVT<RealIntegrator>*  myNVT = NULL;
1504	<	NPTi<RealIntegrator>* myNPTi = NULL;
1505	<	NPTf<RealIntegrator>* myNPTf = NULL;
1506	<	NPTim<RealIntegrator>* myNPTim = NULL;
1507	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1503	>	NVE<RealIntegrator>* myNVE = NULL;
1504	>	NVT<RealIntegrator>* myNVT = NULL;
1505	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1506	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1507	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1508	>
1509	>	for (k = 0; k < nInfo; k++){
1510	>	switch (ensembleCase){
1511	>	case NVE_ENS:
1512	>	if (globals->haveZconstraints()){
1513	>	setupZConstraint(info[k]);
1514	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1515	>	}
1516	>	else{
1517	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1518	>	}
1519	>
1520	>	info->the_integrator = myNVE;
1521	>	break;
1522
1523	<	switch( ensembleCase ){
1523	>	case NVT_ENS:
1524	>	if (globals->haveZconstraints()){
1525	>	setupZConstraint(info[k]);
1526	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1527	>	}
1528	>	else
1529	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1530
1531	<	case NVE_ENS:
1298	<	new NVE<RealIntegrator>( info, the_ff );
1299	<	break;
1531	>	myNVT->setTargetTemp(globals->getTargetTemp());
1532
1533	<	case NVT_ENS:
1534	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1535	<	myNVT->setTargetTemp(globals->getTargetTemp());
1533	>	if (globals->haveTauThermostat())
1534	>	myNVT->setTauThermostat(globals->getTauThermostat());
1535	>	else{
1536	>	sprintf(painCave.errMsg,
1537	>	"SimSetup error: If you use the NVT\n"
1538	>	"\tensemble, you must set tauThermostat.\n");
1539	>	painCave.isFatal = 1;
1540	>	simError();
1541	>	}
1542
1543	<	if (globals->haveTauThermostat())
1544	<	myNVT->setTauThermostat(globals->getTauThermostat());
1543	>	info->the_integrator = myNVT;
1544	>	break;
1545
1546	<	else {
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use the NVT\n"
1549	<	"    ensemble, you must set tauThermostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1315	<	break;
1546	>	case NPTi_ENS:
1547	>	if (globals->haveZconstraints()){
1548	>	setupZConstraint(info[k]);
1549	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1550	>	}
1551	>	else
1552	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1553
1554	<	case NPTi_ENS:
1318	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1319	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1554	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1555
1556	<	if (globals->haveTargetPressure())
1557	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1558	<	else {
1559	<	sprintf( painCave.errMsg,
1560	<	"SimSetup error: If you use a constant pressure\n"
1561	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1562	<	painCave.isFatal = 1;
1563	<	simError();
1564	<	}
1330	<
1331	<	if( globals->haveTauThermostat() )
1332	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1333	<	else{
1334	<	sprintf( painCave.errMsg,
1335	<	"SimSetup error: If you use an NPT\n"
1336	<	"    ensemble, you must set tauThermostat.\n");
1337	<	painCave.isFatal = 1;
1338	<	simError();
1339	<	}
1556	>	if (globals->haveTargetPressure())
1557	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1558	>	else{
1559	>	sprintf(painCave.errMsg,
1560	>	"SimSetup error: If you use a constant pressure\n"
1561	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1562	>	painCave.isFatal = 1;
1563	>	simError();
1564	>	}
1565
1566	<	if( globals->haveTauBarostat() )
1567	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1568	<	else{
1569	<	sprintf( painCave.errMsg,
1570	<	"SimSetup error: If you use an NPT\n"
1571	<	"    ensemble, you must set tauBarostat.\n");
1572	<	painCave.isFatal = 1;
1573	<	simError();
1574	<	}
1350	<	break;
1566	>	if (globals->haveTauThermostat())
1567	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1568	>	else{
1569	>	sprintf(painCave.errMsg,
1570	>	"SimSetup error: If you use an NPT\n"
1571	>	"\tensemble, you must set tauThermostat.\n");
1572	>	painCave.isFatal = 1;
1573	>	simError();
1574	>	}
1575
1576	<	case NPTf_ENS:
1577	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1578	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1576	>	if (globals->haveTauBarostat())
1577	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1578	>	else{
1579	>	sprintf(painCave.errMsg,
1580	>	"SimSetup error: If you use an NPT\n"
1581	>	"\tensemble, you must set tauBarostat.\n");
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585
1586	<	if (globals->haveTargetPressure())
1587	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1358	<	else {
1359	<	sprintf( painCave.errMsg,
1360	<	"SimSetup error: If you use a constant pressure\n"
1361	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1362	<	painCave.isFatal = 1;
1363	<	simError();
1364	<	}
1586	>	info->the_integrator = myNPTi;
1587	>	break;
1588
1589	<	if( globals->haveTauThermostat() )
1590	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1591	<	else{
1592	<	sprintf( painCave.errMsg,
1593	<	"SimSetup error: If you use an NPT\n"
1594	<	"    ensemble, you must set tauThermostat.\n");
1595	<	painCave.isFatal = 1;
1373	<	simError();
1374	<	}
1589	>	case NPTf_ENS:
1590	>	if (globals->haveZconstraints()){
1591	>	setupZConstraint(info[k]);
1592	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1593	>	}
1594	>	else
1595	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1596
1597	<	if( globals->haveTauBarostat() )
1377	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1378	<	else{
1379	<	sprintf( painCave.errMsg,
1380	<	"SimSetup error: If you use an NPT\n"
1381	<	"    ensemble, you must set tauBarostat.\n");
1382	<	painCave.isFatal = 1;
1383	<	simError();
1384	<	}
1385	<	break;
1386	<
1387	<	case NPTim_ENS:
1388	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1389	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1597	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1598
1599	<	if (globals->haveTargetPressure())
1600	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1601	<	else {
1602	<	sprintf( painCave.errMsg,
1603	<	"SimSetup error: If you use a constant pressure\n"
1604	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1605	<	painCave.isFatal = 1;
1606	<	simError();
1607	<	}
1400	<
1401	<	if( globals->haveTauThermostat() )
1402	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1403	<	else{
1404	<	sprintf( painCave.errMsg,
1405	<	"SimSetup error: If you use an NPT\n"
1406	<	"    ensemble, you must set tauThermostat.\n");
1407	<	painCave.isFatal = 1;
1408	<	simError();
1409	<	}
1599	>	if (globals->haveTargetPressure())
1600	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1601	>	else{
1602	>	sprintf(painCave.errMsg,
1603	>	"SimSetup error: If you use a constant pressure\n"
1604	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1605	>	painCave.isFatal = 1;
1606	>	simError();
1607	>	}
1608
1609	<	if( globals->haveTauBarostat() )
1610	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1413	<	else{
1414	<	sprintf( painCave.errMsg,
1415	<	"SimSetup error: If you use an NPT\n"
1416	<	"    ensemble, you must set tauBarostat.\n");
1417	<	painCave.isFatal = 1;
1418	<	simError();
1419	<	}
1420	<	break;
1609	>	if (globals->haveTauThermostat())
1610	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1611
1612	<	case NPTfm_ENS:
1613	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1614	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1612	>	else{
1613	>	sprintf(painCave.errMsg,
1614	>	"SimSetup error: If you use an NPT\n"
1615	>	"\tensemble, you must set tauThermostat.\n");
1616	>	painCave.isFatal = 1;
1617	>	simError();
1618	>	}
1619
1620	<	if (globals->haveTargetPressure())
1621	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1428	<	else {
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use a constant pressure\n"
1431	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<
1436	<	if( globals->haveTauThermostat() )
1437	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1438	<	else{
1439	<	sprintf( painCave.errMsg,
1440	<	"SimSetup error: If you use an NPT\n"
1441	<	"    ensemble, you must set tauThermostat.\n");
1442	<	painCave.isFatal = 1;
1443	<	simError();
1444	<	}
1620	>	if (globals->haveTauBarostat())
1621	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1622
1623	<	if( globals->haveTauBarostat() )
1624	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1625	<	else{
1626	<	sprintf( painCave.errMsg,
1627	<	"SimSetup error: If you use an NPT\n"
1628	<	"    ensemble, you must set tauBarostat.\n");
1629	<	painCave.isFatal = 1;
1453	<	simError();
1454	<	}
1455	<	break;
1623	>	else{
1624	>	sprintf(painCave.errMsg,
1625	>	"SimSetup error: If you use an NPT\n"
1626	>	"\tensemble, you must set tauBarostat.\n");
1627	>	painCave.isFatal = 1;
1628	>	simError();
1629	>	}
1630
1631	<	default:
1632	<	sprintf( painCave.errMsg,
1459	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1460	<	painCave.isFatal = 1;
1461	<	simError();
1462	<	}
1631	>	info->the_integrator = myNPTf;
1632	>	break;
1633
1634	+	case NPTxyz_ENS:
1635	+	if (globals->haveZconstraints()){
1636	+	setupZConstraint(info[k]);
1637	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1638	+	}
1639	+	else
1640	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1641	+
1642	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1643	+
1644	+	if (globals->haveTargetPressure())
1645	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1646	+	else{
1647	+	sprintf(painCave.errMsg,
1648	+	"SimSetup error: If you use a constant pressure\n"
1649	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1650	+	painCave.isFatal = 1;
1651	+	simError();
1652	+	}
1653	+
1654	+	if (globals->haveTauThermostat())
1655	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1656	+	else{
1657	+	sprintf(painCave.errMsg,
1658	+	"SimSetup error: If you use an NPT\n"
1659	+	"\tensemble, you must set tauThermostat.\n");
1660	+	painCave.isFatal = 1;
1661	+	simError();
1662	+	}
1663	+
1664	+	if (globals->haveTauBarostat())
1665	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1666	+	else{
1667	+	sprintf(painCave.errMsg,
1668	+	"SimSetup error: If you use an NPT\n"
1669	+	"\tensemble, you must set tauBarostat.\n");
1670	+	painCave.isFatal = 1;
1671	+	simError();
1672	+	}
1673	+
1674	+	info->the_integrator = myNPTxyz;
1675	+	break;
1676	+
1677	+	default:
1678	+	sprintf(painCave.errMsg,
1679	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1680	+	painCave.isFatal = 1;
1681	+	simError();
1682	+	}
1683	+	}
1684		}
1685
1686	<	void SimSetup::initFortran( void ){
1686	>	void SimSetup::initFortran(void){
1687	>	info[0].refreshSim();
1688
1689	<	info->refreshSim();
1690	<
1470	<	if( !strcmp( info->mixingRule, "standard") ){
1471	<	the_ff->initForceField( LB_MIXING_RULE );
1689	>	if (!strcmp(info[0].mixingRule, "standard")){
1690	>	the_ff->initForceField(LB_MIXING_RULE);
1691		}
1692	<	else if( !strcmp( info->mixingRule, "explicit") ){
1693	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1692	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1693	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1694		}
1695		else{
1696	<	sprintf( painCave.errMsg,
1697	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1479	<	info->mixingRule );
1696	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1697	>	info[0].mixingRule);
1698		painCave.isFatal = 1;
1699		simError();
1700		}
1701
1702
1703		#ifdef IS_MPI
1704	<	strcpy( checkPointMsg,
1487	<	"Successfully intialized the mixingRule for Fortran." );
1704	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1705		MPIcheckPoint();
1706		#endif // is_mpi
1707	+	}
1708
1709	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1710	+	int nZConstraints;
1711	+	ZconStamp** zconStamp;
1712	+
1713	+	if (globals->haveZconstraintTime()){
1714	+	//add sample time of z-constraint  into SimInfo's property list
1715	+	DoubleData* zconsTimeProp = new DoubleData();
1716	+	zconsTimeProp->setID(ZCONSTIME_ID);
1717	+	zconsTimeProp->setData(globals->getZconsTime());
1718	+	theInfo.addProperty(zconsTimeProp);
1719	+	}
1720	+	else{
1721	+	sprintf(painCave.errMsg,
1722	+	"ZConstraint error: If you use a ZConstraint,\n"
1723	+	"\tyou must set zconsTime.\n");
1724	+	painCave.isFatal = 1;
1725	+	simError();
1726	+	}
1727	+
1728	+	//push zconsTol into siminfo, if user does not specify
1729	+	//value for zconsTol, a default value will be used
1730	+	DoubleData* zconsTol = new DoubleData();
1731	+	zconsTol->setID(ZCONSTOL_ID);
1732	+	if (globals->haveZconsTol()){
1733	+	zconsTol->setData(globals->getZconsTol());
1734	+	}
1735	+	else{
1736	+	double defaultZConsTol = 0.01;
1737	+	sprintf(painCave.errMsg,
1738	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1739	+	"\tOOPSE will use a default value of %f.\n"
1740	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1741	+	defaultZConsTol);
1742	+	painCave.isFatal = 0;
1743	+	simError();
1744	+
1745	+	zconsTol->setData(defaultZConsTol);
1746	+	}
1747	+	theInfo.addProperty(zconsTol);
1748	+
1749	+	//set Force Subtraction Policy
1750	+	StringData* zconsForcePolicy = new StringData();
1751	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1752	+
1753	+	if (globals->haveZconsForcePolicy()){
1754	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1755	+	}
1756	+	else{
1757	+	sprintf(painCave.errMsg,
1758	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1759	+	"\tOOPSE will use PolicyByMass.\n"
1760	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1761	+	painCave.isFatal = 0;
1762	+	simError();
1763	+	zconsForcePolicy->setData("BYMASS");
1764	+	}
1765	+
1766	+	theInfo.addProperty(zconsForcePolicy);
1767	+
1768	+	//set zcons gap
1769	+	DoubleData* zconsGap = new DoubleData();
1770	+	zconsGap->setID(ZCONSGAP_ID);
1771	+
1772	+	if (globals->haveZConsGap()){
1773	+	zconsGap->setData(globals->getZconsGap());
1774	+	theInfo.addProperty(zconsGap);
1775	+	}
1776	+
1777	+	//set zcons fixtime
1778	+	DoubleData* zconsFixtime = new DoubleData();
1779	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1780	+
1781	+	if (globals->haveZConsFixTime()){
1782	+	zconsFixtime->setData(globals->getZconsFixtime());
1783	+	theInfo.addProperty(zconsFixtime);
1784	+	}
1785	+
1786	+	//set zconsUsingSMD
1787	+	IntData* zconsUsingSMD = new IntData();
1788	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1789	+
1790	+	if (globals->haveZConsUsingSMD()){
1791	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1792	+	theInfo.addProperty(zconsUsingSMD);
1793	+	}
1794	+
1795	+	//Determine the name of ouput file and add it into SimInfo's property list
1796	+	//Be careful, do not use inFileName, since it is a pointer which
1797	+	//point to a string at master node, and slave nodes do not contain that string
1798	+
1799	+	string zconsOutput(theInfo.finalName);
1800	+
1801	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1802	+
1803	+	StringData* zconsFilename = new StringData();
1804	+	zconsFilename->setID(ZCONSFILENAME_ID);
1805	+	zconsFilename->setData(zconsOutput);
1806	+
1807	+	theInfo.addProperty(zconsFilename);
1808	+
1809	+	//setup index, pos and other parameters of z-constraint molecules
1810	+	nZConstraints = globals->getNzConstraints();
1811	+	theInfo.nZconstraints = nZConstraints;
1812	+
1813	+	zconStamp = globals->getZconStamp();
1814	+	ZConsParaItem tempParaItem;
1815	+
1816	+	ZConsParaData* zconsParaData = new ZConsParaData();
1817	+	zconsParaData->setID(ZCONSPARADATA_ID);
1818	+
1819	+	for (int i = 0; i < nZConstraints; i++){
1820	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1821	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1822	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1823	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1824	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1825	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1826	+	zconsParaData->addItem(tempParaItem);
1827	+	}
1828	+
1829	+	//check the uniqueness of index
1830	+	if(!zconsParaData->isIndexUnique()){
1831	+	sprintf(painCave.errMsg,
1832	+	"ZConstraint Error: molIndex is not unique!\n");
1833	+	painCave.isFatal = 1;
1834	+	simError();
1835	+	}
1836	+
1837	+	//sort the parameters by index of molecules
1838	+	zconsParaData->sortByIndex();
1839	+
1840	+	//push data into siminfo, therefore, we can retrieve later
1841	+	theInfo.addProperty(zconsParaData);
1842		}
1843	+
1844	+	void SimSetup::makeMinimizer(){
1845	+
1846	+	OOPSEMinimizer* myOOPSEMinimizer;
1847	+	MinimizerParameterSet* param;
1848	+	char minimizerName[100];
1849	+
1850	+	for (int i = 0; i < nInfo; i++){
1851	+
1852	+	//prepare parameter set for minimizer
1853	+	param = new MinimizerParameterSet();
1854	+	param->setDefaultParameter();
1855	+
1856	+	if (globals->haveMinimizer()){
1857	+	param->setFTol(globals->getMinFTol());
1858	+	}
1859	+
1860	+	if (globals->haveMinGTol()){
1861	+	param->setGTol(globals->getMinGTol());
1862	+	}
1863	+
1864	+	if (globals->haveMinMaxIter()){
1865	+	param->setMaxIteration(globals->getMinMaxIter());
1866	+	}
1867	+
1868	+	if (globals->haveMinWriteFrq()){
1869	+	param->setMaxIteration(globals->getMinMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinWriteFrq()){
1873	+	param->setWriteFrq(globals->getMinWriteFrq());
1874	+	}
1875	+
1876	+	if (globals->haveMinStepSize()){
1877	+	param->setStepSize(globals->getMinStepSize());
1878	+	}
1879	+
1880	+	if (globals->haveMinLSMaxIter()){
1881	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1882	+	}
1883	+
1884	+	if (globals->haveMinLSTol()){
1885	+	param->setLineSearchTol(globals->getMinLSTol());
1886	+	}
1887	+
1888	+	strcpy(minimizerName, globals->getMinimizer());
1889	+
1890	+	if (!strcasecmp(minimizerName, "CG")){
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	else if (!strcasecmp(minimizerName, "SD")){
1894	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1895	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1896	+	}
1897	+	else{
1898	+	sprintf(painCave.errMsg,
1899	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1900	+	painCave.isFatal = 0;
1901	+	simError();
1902	+
1903	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1904	+	}
1905	+	info[i].the_integrator = myOOPSEMinimizer;
1906	+
1907	+	//store the minimizer into simInfo
1908	+	info[i].the_minimizer = myOOPSEMinimizer;
1909	+	info[i].has_minimizer = true;
1910	+	}
1911	+
1912	+	}

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