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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 16 | 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
24	<	#define NPTfm_ENS 5
25	<	#define NVEZCONS_ENS 6
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	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
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 51 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
86	<	}
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 ){
62	<
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();
90	<	mpiEventLoop();
91	<
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
98	–	int i, j, k, globalAtomIndex;
99	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 106 | 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();
120	–
121	–	// make the integrator
150
123	–	makeIntegrator();
124	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 130 | 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
134	–
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
159	–
201		// init the atoms
202
203	<	double ux, uy, uz, u, uSqr;
163	<
164	<	atomOffset = 0;
165	<	excludeOffset = 0;
166	<	for(i=0; i<info->n_mol; i++){
167	<
168	<	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();
172	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
173	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
174	<	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];
177	<	molInfo.myExcludes = &the_excludes[excludeOffset];
178	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
179	<	molInfo.myBends = new Bend*[molInfo.nBends];
180	<	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 );
191	<	if( currentAtom->haveOrientation() ){
192	<
193	<	dAtom = new DirectionalAtom(j + atomOffset);
194	<	info->n_oriented++;
195	<	molInfo.myAtoms[j] = dAtom;
196	<
197	<	ux = currentAtom->getOrntX();
198	<	uy = currentAtom->getOrntY();
199	<	uz = currentAtom->getOrntZ();
200	<
201	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	<
203	<	u = sqrt( uSqr );
204	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx( ux );
209	<	dAtom->setSUy( uy );
210	<	dAtom->setSUz( uz );
211	<	}
212	<	else{
213	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
214	<	}
215	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
216	<
217	<	#ifdef IS_MPI
218	<
219	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
220	<
221	<	#endif // is_mpi
222	<	}
223	<
224	<	// make the bonds
225	<	for(j=0; j<molInfo.nBonds; j++){
226	<
227	<	currentBond = comp_stamps[stampID]->getBond( j );
228	<	theBonds[j].a = currentBond->getA() + atomOffset;
229	<	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;
238	<	exJ = tempEx;
239	<	}
240	<	#ifdef IS_MPI
241	<	tempEx = exI;
242	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
243	<	tempEx = exJ;
244	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
245	<
246	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
247	<	#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
335	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
336	<	#endif  //is_mpi
337	<	}
338	<	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++){
341	<
342	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
343	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
344	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
345	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
346	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
347	<
348	<	exI = theTorsions[j].a;
349	<	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	<	}
368	<	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
394	–	the_ff->calcRcut();
395	–	the_ff->cleanMe();
540
541	<	}
541	>	if (!globals->haveLJrcut()){
542
543	<	void SimSetup::initFromBass( void ){
543	>	the_ff->calcRcut();
544
545	+	} else {
546	+
547	+	the_ff->setRcut( globals->getLJrcut() );
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 406 | 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;
421	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
422	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
423	<	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 442 | 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,
450	<	j * celly,
451	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
454	<	j * celly + 0.5 * celly,
455	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	makeElement( i * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz + 0.5 * cellz );
460	<
461	<	makeElement( i * cellx + 0.5 * cellx,
462	<	j * celly,
463	<	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	<	}
482	<	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 ){
492	<	makeElement( i * cellx + 0.5 * cellx,
493	<	j * celly + 0.5 * celly,
494	<	k * cellz );
495	<	done = ( current_mol >= tot_nmol );
496	<	}
497	<
498	<	if( !done && n_per_extra > 2){
499	<	makeElement( i * cellx,
500	<	j * celly + 0.5 * celly,
501	<	k * cellz + 0.5 * cellz );
502	<	done = ( current_mol >= tot_nmol );
503	<	}
504	<
505	<	if( !done && n_per_extra > 3){
506	<	makeElement( i * cellx + 0.5 * cellx,
507	<	j * celly,
508	<	k * cellz + 0.5 * cellz );
509	<	done = ( current_mol >= tot_nmol );
510	<	}
511	<	}
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++ ){
518	<	info->atoms[i]->set_vx( 0.0 );
519	<	info->atoms[i]->set_vy( 0.0 );
520	<	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 ){
525	<
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",
540	<	comp_stamps[current_comp]->getID(),
541	<	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 563 | 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 572 | 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] ){
576	<
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
589	–	// get the stamps and globals;
590	–	stamps = stamps;
591	–	globals = globals;
592	–
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;
612	<	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;
776	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_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		}
637	–	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;
664	<	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 669 | 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		}
689	–	else{
690	–	info->sampleTime = globals->getRunTime();
691	–	info->statusTime = info->sampleTime;
692	–	info->thermalTime = info->sampleTime;
693	–	}
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();
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	<	// get some of the tricky things that may still be in the globals
877	>	// set the status, sample, and thermal kick times
878
879	<	double boxVector[3];
880	<	if( globals->haveBox() ){
881	<	boxVector[0] = globals->getBox();
882	<	boxVector[1] = globals->getBox();
883	<	boxVector[2] = globals->getBox();
884	<
885	<	info->setBox( boxVector );
886	<	}
887	<	else if( globals->haveDensity() ){
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	<	double vol;
890	<	vol = (double)tot_nmol / globals->getDensity();
721	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
722	<	boxVector[1] = boxVector[0];
723	<	boxVector[2] = boxVector[0];
724	<
725	<	info->setBox( boxVector );
726	<	}
727	<	else{
728	<	if( !globals->haveBoxX() ){
729	<	sprintf( painCave.errMsg,
730	<	"SimSetup error, no periodic BoxX size given.\n" );
731	<	painCave.isFatal = 1;
732	<	simError();
889	>	if (globals->haveStatusTime()){
890	>	info[i].statusTime = globals->getStatusTime();
891		}
734	–	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;
740	<	simError();
893	>	if (globals->haveThermalTime()){
894	>	info[i].thermalTime = globals->getThermalTime();
895	>	} else {
896	>	info[i].thermalTime = globals->getRunTime();
897		}
742	–	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;
748	<	simError();
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903		}
750	–	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	>	info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915	>
916	>
917		}
918	+
919	+	//setup seed for random number generator
920	+	int seedValue;
921
922	+	if (globals->haveSeed()){
923	+	seedValue = globals->getSeed();
924
925	+	if(seedValue / 1E9 == 0){
926	+	sprintf(painCave.errMsg,
927	+	"Seed for sprng library should contain at least 9 digits\n"
928	+	"OOPSE will generate a seed for user\n");
929	+	painCave.isFatal = 0;
930	+	simError();
931	+
932	+	//using seed generated by system instead of invalid seed set by user
933	+	#ifndef IS_MPI
934	+	seedValue = make_sprng_seed();
935	+	#else
936	+	if (worldRank == 0){
937	+	seedValue = make_sprng_seed();
938	+	}
939	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
940	+	#endif
941	+	}
942	+	}//end of if branch of globals->haveSeed()
943	+	else{
944
945	+	#ifndef IS_MPI
946	+	seedValue = make_sprng_seed();
947	+	#else
948	+	if (worldRank == 0){
949	+	seedValue = make_sprng_seed();
950	+	}
951	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
952	+	#endif
953	+	}//end of globals->haveSeed()
954	+
955	+	for (int i = 0; i < nInfo; i++){
956	+	info[i].setSeed(seedValue);
957	+	}
958	+
959		#ifdef IS_MPI
960	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
960	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
961		MPIcheckPoint();
962		#endif // is_mpi
761	–
963		}
964
965
966	<	void SimSetup::finalInfoCheck( void ){
966	>	void SimSetup::finalInfoCheck(void){
967		int index;
968		int usesDipoles;
969	<
969	>	int usesCharges;
970	>	int i;
971
972	<	// check electrostatic parameters
973	<
974	<	index = 0;
975	<	usesDipoles = 0;
976	<	while( (index < info->n_atoms) && !usesDipoles ){
977	<	usesDipoles = ((info->atoms)[index])->hasDipole();
978	<	index++;
979	<	}
980	<
972	>	for (i = 0; i < nInfo; i++){
973	>	// check electrostatic parameters
974	>
975	>	index = 0;
976	>	usesDipoles = 0;
977	>	while ((index < info[i].n_atoms) && !usesDipoles){
978	>	usesDipoles = (info[i].atoms[index])->hasDipole();
979	>	index++;
980	>	}
981	>	index = 0;
982	>	usesCharges = 0;
983	>	while ((index < info[i].n_atoms) && !usesCharges){
984	>	usesCharges= (info[i].atoms[index])->hasCharge();
985	>	index++;
986	>	}
987		#ifdef IS_MPI
988	<	int myUse = usesDipoles;
989	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
988	>	int myUse = usesDipoles;
989	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
990		#endif //is_mpi
991
992	<	double theEcr, theEst;
992	>	double theEcr, theEst;
993
994	<	if (globals->getUseRF() ) {
995	<	info->useReactionField = 1;
788	<
789	<	if( !globals->haveECR() ){
790	<	sprintf( painCave.errMsg,
791	<	"SimSetup Warning: using default value of 1/2 the smallest "
792	<	"box length for the electrostaticCutoffRadius.\n"
793	<	"I hope you have a very fast processor!\n");
794	<	painCave.isFatal = 0;
795	<	simError();
796	<	double smallest;
797	<	smallest = info->boxL[0];
798	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
799	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
800	<	theEcr = 0.5 * smallest;
801	<	} else {
802	<	theEcr = globals->getECR();
803	<	}
994	>	if (globals->getUseRF()){
995	>	info[i].useReactionField = 1;
996
997	<	if( !globals->haveEST() ){
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Warning: using default value of 0.05 * the "
1000	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1001	<	);
1002	<	painCave.isFatal = 0;
1003	<	simError();
1004	<	theEst = 0.05 * theEcr;
1005	<	} else {
1006	<	theEst= globals->getEST();
1007	<	}
997	>	if (!globals->haveECR()){
998	>	sprintf(painCave.errMsg,
999	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1000	>	"\tOOPSE will use a default value of 15.0 angstroms"
1001	>	"\tfor the electrostaticCutoffRadius.\n");
1002	>	painCave.isFatal = 0;
1003	>	simError();
1004	>	theEcr = 15.0;
1005	>	}
1006	>	else{
1007	>	theEcr = globals->getECR();
1008	>	}
1009
1010	<	info->setEcr( theEcr, theEst );
1011	<
1012	<	if(!globals->haveDielectric() ){
1013	<	sprintf( painCave.errMsg,
1014	<	"SimSetup Error: You are trying to use Reaction Field without"
1015	<	"setting a dielectric constant!\n"
1016	<	);
1017	<	painCave.isFatal = 1;
1018	<	simError();
826	<	}
827	<	info->dielectric = globals->getDielectric();
828	<	}
829	<	else {
830	<	if (usesDipoles) {
831	<
832	<	if( !globals->haveECR() ){
833	<	sprintf( painCave.errMsg,
834	<	"SimSetup Warning: using default value of 1/2 the smallest "
835	<	"box length for the electrostaticCutoffRadius.\n"
836	<	"I hope you have a very fast processor!\n");
837	<	painCave.isFatal = 0;
838	<	simError();
839	<	double smallest;
840	<	smallest = info->boxL[0];
841	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
842	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
843	<	theEcr = 0.5 * smallest;
844	<	} else {
845	<	theEcr = globals->getECR();
1010	>	if (!globals->haveEST()){
1011	>	sprintf(painCave.errMsg,
1012	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1013	>	"\tOOPSE will use a default value of\n"
1014	>	"\t0.05 * electrostaticCutoffRadius\n"
1015	>	"\tfor the electrostaticSkinThickness\n");
1016	>	painCave.isFatal = 0;
1017	>	simError();
1018	>	theEst = 0.05 * theEcr;
1019		}
1020	<
1021	<	if( !globals->haveEST() ){
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup Warning: using default value of 0.05 * the "
851	<	"electrostaticCutoffRadius for the "
852	<	"electrostaticSkinThickness\n"
853	<	);
854	<	painCave.isFatal = 0;
855	<	simError();
856	<	theEst = 0.05 * theEcr;
857	<	} else {
858	<	theEst= globals->getEST();
1020	>	else{
1021	>	theEst = globals->getEST();
1022		}
1023
1024	<	info->setEcr( theEcr, theEst );
862	<	}
863	<	}
1024	>	info[i].setDefaultEcr(theEcr, theEst);
1025
1026	+	if (!globals->haveDielectric()){
1027	+	sprintf(painCave.errMsg,
1028	+	"SimSetup Error: No Dielectric constant was set.\n"
1029	+	"\tYou are trying to use Reaction Field without"
1030	+	"\tsetting a dielectric constant!\n");
1031	+	painCave.isFatal = 1;
1032	+	simError();
1033	+	}
1034	+	info[i].dielectric = globals->getDielectric();
1035	+	}
1036	+	else{
1037	+	if (usesDipoles || usesCharges){
1038	+	if (!globals->haveECR()){
1039	+	sprintf(painCave.errMsg,
1040	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1041	+	"\tOOPSE will use a default value of 15.0 angstroms"
1042	+	"\tfor the electrostaticCutoffRadius.\n");
1043	+	painCave.isFatal = 0;
1044	+	simError();
1045	+	theEcr = 15.0;
1046	+	}
1047	+	else{
1048	+	theEcr = globals->getECR();
1049	+	}
1050	+
1051	+	if (!globals->haveEST()){
1052	+	sprintf(painCave.errMsg,
1053	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1054	+	"\tOOPSE will use a default value of\n"
1055	+	"\t0.05 * electrostaticCutoffRadius\n"
1056	+	"\tfor the electrostaticSkinThickness\n");
1057	+	painCave.isFatal = 0;
1058	+	simError();
1059	+	theEst = 0.05 * theEcr;
1060	+	}
1061	+	else{
1062	+	theEst = globals->getEST();
1063	+	}
1064	+
1065	+	info[i].setDefaultEcr(theEcr, theEst);
1066	+	}
1067	+	}
1068	+	}
1069		#ifdef IS_MPI
1070	<	strcpy( checkPointMsg, "post processing checks out" );
1070	>	strcpy(checkPointMsg, "post processing checks out");
1071		MPIcheckPoint();
1072		#endif // is_mpi
869	–
1073		}
1074	+
1075	+	void SimSetup::initSystemCoords(void){
1076	+	int i;
1077
1078	<	void SimSetup::initSystemCoords( void ){
1078	>	char* inName;
1079
1080	<	if( globals->haveInitialConfig() ){
1081	<
1082	<	InitializeFromFile* fileInit;
1080	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1081	>
1082	>	for (i = 0; i < info[0].n_atoms; i++)
1083	>	info[0].atoms[i]->setCoords();
1084	>
1085	>	if (globals->haveInitialConfig()){
1086	>	InitializeFromFile* fileInit;
1087		#ifdef IS_MPI // is_mpi
1088	<	if( worldRank == 0 ){
1088	>	if (worldRank == 0){
1089		#endif //is_mpi
1090	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1090	>	inName = globals->getInitialConfig();
1091	>	fileInit = new InitializeFromFile(inName);
1092		#ifdef IS_MPI
1093	<	}else fileInit = new InitializeFromFile( NULL );
1093	>	}
1094	>	else
1095	>	fileInit = new InitializeFromFile(NULL);
1096		#endif
1097	<	fileInit->readInit( info ); // default velocities on
1097	>	fileInit->readInit(info); // default velocities on
1098
1099	<	delete fileInit;
1100	<	}
1101	<	else{
1099	>	delete fileInit;
1100	>	}
1101	>	else{
1102	>
1103	>	// no init from bass
1104	>
1105	>	sprintf(painCave.errMsg,
1106	>	"Cannot intialize a simulation without an initial configuration file.\n");
1107	>	painCave.isFatal = 1;;
1108	>	simError();
1109	>
1110	>	}
1111
890	–	#ifdef IS_MPI
891	–
892	–	// no init from bass
893	–
894	–	sprintf( painCave.errMsg,
895	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
896	–	painCave.isFatal;
897	–	simError();
898	–
899	–	#else
900	–
901	–	initFromBass();
902	–
903	–
904	–	#endif
905	–	}
906	–
1112		#ifdef IS_MPI
1113	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1113	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1114		MPIcheckPoint();
1115		#endif // is_mpi
911	–
1116		}
1117
1118
1119	<	void SimSetup::makeOutNames( void ){
1119	>	void SimSetup::makeOutNames(void){
1120	>	int k;
1121
1122	+
1123	+	for (k = 0; k < nInfo; k++){
1124		#ifdef IS_MPI
1125	<	if( worldRank == 0 ){
1125	>	if (worldRank == 0){
1126		#endif // is_mpi
1127	<
1128	<	if( globals->haveFinalConfig() ){
1129	<	strcpy( info->finalName, globals->getFinalConfig() );
923	<	}
924	<	else{
925	<	strcpy( info->finalName, inFileName );
926	<	char* endTest;
927	<	int nameLength = strlen( info->finalName );
928	<	endTest = &(info->finalName[nameLength - 5]);
929	<	if( !strcmp( endTest, ".bass" ) ){
930	<	strcpy( endTest, ".eor" );
1127	>
1128	>	if (globals->haveFinalConfig()){
1129	>	strcpy(info[k].finalName, globals->getFinalConfig());
1130		}
932	–	else if( !strcmp( endTest, ".BASS" ) ){
933	–	strcpy( endTest, ".eor" );
934	–	}
1131		else{
1132	<	endTest = &(info->finalName[nameLength - 4]);
1133	<	if( !strcmp( endTest, ".bss" ) ){
1134	<	strcpy( endTest, ".eor" );
1135	<	}
1136	<	else if( !strcmp( endTest, ".mdl" ) ){
1137	<	strcpy( endTest, ".eor" );
1138	<	}
1139	<	else{
1140	<	strcat( info->finalName, ".eor" );
1141	<	}
1132	>	strcpy(info[k].finalName, inFileName);
1133	>	char* endTest;
1134	>	int nameLength = strlen(info[k].finalName);
1135	>	endTest = &(info[k].finalName[nameLength - 5]);
1136	>	if (!strcmp(endTest, ".bass")){
1137	>	strcpy(endTest, ".eor");
1138	>	}
1139	>	else if (!strcmp(endTest, ".BASS")){
1140	>	strcpy(endTest, ".eor");
1141	>	}
1142	>	else{
1143	>	endTest = &(info[k].finalName[nameLength - 4]);
1144	>	if (!strcmp(endTest, ".bss")){
1145	>	strcpy(endTest, ".eor");
1146	>	}
1147	>	else if (!strcmp(endTest, ".mdl")){
1148	>	strcpy(endTest, ".eor");
1149	>	}
1150	>	else{
1151	>	strcat(info[k].finalName, ".eor");
1152	>	}
1153	>	}
1154		}
1155	<	}
1156	<
1157	<	// make the sample and status out names
1158	<
1159	<	strcpy( info->sampleName, inFileName );
1160	<	char* endTest;
1161	<	int nameLength = strlen( info->sampleName );
1162	<	endTest = &(info->sampleName[nameLength - 5]);
1163	<	if( !strcmp( endTest, ".bass" ) ){
956	<	strcpy( endTest, ".dump" );
957	<	}
958	<	else if( !strcmp( endTest, ".BASS" ) ){
959	<	strcpy( endTest, ".dump" );
960	<	}
961	<	else{
962	<	endTest = &(info->sampleName[nameLength - 4]);
963	<	if( !strcmp( endTest, ".bss" ) ){
964	<	strcpy( endTest, ".dump" );
1155	>
1156	>	// make the sample and status out names
1157	>
1158	>	strcpy(info[k].sampleName, inFileName);
1159	>	char* endTest;
1160	>	int nameLength = strlen(info[k].sampleName);
1161	>	endTest = &(info[k].sampleName[nameLength - 5]);
1162	>	if (!strcmp(endTest, ".bass")){
1163	>	strcpy(endTest, ".dump");
1164		}
1165	<	else if( !strcmp( endTest, ".mdl" ) ){
1166	<	strcpy( endTest, ".dump" );
1165	>	else if (!strcmp(endTest, ".BASS")){
1166	>	strcpy(endTest, ".dump");
1167		}
1168		else{
1169	<	strcat( info->sampleName, ".dump" );
1169	>	endTest = &(info[k].sampleName[nameLength - 4]);
1170	>	if (!strcmp(endTest, ".bss")){
1171	>	strcpy(endTest, ".dump");
1172	>	}
1173	>	else if (!strcmp(endTest, ".mdl")){
1174	>	strcpy(endTest, ".dump");
1175	>	}
1176	>	else{
1177	>	strcat(info[k].sampleName, ".dump");
1178	>	}
1179		}
1180	<	}
1181	<
1182	<	strcpy( info->statusName, inFileName );
1183	<	nameLength = strlen( info->statusName );
1184	<	endTest = &(info->statusName[nameLength - 5]);
1185	<	if( !strcmp( endTest, ".bass" ) ){
978	<	strcpy( endTest, ".stat" );
979	<	}
980	<	else if( !strcmp( endTest, ".BASS" ) ){
981	<	strcpy( endTest, ".stat" );
982	<	}
983	<	else{
984	<	endTest = &(info->statusName[nameLength - 4]);
985	<	if( !strcmp( endTest, ".bss" ) ){
986	<	strcpy( endTest, ".stat" );
1180	>
1181	>	strcpy(info[k].statusName, inFileName);
1182	>	nameLength = strlen(info[k].statusName);
1183	>	endTest = &(info[k].statusName[nameLength - 5]);
1184	>	if (!strcmp(endTest, ".bass")){
1185	>	strcpy(endTest, ".stat");
1186		}
1187	<	else if( !strcmp( endTest, ".mdl" ) ){
1188	<	strcpy( endTest, ".stat" );
1187	>	else if (!strcmp(endTest, ".BASS")){
1188	>	strcpy(endTest, ".stat");
1189		}
1190		else{
1191	<	strcat( info->statusName, ".stat" );
1191	>	endTest = &(info[k].statusName[nameLength - 4]);
1192	>	if (!strcmp(endTest, ".bss")){
1193	>	strcpy(endTest, ".stat");
1194	>	}
1195	>	else if (!strcmp(endTest, ".mdl")){
1196	>	strcpy(endTest, ".stat");
1197	>	}
1198	>	else{
1199	>	strcat(info[k].statusName, ".stat");
1200	>	}
1201		}
1202	<	}
995	<
1202	>
1203		#ifdef IS_MPI
997	–	}
998	–	#endif // is_mpi
1204
1205	+	}
1206	+	#endif // is_mpi
1207	+	}
1208		}
1209
1210
1211	<	void SimSetup::sysObjectsCreation( void ){
1211	>	void SimSetup::sysObjectsCreation(void){
1212	>	int i, k;
1213
1005	–	int i;
1006	–
1214		// create the forceField
1215
1216		createFF();
#	Line 1018 | Line 1225 | void SimSetup::sysObjectsCreation( void ){
1225
1226		#ifdef IS_MPI
1227		// divide the molecules among the processors
1228	<
1228	>
1229		mpiMolDivide();
1230		#endif //is_mpi
1231	<
1231	>
1232		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1233	<
1233	>
1234		makeSysArrays();
1235
1236		// make and initialize the molecules (all but atomic coordinates)
1237	<
1237	>
1238		makeMolecules();
1032	–	info->identArray = new int[info->n_atoms];
1033	–	for(i=0; i<info->n_atoms; i++){
1034	–	info->identArray[i] = the_atoms[i]->getIdent();
1035	–	}
1036	–
1239
1240	<
1240	>	for (k = 0; k < nInfo; k++){
1241	>	info[k].identArray = new int[info[k].n_atoms];
1242	>	for (i = 0; i < info[k].n_atoms; i++){
1243	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1244	>	}
1245	>	}
1246		}
1247
1248
1249	<	void SimSetup::createFF( void ){
1249	>	void SimSetup::createFF(void){
1250	>	switch (ffCase){
1251	>	case FF_DUFF:
1252	>	the_ff = new DUFF();
1253	>	break;
1254
1255	<	switch( ffCase ){
1255	>	case FF_LJ:
1256	>	the_ff = new LJFF();
1257	>	break;
1258
1259	<	case FF_DUFF:
1260	<	the_ff = new DUFF();
1261	<	break;
1259	>	case FF_EAM:
1260	>	the_ff = new EAM_FF();
1261	>	break;
1262
1263	<	case FF_LJ:
1264	<	the_ff = new LJFF();
1265	<	break;
1263	>	case FF_H2O:
1264	>	the_ff = new WATER();
1265	>	break;
1266
1267	<	case FF_EAM:
1268	<	the_ff = new EAM_FF();
1269	<	break;
1270	<
1271	<	default:
1059	<	sprintf( painCave.errMsg,
1060	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1061	<	painCave.isFatal = 1;
1062	<	simError();
1267	>	default:
1268	>	sprintf(painCave.errMsg,
1269	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1270	>	painCave.isFatal = 1;
1271	>	simError();
1272		}
1273
1274		#ifdef IS_MPI
1275	<	strcpy( checkPointMsg, "ForceField creation successful" );
1275	>	strcpy(checkPointMsg, "ForceField creation successful");
1276		MPIcheckPoint();
1277		#endif // is_mpi
1069	–
1278		}
1279
1280
1281	<	void SimSetup::compList( void ){
1074	<
1281	>	void SimSetup::compList(void){
1282		int i;
1283	+	char* id;
1284	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1285	+	LinkedMolStamp* currentStamp = NULL;
1286	+	comp_stamps = new MoleculeStamp * [n_components];
1287
1077	–	comp_stamps = new MoleculeStamp*[n_components];
1078	–
1288		// make an array of molecule stamps that match the components used.
1289		// also extract the used stamps out into a separate linked list
1290
1291	<	info->nComponents = n_components;
1292	<	info->componentsNmol = components_nmol;
1293	<	info->compStamps = comp_stamps;
1294	<	info->headStamp = new LinkedMolStamp();
1295	<
1296	<	char* id;
1088	<	LinkedMolStamp* headStamp = info->headStamp;
1089	<	LinkedMolStamp* currentStamp = NULL;
1090	<	for( i=0; i<n_components; i++ ){
1291	>	for (i = 0; i < nInfo; i++){
1292	>	info[i].nComponents = n_components;
1293	>	info[i].componentsNmol = components_nmol;
1294	>	info[i].compStamps = comp_stamps;
1295	>	info[i].headStamp = headStamp;
1296	>	}
1297
1298	+
1299	+	for (i = 0; i < n_components; i++){
1300		id = the_components[i]->getType();
1301		comp_stamps[i] = NULL;
1302	<
1302	>
1303		// check to make sure the component isn't already in the list
1304
1305	<	comp_stamps[i] = headStamp->match( id );
1306	<	if( comp_stamps[i] == NULL ){
1099	<
1305	>	comp_stamps[i] = headStamp->match(id);
1306	>	if (comp_stamps[i] == NULL){
1307		// extract the component from the list;
1308	<
1309	<	currentStamp = stamps->extractMolStamp( id );
1310	<	if( currentStamp == NULL ){
1311	<	sprintf( painCave.errMsg,
1312	<	"SimSetup error: Component \"%s\" was not found in the "
1313	<	"list of declared molecules\n",
1314	<	id );
1315	<	painCave.isFatal = 1;
1316	<	simError();
1308	>
1309	>	currentStamp = stamps->extractMolStamp(id);
1310	>	if (currentStamp == NULL){
1311	>	sprintf(painCave.errMsg,
1312	>	"SimSetup error: Component \"%s\" was not found in the "
1313	>	"list of declared molecules\n",
1314	>	id);
1315	>	painCave.isFatal = 1;
1316	>	simError();
1317		}
1318	<
1319	<	headStamp->add( currentStamp );
1320	<	comp_stamps[i] = headStamp->match( id );
1318	>
1319	>	headStamp->add(currentStamp);
1320	>	comp_stamps[i] = headStamp->match(id);
1321		}
1322		}
1323
1324		#ifdef IS_MPI
1325	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1325	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1326		MPIcheckPoint();
1327		#endif // is_mpi
1121	–
1122	–
1328		}
1329
1330	<	void SimSetup::calcSysValues( void ){
1331	<	int i, j, k;
1330	>	void SimSetup::calcSysValues(void){
1331	>	int i;
1332
1333	+	int* molMembershipArray;
1334
1335		tot_atoms = 0;
1336		tot_bonds = 0;
1337		tot_bends = 0;
1338		tot_torsions = 0;
1339	<	for( i=0; i<n_components; i++ ){
1340	<
1341	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1342	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1343	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1339	>	tot_rigid = 0;
1340	>	for (i = 0; i < n_components; i++){
1341	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1342	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1343	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1344		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1345	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1346		}
1347	<
1347	>
1348		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1349	+	molMembershipArray = new int[tot_atoms];
1350
1351	<	info->n_atoms = tot_atoms;
1352	<	info->n_bonds = tot_bonds;
1353	<	info->n_bends = tot_bends;
1354	<	info->n_torsions = tot_torsions;
1355	<	info->n_SRI = tot_SRI;
1356	<	info->n_mol = tot_nmol;
1357	<
1358	<	info->molMembershipArray = new int[tot_atoms];
1351	>	for (i = 0; i < nInfo; i++){
1352	>	info[i].n_atoms = tot_atoms;
1353	>	info[i].n_bonds = tot_bonds;
1354	>	info[i].n_bends = tot_bends;
1355	>	info[i].n_torsions = tot_torsions;
1356	>	info[i].n_SRI = tot_SRI;
1357	>	info[i].n_mol = tot_nmol;
1358	>
1359	>	info[i].molMembershipArray = molMembershipArray;
1360	>	}
1361		}
1362
1153	–
1363		#ifdef IS_MPI
1364
1365	<	void SimSetup::mpiMolDivide( void ){
1157	<
1365	>	void SimSetup::mpiMolDivide(void){
1366		int i, j, k;
1367		int localMol, allMol;
1368		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369	+	int local_rigid;
1370	+	vector<int> globalMolIndex;
1371
1372	<	mpiSim = new mpiSimulation( info );
1163	<
1164	<	globalIndex = mpiSim->divideLabor();
1372	>	mpiSim = new mpiSimulation(info);
1373
1374	+	mpiSim->divideLabor();
1375	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1377	+
1378		// set up the local variables
1379	<
1379	>
1380		mol2proc = mpiSim->getMolToProcMap();
1381		molCompType = mpiSim->getMolComponentType();
1382	<
1382	>
1383		allMol = 0;
1384		localMol = 0;
1385		local_atoms = 0;
1386		local_bonds = 0;
1387		local_bends = 0;
1388		local_torsions = 0;
1389	<	globalAtomIndex = 0;
1389	>	local_rigid = 0;
1390	>	globalAtomCounter = 0;
1391
1392	<
1393	<	for( i=0; i<n_components; i++ ){
1394	<
1395	<	for( j=0; j<components_nmol[i]; j++ ){
1396	<
1397	<	if( mol2proc[allMol] == worldRank ){
1398	<
1399	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1400	<	local_bonds +=    comp_stamps[i]->getNBonds();
1188	<	local_bends +=    comp_stamps[i]->getNBends();
1189	<	local_torsions += comp_stamps[i]->getNTorsions();
1190	<	localMol++;
1392	>	for (i = 0; i < n_components; i++){
1393	>	for (j = 0; j < components_nmol[i]; j++){
1394	>	if (mol2proc[allMol] == worldRank){
1395	>	local_atoms += comp_stamps[i]->getNAtoms();
1396	>	local_bonds += comp_stamps[i]->getNBonds();
1397	>	local_bends += comp_stamps[i]->getNBends();
1398	>	local_torsions += comp_stamps[i]->getNTorsions();
1399	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1400	>	localMol++;
1401		}
1402	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1403	<	info->molMembershipArray[globalAtomIndex] = allMol;
1404	<	globalAtomIndex++;
1402	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1403	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1404	>	globalAtomCounter++;
1405		}
1406
1407	<	allMol++;
1407	>	allMol++;
1408		}
1409		}
1410		local_SRI = local_bonds + local_bends + local_torsions;
1411	+
1412	+	info[0].n_atoms = mpiSim->getMyNlocal();
1413
1414	<	info->n_atoms = mpiSim->getMyNlocal();
1415	<
1416	<	if( local_atoms != info->n_atoms ){
1417	<	sprintf( painCave.errMsg,
1418	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1419	<	" localAtom (%d) are not equal.\n",
1208	<	info->n_atoms,
1209	<	local_atoms );
1414	>
1415	>	if (local_atoms != info[0].n_atoms){
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1418	>	"\tlocalAtom (%d) are not equal.\n",
1419	>	info[0].n_atoms, local_atoms);
1420		painCave.isFatal = 1;
1421		simError();
1422		}
1423
1424	<	info->n_bonds = local_bonds;
1425	<	info->n_bends = local_bends;
1426	<	info->n_torsions = local_torsions;
1427	<	info->n_SRI = local_SRI;
1428	<	info->n_mol = localMol;
1424	>	info[0].n_bonds = local_bonds;
1425	>	info[0].n_bends = local_bends;
1426	>	info[0].n_torsions = local_torsions;
1427	>	info[0].n_SRI = local_SRI;
1428	>	info[0].n_mol = localMol;
1429
1430	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1430	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1431		MPIcheckPoint();
1432		}
1433	<
1433	>
1434		#endif // is_mpi
1435
1436
1437	<	void SimSetup::makeSysArrays( void ){
1438	<	int i, j, k;
1437	>	void SimSetup::makeSysArrays(void){
1438	>
1439	>	#ifndef IS_MPI
1440	>	int k, j;
1441	>	#endif // is_mpi
1442	>	int i, l;
1443
1444	+	Atom** the_atoms;
1445	+	Molecule* the_molecules;
1446
1447	<	// create the atom and short range interaction arrays
1447	>	for (l = 0; l < nInfo; l++){
1448	>	// create the atom and short range interaction arrays
1449
1450	<	Atom::createArrays(info->n_atoms);
1451	<	the_atoms = new Atom*[info->n_atoms];
1452	<	the_molecules = new Molecule[info->n_mol];
1236	<	int molIndex;
1450	>	the_atoms = new Atom * [info[l].n_atoms];
1451	>	the_molecules = new Molecule[info[l].n_mol];
1452	>	int molIndex;
1453
1454	<	// initialize the molecule's stampID's
1454	>	// initialize the molecule's stampID's
1455
1456		#ifdef IS_MPI
1241	–
1457
1458	<	molIndex = 0;
1459	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1460	<
1461	<	if(mol2proc[i] == worldRank ){
1462	<	the_molecules[molIndex].setStampID( molCompType[i] );
1463	<	the_molecules[molIndex].setMyIndex( molIndex );
1464	<	the_molecules[molIndex].setGlobalIndex( i );
1465	<	molIndex++;
1458	>
1459	>	molIndex = 0;
1460	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1461	>	if (mol2proc[i] == worldRank){
1462	>	the_molecules[molIndex].setStampID(molCompType[i]);
1463	>	the_molecules[molIndex].setMyIndex(molIndex);
1464	>	the_molecules[molIndex].setGlobalIndex(i);
1465	>	molIndex++;
1466	>	}
1467		}
1252	–	}
1468
1469		#else // is_mpi
1470	<
1471	<	molIndex = 0;
1472	<	globalAtomIndex = 0;
1473	<	for(i=0; i<n_components; i++){
1474	<	for(j=0; j<components_nmol[i]; j++ ){
1475	<	the_molecules[molIndex].setStampID( i );
1476	<	the_molecules[molIndex].setMyIndex( molIndex );
1477	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1478	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1479	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1480	<	globalAtomIndex++;
1470	>
1471	>	molIndex = 0;
1472	>	globalAtomCounter = 0;
1473	>	for (i = 0; i < n_components; i++){
1474	>	for (j = 0; j < components_nmol[i]; j++){
1475	>	the_molecules[molIndex].setStampID(i);
1476	>	the_molecules[molIndex].setMyIndex(molIndex);
1477	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1478	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1479	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1480	>	globalAtomCounter++;
1481	>	}
1482	>	molIndex++;
1483		}
1267	–	molIndex++;
1484		}
1269	–	}
1270	–
1485
1486	+
1487		#endif // is_mpi
1488
1489	<
1490	<	if( info->n_SRI ){
1489	>	info[l].globalExcludes = new int;
1490	>	info[l].globalExcludes[0] = 0;
1491
1492	<	Exclude::createArray(info->n_SRI);
1278	<	the_excludes = new Exclude*[info->n_SRI];
1279	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1280	<	info->globalExcludes = new int;
1281	<	info->n_exclude = info->n_SRI;
1282	<	}
1283	<	else{
1284	<
1285	<	Exclude::createArray( 1 );
1286	<	the_excludes = new Exclude*;
1287	<	the_excludes[0] = new Exclude(0);
1288	<	the_excludes[0]->setPair( 0,0 );
1289	<	info->globalExcludes = new int;
1290	<	info->globalExcludes[0] = 0;
1291	<	info->n_exclude = 0;
1292	<	}
1492	>	// set the arrays into the SimInfo object
1493
1494	<	// set the arrays into the SimInfo object
1494	>	info[l].atoms = the_atoms;
1495	>	info[l].molecules = the_molecules;
1496	>	info[l].nGlobalExcludes = 0;
1497
1498	<	info->atoms = the_atoms;
1499	<	info->molecules = the_molecules;
1298	<	info->nGlobalExcludes = 0;
1299	<	info->excludes = the_excludes;
1300	<
1301	<	the_ff->setSimInfo( info );
1302	<
1498	>	the_ff->setSimInfo(info);
1499	>	}
1500		}
1501
1502	<	void SimSetup::makeIntegrator( void ){
1502	>	void SimSetup::makeIntegrator(void){
1503	>	int k;
1504
1505	<	NVT<RealIntegrator>*  myNVT = NULL;
1506	<	NPTi<RealIntegrator>* myNPTi = NULL;
1507	<	NPTf<RealIntegrator>* myNPTf = NULL;
1508	<	NPTim<RealIntegrator>* myNPTim = NULL;
1509	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1312	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1313	<
1314	<	cerr << "setting integrator" <<endl;
1505	>	NVE<RealIntegrator>* myNVE = NULL;
1506	>	NVT<RealIntegrator>* myNVT = NULL;
1507	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1508	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1509	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1510
1511	<	switch( ensembleCase ){
1511	>	for (k = 0; k < nInfo; k++){
1512	>	switch (ensembleCase){
1513	>	case NVE_ENS:
1514	>	if (globals->haveZconstraints()){
1515	>	setupZConstraint(info[k]);
1516	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1517	>	}
1518	>	else{
1519	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1520	>	}
1521	>
1522	>	info->the_integrator = myNVE;
1523	>	break;
1524
1525	<	case NVE_ENS:
1526	<	new NVE<RealIntegrator>( info, the_ff );
1527	<	break;
1525	>	case NVT_ENS:
1526	>	if (globals->haveZconstraints()){
1527	>	setupZConstraint(info[k]);
1528	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1529	>	}
1530	>	else
1531	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1532
1533	<	case NVT_ENS:
1323	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1324	<	myNVT->setTargetTemp(globals->getTargetTemp());
1533	>	myNVT->setTargetTemp(globals->getTargetTemp());
1534
1535	<	if (globals->haveTauThermostat())
1536	<	myNVT->setTauThermostat(globals->getTauThermostat());
1535	>	if (globals->haveTauThermostat())
1536	>	myNVT->setTauThermostat(globals->getTauThermostat());
1537	>	else{
1538	>	sprintf(painCave.errMsg,
1539	>	"SimSetup error: If you use the NVT\n"
1540	>	"\tensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544
1545	<	else {
1546	<	sprintf( painCave.errMsg,
1331	<	"SimSetup error: If you use the NVT\n"
1332	<	"    ensemble, you must set tauThermostat.\n");
1333	<	painCave.isFatal = 1;
1334	<	simError();
1335	<	}
1336	<	break;
1545	>	info->the_integrator = myNVT;
1546	>	break;
1547
1548	<	case NPTi_ENS:
1549	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1550	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1548	>	case NPTi_ENS:
1549	>	if (globals->haveZconstraints()){
1550	>	setupZConstraint(info[k]);
1551	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1552	>	}
1553	>	else
1554	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1555
1556	<	if (globals->haveTargetPressure())
1343	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1344	<	else {
1345	<	sprintf( painCave.errMsg,
1346	<	"SimSetup error: If you use a constant pressure\n"
1347	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1348	<	painCave.isFatal = 1;
1349	<	simError();
1350	<	}
1351	<
1352	<	if( globals->haveTauThermostat() )
1353	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1354	<	else{
1355	<	sprintf( painCave.errMsg,
1356	<	"SimSetup error: If you use an NPT\n"
1357	<	"    ensemble, you must set tauThermostat.\n");
1358	<	painCave.isFatal = 1;
1359	<	simError();
1360	<	}
1556	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1557
1558	<	if( globals->haveTauBarostat() )
1559	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1560	<	else{
1561	<	sprintf( painCave.errMsg,
1562	<	"SimSetup error: If you use an NPT\n"
1563	<	"    ensemble, you must set tauBarostat.\n");
1564	<	painCave.isFatal = 1;
1565	<	simError();
1566	<	}
1371	<	break;
1558	>	if (globals->haveTargetPressure())
1559	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1560	>	else{
1561	>	sprintf(painCave.errMsg,
1562	>	"SimSetup error: If you use a constant pressure\n"
1563	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1564	>	painCave.isFatal = 1;
1565	>	simError();
1566	>	}
1567
1568	<	case NPTf_ENS:
1569	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1570	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1568	>	if (globals->haveTauThermostat())
1569	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1570	>	else{
1571	>	sprintf(painCave.errMsg,
1572	>	"SimSetup error: If you use an NPT\n"
1573	>	"\tensemble, you must set tauThermostat.\n");
1574	>	painCave.isFatal = 1;
1575	>	simError();
1576	>	}
1577
1578	<	if (globals->haveTargetPressure())
1579	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1580	<	else {
1581	<	sprintf( painCave.errMsg,
1582	<	"SimSetup error: If you use a constant pressure\n"
1583	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1584	<	painCave.isFatal = 1;
1585	<	simError();
1586	<	}
1578	>	if (globals->haveTauBarostat())
1579	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1580	>	else{
1581	>	sprintf(painCave.errMsg,
1582	>	"SimSetup error: If you use an NPT\n"
1583	>	"\tensemble, you must set tauBarostat.\n");
1584	>	painCave.isFatal = 1;
1585	>	simError();
1586	>	}
1587
1588	<	if( globals->haveTauThermostat() )
1589	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1389	<	else{
1390	<	sprintf( painCave.errMsg,
1391	<	"SimSetup error: If you use an NPT\n"
1392	<	"    ensemble, you must set tauThermostat.\n");
1393	<	painCave.isFatal = 1;
1394	<	simError();
1395	<	}
1588	>	info->the_integrator = myNPTi;
1589	>	break;
1590
1591	<	if( globals->haveTauBarostat() )
1592	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1593	<	else{
1594	<	sprintf( painCave.errMsg,
1595	<	"SimSetup error: If you use an NPT\n"
1596	<	"    ensemble, you must set tauBarostat.\n");
1597	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1406	<	break;
1407	<
1408	<	case NPTim_ENS:
1409	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1410	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1591	>	case NPTf_ENS:
1592	>	if (globals->haveZconstraints()){
1593	>	setupZConstraint(info[k]);
1594	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1595	>	}
1596	>	else
1597	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1598
1599	<	if (globals->haveTargetPressure())
1413	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1414	<	else {
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use a constant pressure\n"
1417	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<
1422	<	if( globals->haveTauThermostat() )
1423	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1424	<	else{
1425	<	sprintf( painCave.errMsg,
1426	<	"SimSetup error: If you use an NPT\n"
1427	<	"    ensemble, you must set tauThermostat.\n");
1428	<	painCave.isFatal = 1;
1429	<	simError();
1430	<	}
1599	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1600
1601	<	if( globals->haveTauBarostat() )
1602	<	myNPTim->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;
1608	<	simError();
1609	<	}
1441	<	break;
1601	>	if (globals->haveTargetPressure())
1602	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1603	>	else{
1604	>	sprintf(painCave.errMsg,
1605	>	"SimSetup error: If you use a constant pressure\n"
1606	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1607	>	painCave.isFatal = 1;
1608	>	simError();
1609	>	}
1610
1611	<	case NPTfm_ENS:
1612	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1445	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1611	>	if (globals->haveTauThermostat())
1612	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1613
1614	<	if (globals->haveTargetPressure())
1615	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1616	<	else {
1617	<	sprintf( painCave.errMsg,
1618	<	"SimSetup error: If you use a constant pressure\n"
1619	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1620	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1614	>	else{
1615	>	sprintf(painCave.errMsg,
1616	>	"SimSetup error: If you use an NPT\n"
1617	>	"\tensemble, you must set tauThermostat.\n");
1618	>	painCave.isFatal = 1;
1619	>	simError();
1620	>	}
1621
1622	<	if( globals->haveTauBarostat() )
1623	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NVEZCONS_ENS:
1479	<	{
1622	>	if (globals->haveTauBarostat())
1623	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1624
1625	<	if(globals->haveZConsTime()){
1626	<
1627	<	//add sample time of z-constraint  into SimInfo's property list
1628	<	DoubleData* zconsTimeProp = new DoubleData();
1629	<	zconsTimeProp->setID("zconstime");
1630	<	zconsTimeProp->setData(globals->getZConsTime());
1631	<	info->addProperty(zconsTimeProp);
1488	<	}
1489	<	else{
1490	<	sprintf( painCave.errMsg,
1491	<	"ZConstraint error: If you use an ZConstraint\n"
1492	<	" , you must set sample time.\n");
1493	<	painCave.isFatal = 1;
1494	<	simError();
1495	<	}
1496	<
1497	<	if(globals->haveIndexOfAllZConsMols()){
1498	<
1499	<	//add index of z-constraint molecules into SimInfo's property list
1500	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1501	<	sort(tempIndex.begin(), tempIndex.end());
1502	<
1503	<	IndexData* zconsIndex = new IndexData();
1504	<	zconsIndex->setID("zconsindex");
1505	<	zconsIndex->setIndexData(tempIndex);
1506	<	info->addProperty(zconsIndex);
1507	<	}
1508	<	else{
1509	<	sprintf( painCave.errMsg,
1510	<	"SimSetup error: If you use an ZConstraint\n"
1511	<	" , you must set index of z-constraint molecules.\n");
1512	<	painCave.isFatal = 1;
1513	<	simError();
1514	<
1515	<	}
1625	>	else{
1626	>	sprintf(painCave.errMsg,
1627	>	"SimSetup error: If you use an NPT\n"
1628	>	"\tensemble, you must set tauBarostat.\n");
1629	>	painCave.isFatal = 1;
1630	>	simError();
1631	>	}
1632
1633	<	//Determine the name of ouput file and add it into SimInfo's property list
1634	<	//Be careful, do not use inFileName, since it is a pointer which
1519	<	//point to a string at master node, and slave nodes do not contain that string
1520	<
1521	<	string zconsOutput(info->finalName);
1522	<
1523	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1524	<
1525	<	StringData* zconsFilename = new StringData();
1526	<	zconsFilename->setID("zconsfilename");
1527	<	zconsFilename->setData(zconsOutput);
1633	>	info->the_integrator = myNPTf;
1634	>	break;
1635
1636	<	info->addProperty(zconsFilename);
1637	<
1638	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1639	<
1640	<	break;
1636	>	case NPTxyz_ENS:
1637	>	if (globals->haveZconstraints()){
1638	>	setupZConstraint(info[k]);
1639	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1640	>	}
1641	>	else
1642	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1643	>
1644	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1645	>
1646	>	if (globals->haveTargetPressure())
1647	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1648	>	else{
1649	>	sprintf(painCave.errMsg,
1650	>	"SimSetup error: If you use a constant pressure\n"
1651	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1652	>	painCave.isFatal = 1;
1653	>	simError();
1654	>	}
1655	>
1656	>	if (globals->haveTauThermostat())
1657	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1658	>	else{
1659	>	sprintf(painCave.errMsg,
1660	>	"SimSetup error: If you use an NPT\n"
1661	>	"\tensemble, you must set tauThermostat.\n");
1662	>	painCave.isFatal = 1;
1663	>	simError();
1664	>	}
1665	>
1666	>	if (globals->haveTauBarostat())
1667	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1668	>	else{
1669	>	sprintf(painCave.errMsg,
1670	>	"SimSetup error: If you use an NPT\n"
1671	>	"\tensemble, you must set tauBarostat.\n");
1672	>	painCave.isFatal = 1;
1673	>	simError();
1674	>	}
1675	>
1676	>	info->the_integrator = myNPTxyz;
1677	>	break;
1678	>
1679	>	default:
1680	>	sprintf(painCave.errMsg,
1681	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1682	>	painCave.isFatal = 1;
1683	>	simError();
1684		}
1535	–
1536	–	default:
1537	–	sprintf( painCave.errMsg,
1538	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1539	–	painCave.isFatal = 1;
1540	–	simError();
1685		}
1542	–
1686		}
1687
1688	<	void SimSetup::initFortran( void ){
1688	>	void SimSetup::initFortran(void){
1689	>	info[0].refreshSim();
1690
1691	<	info->refreshSim();
1692	<
1549	<	if( !strcmp( info->mixingRule, "standard") ){
1550	<	the_ff->initForceField( LB_MIXING_RULE );
1691	>	if (!strcmp(info[0].mixingRule, "standard")){
1692	>	the_ff->initForceField(LB_MIXING_RULE);
1693		}
1694	<	else if( !strcmp( info->mixingRule, "explicit") ){
1695	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1694	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1695	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1696		}
1697		else{
1698	<	sprintf( painCave.errMsg,
1699	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1558	<	info->mixingRule );
1698	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1699	>	info[0].mixingRule);
1700		painCave.isFatal = 1;
1701		simError();
1702		}
1703
1704
1705		#ifdef IS_MPI
1706	<	strcpy( checkPointMsg,
1566	<	"Successfully intialized the mixingRule for Fortran." );
1706	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1707		MPIcheckPoint();
1708		#endif // is_mpi
1709	+	}
1710
1711	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1712	+	int nZConstraints;
1713	+	ZconStamp** zconStamp;
1714	+
1715	+	if (globals->haveZconstraintTime()){
1716	+	//add sample time of z-constraint  into SimInfo's property list
1717	+	DoubleData* zconsTimeProp = new DoubleData();
1718	+	zconsTimeProp->setID(ZCONSTIME_ID);
1719	+	zconsTimeProp->setData(globals->getZconsTime());
1720	+	theInfo.addProperty(zconsTimeProp);
1721	+	}
1722	+	else{
1723	+	sprintf(painCave.errMsg,
1724	+	"ZConstraint error: If you use a ZConstraint,\n"
1725	+	"\tyou must set zconsTime.\n");
1726	+	painCave.isFatal = 1;
1727	+	simError();
1728	+	}
1729	+
1730	+	//push zconsTol into siminfo, if user does not specify
1731	+	//value for zconsTol, a default value will be used
1732	+	DoubleData* zconsTol = new DoubleData();
1733	+	zconsTol->setID(ZCONSTOL_ID);
1734	+	if (globals->haveZconsTol()){
1735	+	zconsTol->setData(globals->getZconsTol());
1736	+	}
1737	+	else{
1738	+	double defaultZConsTol = 0.01;
1739	+	sprintf(painCave.errMsg,
1740	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1741	+	"\tOOPSE will use a default value of %f.\n"
1742	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1743	+	defaultZConsTol);
1744	+	painCave.isFatal = 0;
1745	+	simError();
1746	+
1747	+	zconsTol->setData(defaultZConsTol);
1748	+	}
1749	+	theInfo.addProperty(zconsTol);
1750	+
1751	+	//set Force Subtraction Policy
1752	+	StringData* zconsForcePolicy = new StringData();
1753	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1754	+
1755	+	if (globals->haveZconsForcePolicy()){
1756	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1757	+	}
1758	+	else{
1759	+	sprintf(painCave.errMsg,
1760	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1761	+	"\tOOPSE will use PolicyByMass.\n"
1762	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1763	+	painCave.isFatal = 0;
1764	+	simError();
1765	+	zconsForcePolicy->setData("BYMASS");
1766	+	}
1767	+
1768	+	theInfo.addProperty(zconsForcePolicy);
1769	+
1770	+	//set zcons gap
1771	+	DoubleData* zconsGap = new DoubleData();
1772	+	zconsGap->setID(ZCONSGAP_ID);
1773	+
1774	+	if (globals->haveZConsGap()){
1775	+	zconsGap->setData(globals->getZconsGap());
1776	+	theInfo.addProperty(zconsGap);
1777	+	}
1778	+
1779	+	//set zcons fixtime
1780	+	DoubleData* zconsFixtime = new DoubleData();
1781	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1782	+
1783	+	if (globals->haveZConsFixTime()){
1784	+	zconsFixtime->setData(globals->getZconsFixtime());
1785	+	theInfo.addProperty(zconsFixtime);
1786	+	}
1787	+
1788	+	//set zconsUsingSMD
1789	+	IntData* zconsUsingSMD = new IntData();
1790	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1791	+
1792	+	if (globals->haveZConsUsingSMD()){
1793	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1794	+	theInfo.addProperty(zconsUsingSMD);
1795	+	}
1796	+
1797	+	//Determine the name of ouput file and add it into SimInfo's property list
1798	+	//Be careful, do not use inFileName, since it is a pointer which
1799	+	//point to a string at master node, and slave nodes do not contain that string
1800	+
1801	+	string zconsOutput(theInfo.finalName);
1802	+
1803	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1804	+
1805	+	StringData* zconsFilename = new StringData();
1806	+	zconsFilename->setID(ZCONSFILENAME_ID);
1807	+	zconsFilename->setData(zconsOutput);
1808	+
1809	+	theInfo.addProperty(zconsFilename);
1810	+
1811	+	//setup index, pos and other parameters of z-constraint molecules
1812	+	nZConstraints = globals->getNzConstraints();
1813	+	theInfo.nZconstraints = nZConstraints;
1814	+
1815	+	zconStamp = globals->getZconStamp();
1816	+	ZConsParaItem tempParaItem;
1817	+
1818	+	ZConsParaData* zconsParaData = new ZConsParaData();
1819	+	zconsParaData->setID(ZCONSPARADATA_ID);
1820	+
1821	+	for (int i = 0; i < nZConstraints; i++){
1822	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1823	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1824	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1825	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1826	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1827	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1828	+	zconsParaData->addItem(tempParaItem);
1829	+	}
1830	+
1831	+	//check the uniqueness of index
1832	+	if(!zconsParaData->isIndexUnique()){
1833	+	sprintf(painCave.errMsg,
1834	+	"ZConstraint Error: molIndex is not unique!\n");
1835	+	painCave.isFatal = 1;
1836	+	simError();
1837	+	}
1838	+
1839	+	//sort the parameters by index of molecules
1840	+	zconsParaData->sortByIndex();
1841	+
1842	+	//push data into siminfo, therefore, we can retrieve later
1843	+	theInfo.addProperty(zconsParaData);
1844		}
1845	+
1846	+	void SimSetup::makeMinimizer(){
1847	+
1848	+	OOPSEMinimizer* myOOPSEMinimizer;
1849	+	MinimizerParameterSet* param;
1850	+	char minimizerName[100];
1851	+
1852	+	for (int i = 0; i < nInfo; i++){
1853	+
1854	+	//prepare parameter set for minimizer
1855	+	param = new MinimizerParameterSet();
1856	+	param->setDefaultParameter();
1857	+
1858	+	if (globals->haveMinimizer()){
1859	+	param->setFTol(globals->getMinFTol());
1860	+	}
1861	+
1862	+	if (globals->haveMinGTol()){
1863	+	param->setGTol(globals->getMinGTol());
1864	+	}
1865	+
1866	+	if (globals->haveMinMaxIter()){
1867	+	param->setMaxIteration(globals->getMinMaxIter());
1868	+	}
1869	+
1870	+	if (globals->haveMinWriteFrq()){
1871	+	param->setMaxIteration(globals->getMinMaxIter());
1872	+	}
1873	+
1874	+	if (globals->haveMinWriteFrq()){
1875	+	param->setWriteFrq(globals->getMinWriteFrq());
1876	+	}
1877	+
1878	+	if (globals->haveMinStepSize()){
1879	+	param->setStepSize(globals->getMinStepSize());
1880	+	}
1881	+
1882	+	if (globals->haveMinLSMaxIter()){
1883	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1884	+	}
1885	+
1886	+	if (globals->haveMinLSTol()){
1887	+	param->setLineSearchTol(globals->getMinLSTol());
1888	+	}
1889	+
1890	+	strcpy(minimizerName, globals->getMinimizer());
1891	+
1892	+	if (!strcasecmp(minimizerName, "CG")){
1893	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1894	+	}
1895	+	else if (!strcasecmp(minimizerName, "SD")){
1896	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1897	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1898	+	}
1899	+	else{
1900	+	sprintf(painCave.errMsg,
1901	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1902	+	painCave.isFatal = 0;
1903	+	simError();
1904	+
1905	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1906	+	}
1907	+	info[i].the_integrator = myOOPSEMinimizer;
1908	+
1909	+	//store the minimizer into simInfo
1910	+	info[i].the_minimizer = myOOPSEMinimizer;
1911	+	info[i].has_minimizer = true;
1912	+	}
1913	+
1914	+	}

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