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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 644 by mmeineke, Tue Jul 22 16:41:08 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 41 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
81	–	int i, j, k, globalAtomIndex;
82	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 89 | Line 132 | void SimSetup::createSim( void ){
132		sysObjectsCreation();
133
134		// check on the post processing info
135	<
135	>
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	initSystemCoords();
141	<
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
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	<
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>
189		bond_pair* theBonds;
190		bend_set* theBends;
191		torsion_set* theTorsions;
192
193	<
193	>	set<int> skipList;
194	>
195	>	double phi, theta, psi;
196	>	char* molName;
197	>	char rbName[100];
198	>
199		//init the forceField paramters
200
201		the_ff->readParams();
202
142	–
203		// init the atoms
204
205	<	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();
205	>	int nMembers, nNew, rb1, rb2;
206
207	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
208	<	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;
207	>	for (k = 0; k < nInfo; k++){
208	>	the_ff->setSimInfo(&(info[k]));
209
210	<	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];
210	>	atomOffset = 0;
211
212	<	theBonds = new bond_pair[molInfo.nBonds];
213	<	theBends = new bend_set[molInfo.nBends];
214	<	theTorsions = new torsion_set[molInfo.nTorsions];
215	<
216	<	// make the Atoms
217	<
218	<	for(j=0; j<molInfo.nAtoms; j++){
212	>	for (i = 0; i < info[k].n_mol; i++){
213	>	stampID = info[k].molecules[i].getStampID();
214	>	molName = comp_stamps[stampID]->getID();
215	>
216	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
219	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222
223	<	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;
223	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
224
225	<	exI = theBonds[j].a;
226	<	exJ = theBonds[j].b;
225	>	if (molInfo.nBonds > 0)
226	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	>	else
228	>	molInfo.myBonds = NULL;
229
230	<	// exclude_I must always be the smaller of the pair
231	<	if( exI > exJ ){
232	<	tempEx = exI;
233	<	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
230	>	if (molInfo.nBends > 0)
231	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	>	else
233	>	molInfo.myBends = NULL;
234
235	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
236	<	#endif  //is_mpi
237	<	}
238	<	excludeOffset += molInfo.nBonds;
235	>	if (molInfo.nTorsions > 0)
236	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	>	else
238	>	molInfo.myTorsions = NULL;
239
240	<	//make the bends
241	<	for(j=0; j<molInfo.nBends; j++){
240	>	theBonds = new bond_pair[molInfo.nBonds];
241	>	theBends = new bend_set[molInfo.nBends];
242	>	theTorsions = new torsion_set[molInfo.nTorsions];
243
244	<	currentBend = comp_stamps[stampID]->getBend( j );
245	<	theBends[j].a = currentBend->getA() + atomOffset;
246	<	theBends[j].b = currentBend->getB() + atomOffset;
247	<	theBends[j].c = currentBend->getC() + atomOffset;
248	<
249	<	if( currentBend->haveExtras() ){
250	<
251	<	extras = currentBend->getExtras();
252	<	current_extra = extras;
253	<
254	<	while( current_extra != NULL ){
255	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
256	<
257	<	switch( current_extra->getType() ){
258	<
259	<	case 0:
260	<	theBends[j].ghost =
261	<	current_extra->getInt() + atomOffset;
262	<	theBends[j].isGhost = 1;
263	<	break;
264	<
265	<	case 1:
266	<	theBends[j].ghost =
267	<	(int)current_extra->getDouble() + atomOffset;
268	<	theBends[j].isGhost = 1;
269	<	break;
270	<
271	<	default:
272	<	sprintf( painCave.errMsg,
273	<	"SimSetup Error: ghostVectorSource was neither a "
274	<	"double nor an int.\n"
275	<	"-->Bend[%d] in %s\n",
276	<	j, comp_stamps[stampID]->getID() );
277	<	painCave.isFatal = 1;
278	<	simError();
279	<	}
280	<	}
281	<
282	<	else{
283	<
284	<	sprintf( painCave.errMsg,
285	<	"SimSetup Error: unhandled bend assignment:\n"
286	<	"    -->%s in Bend[%d] in %s\n",
287	<	current_extra->getlhs(),
288	<	j, comp_stamps[stampID]->getID() );
289	<	painCave.isFatal = 1;
290	<	simError();
291	<	}
292	<
293	<	current_extra = current_extra->getNext();
294	<	}
244	>	// make the Atoms
245	>
246	>	for (j = 0; j < molInfo.nAtoms; j++){
247	>	currentAtom = comp_stamps[stampID]->getAtom(j);
248	>
249	>	if (currentAtom->haveOrientation()){
250	>	dAtom = new DirectionalAtom((j + atomOffset),
251	>	info[k].getConfiguration());
252	>	info[k].n_oriented++;
253	>	molInfo.myAtoms[j] = dAtom;
254	>
255	>	// Directional Atoms have standard unit vectors which are oriented
256	>	// in space using the three Euler angles.  We assume the standard
257	>	// unit vector was originally along the z axis below.
258	>
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262	>
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267	>
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269	>
270	>	}
271	>
272	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
273	>	#ifdef IS_MPI
274	>
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276	>
277	>	#endif // is_mpi
278	>	}
279	>
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285	>
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288	>
289	>	#ifdef IS_MPI
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296	>
297	>	info[k].excludes->addPair(exI, exJ);
298		}
299	<
300	<	if( !theBends[j].isGhost ){
301	<
302	<	exI = theBends[j].a;
303	<	exJ = theBends[j].c;
304	<	}
305	<	else{
306	<
307	<	exI = theBends[j].a;
308	<	exJ = theBends[j].b;
309	<	}
310	<
311	<	// exclude_I must always be the smaller of the pair
312	<	if( exI > exJ ){
313	<	tempEx = exI;
314	<	exI = exJ;
315	<	exJ = tempEx;
316	<	}
299	>
300	>	//make the bends
301	>	for (j = 0; j < molInfo.nBends; j++){
302	>	currentBend = comp_stamps[stampID]->getBend(j);
303	>	theBends[j].a = currentBend->getA() + atomOffset;
304	>	theBends[j].b = currentBend->getB() + atomOffset;
305	>	theBends[j].c = currentBend->getC() + atomOffset;
306	>
307	>	if (currentBend->haveExtras()){
308	>	extras = currentBend->getExtras();
309	>	current_extra = extras;
310	>
311	>	while (current_extra != NULL){
312	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
313	>	switch (current_extra->getType()){
314	>	case 0:
315	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
316	>	theBends[j].isGhost = 1;
317	>	break;
318	>
319	>	case 1:
320	>	theBends[j].ghost = (int) current_extra->getDouble() +
321	>	atomOffset;
322	>	theBends[j].isGhost = 1;
323	>	break;
324	>
325	>	default:
326	>	sprintf(painCave.errMsg,
327	>	"SimSetup Error: ghostVectorSource was neither a "
328	>	"double nor an int.\n"
329	>	"-->Bend[%d] in %s\n",
330	>	j, comp_stamps[stampID]->getID());
331	>	painCave.isFatal = 1;
332	>	simError();
333	>	}
334	>	}
335	>	else{
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: unhandled bend assignment:\n"
338	>	"    -->%s in Bend[%d] in %s\n",
339	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343	>
344	>	current_extra = current_extra->getNext();
345	>	}
346	>	}
347	>
348	>	if (theBends[j].isGhost) {
349	>
350	>	tempI = theBends[j].a;
351	>	tempJ = theBends[j].b;
352	>
353		#ifdef IS_MPI
354	<	tempEx = exI;
355	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
356	<	tempEx = exJ;
357	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
358	<
359	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
360	<	#else  // isn't MPI
318	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319	<	#endif  //is_mpi
320	<	}
321	<	excludeOffset += molInfo.nBends;
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	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;
362	>	} else {
363
364	<	// exclude_I must always be the smaller of the pair
365	<	if( exI > exJ ){
366	<	tempEx = exI;
367	<	exI = exJ;
368	<	exJ = tempEx;
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
383	+
384	+	for (j = 0; j < molInfo.nTorsions; j++){
385	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
386	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
387	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
388	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
389	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
390	+
391	+	tempI = theTorsions[j].a;
392	+	tempJ = theTorsions[j].b;
393	+	tempK = theTorsions[j].c;
394	+	tempL = theTorsions[j].d;
395	+
396		#ifdef IS_MPI
397	<	tempEx = exI;
398	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
399	<	tempEx = exJ;
400	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
401	<
402	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
403	<	#else  // isn't MPI
404	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
405	<	#endif  //is_mpi
406	<	}
351	<	excludeOffset += molInfo.nTorsions;
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406	>	#endif
407
408	<
409	<	// send the arrays off to the forceField for init.
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415
416	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
417	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
418	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
419	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
416	>
417	>	molInfo.myRigidBodies.clear();
418	>
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420
421	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	+	nMembers = currentRigidBody->getNMembers();
423
424	<	the_molecules[i].initialize( molInfo );
424	>	// Create the Rigid Body:
425
426	+	myRB = new RigidBody();
427
428	<	atomOffset += molInfo.nAtoms;
429	<	delete[] theBonds;
430	<	delete[] theBends;
431	<	delete[] theTorsions;
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432	>
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435	>
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438	>
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442	>
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445	>
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449	>	#ifdef IS_MPI
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469	>	#ifdef IS_MPI
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481	>
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484	>	}
485	>
486	>
487	>	//creat cutoff group for molecule
488	>	molInfo.myCutoffGroups.clear();
489	>	for (j = 0; j < molInfo.nCutoffGroups; j++){
490	>
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493	>
494	>	myCutoffGroup = new CutoffGroup();
495	>
496	>	for (int cg = 0; cg < nMembers; cg++) {
497	>
498	>	// molI is atom numbering inside this molecule
499	>	molI = currentCutoffGroup->getMember(cg);
500	>
501	>	// tempI is atom numbering on local processor
502	>	tempI = molI + atomOffset;
503	>
504	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	>	}
506	>
507	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	>
510	>
511	>
512	>	// After this is all set up, scan through the atoms to
513	>	// see if they can be added to the integrableObjects:
514	>
515	>	molInfo.myIntegrableObjects.clear();
516	>
517	>
518	>	for (j = 0; j < molInfo.nAtoms; j++){
519	>
520	>	#ifdef IS_MPI
521	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	>	#else
523	>	slJ = j+atomOffset;
524	>	#endif
525	>
526	>	// if they aren't on the skip list, then they can be integrated
527	>
528	>	if (skipList.find(slJ) == skipList.end()) {
529	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	>	info[k].integrableObjects.push_back(mySD);
531	>	molInfo.myIntegrableObjects.push_back(mySD);
532	>	}
533	>	}
534	>
535	>	// all rigid bodies are integrated:
536	>
537	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	>	info[k].integrableObjects.push_back(mySD);
540	>	molInfo.myIntegrableObjects.push_back(mySD);
541	>	}
542	>
543	>
544	>	// send the arrays off to the forceField for init.
545	>
546	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550	>	theTorsions);
551	>
552	>	info[k].molecules[i].initialize(molInfo);
553	>
554	>
555	>	atomOffset += molInfo.nAtoms;
556	>	delete[] theBonds;
557	>	delete[] theBends;
558	>	delete[] theTorsions;
559	>	}
560		}
561
562		#ifdef IS_MPI
563	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
563	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
564		MPIcheckPoint();
565		#endif // is_mpi
566
567		// clean up the forcefield
377	–	the_ff->calcRcut();
378	–	the_ff->cleanMe();
568
569	<	}
569	>	if (!globals->haveRcut()){
570
571	<	void SimSetup::initFromBass( void ){
571	>	the_ff->calcRcut();
572
573	+	} else {
574	+
575	+	the_ff->setRcut( globals->getRcut() );
576	+	}
577	+
578	+	the_ff->cleanMe();
579	+	}
580	+
581	+	void SimSetup::initFromBass(void){
582		int i, j, k;
583		int n_cells;
584		double cellx, celly, cellz;
#	Line 389 | Line 587 | void SimSetup::initFromBass( void ){
587		int n_extra;
588		int have_extra, done;
589
590	<	temp1 = (double)tot_nmol / 4.0;
591	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
592	<	temp3 = ceil( temp2 );
590	>	double vel[3];
591	>	vel[0] = 0.0;
592	>	vel[1] = 0.0;
593	>	vel[2] = 0.0;
594
595	<	have_extra =0;
596	<	if( temp2 < temp3 ){ // we have a non-complete lattice
597	<	have_extra =1;
595	>	temp1 = (double) tot_nmol / 4.0;
596	>	temp2 = pow(temp1, (1.0 / 3.0));
597	>	temp3 = ceil(temp2);
598
599	<	n_cells = (int)temp3 - 1;
600	<	cellx = info->boxL[0] / temp3;
601	<	celly = info->boxL[1] / temp3;
602	<	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 );
599	>	have_extra = 0;
600	>	if (temp2 < temp3){
601	>	// we have a non-complete lattice
602	>	have_extra = 1;
603
604	<	if( n_per_extra > 4){
605	<	sprintf( painCave.errMsg,
606	<	"SimSetup error. There has been an error in constructing"
607	<	" the non-complete lattice.\n" );
604	>	n_cells = (int) temp3 - 1;
605	>	cellx = info[0].boxL[0] / temp3;
606	>	celly = info[0].boxL[1] / temp3;
607	>	cellz = info[0].boxL[2] / temp3;
608	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
609	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
610	>	n_per_extra = (int) ceil(temp1);
611	>
612	>	if (n_per_extra > 4){
613	>	sprintf(painCave.errMsg,
614	>	"SimSetup error. There has been an error in constructing"
615	>	" the non-complete lattice.\n");
616		painCave.isFatal = 1;
617		simError();
618		}
619		}
620		else{
621	<	n_cells = (int)temp3;
622	<	cellx = info->boxL[0] / temp3;
623	<	celly = info->boxL[1] / temp3;
624	<	cellz = info->boxL[2] / temp3;
621	>	n_cells = (int) temp3;
622	>	cellx = info[0].boxL[0] / temp3;
623	>	celly = info[0].boxL[1] / temp3;
624	>	cellz = info[0].boxL[2] / temp3;
625		}
626
627		current_mol = 0;
#	Line 425 | Line 629 | void SimSetup::initFromBass( void ){
629		current_comp = 0;
630		current_atom_ndx = 0;
631
632	<	for( i=0; i < n_cells ; i++ ){
633	<	for( j=0; j < n_cells; j++ ){
634	<	for( k=0; k < n_cells; k++ ){
632	>	for (i = 0; i < n_cells ; i++){
633	>	for (j = 0; j < n_cells; j++){
634	>	for (k = 0; k < n_cells; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636
637	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
637	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
638
639	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
639	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
640
641	<	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 );
641	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
642		}
643		}
644		}
645
646	<	if( have_extra ){
646	>	if (have_extra){
647		done = 0;
648
649		int start_ndx;
650	<	for( i=0; i < (n_cells+1) && !done; i++ ){
651	<	for( j=0; j < (n_cells+1) && !done; j++ ){
650	>	for (i = 0; i < (n_cells + 1) && !done; i++){
651	>	for (j = 0; j < (n_cells + 1) && !done; j++){
652	>	if (i < n_cells){
653	>	if (j < n_cells){
654	>	start_ndx = n_cells;
655	>	}
656	>	else
657	>	start_ndx = 0;
658	>	}
659	>	else
660	>	start_ndx = 0;
661
662	<	if( i < n_cells ){
662	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
663	>	makeElement(i * cellx, j * celly, k * cellz);
664	>	done = (current_mol >= tot_nmol);
665
666	<	if( j < n_cells ){
667	<	start_ndx = n_cells;
668	<	}
669	<	else start_ndx = 0;
670	<	}
465	<	else start_ndx = 0;
466	<
467	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
666	>	if (!done && n_per_extra > 1){
667	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
668	>	k * cellz);
669	>	done = (current_mol >= tot_nmol);
670	>	}
671
672	<	makeElement( i * cellx,
673	<	j * celly,
674	<	k * cellz );
675	<	done = ( current_mol >= tot_nmol );
672	>	if (!done && n_per_extra > 2){
673	>	makeElement(i * cellx, j * celly + 0.5 * celly,
674	>	k * cellz + 0.5 * cellz);
675	>	done = (current_mol >= tot_nmol);
676	>	}
677
678	<	if( !done && n_per_extra > 1 ){
679	<	makeElement( i * cellx + 0.5 * cellx,
680	<	j * celly + 0.5 * celly,
681	<	k * cellz );
682	<	done = ( current_mol >= tot_nmol );
683	<	}
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	<	}
678	>	if (!done && n_per_extra > 3){
679	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
680	>	k * cellz + 0.5 * cellz);
681	>	done = (current_mol >= tot_nmol);
682	>	}
683	>	}
684		}
685		}
686		}
687
688	<
689	<	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 );
688	>	for (i = 0; i < info[0].n_atoms; i++){
689	>	info[0].atoms[i]->setVel(vel);
690		}
691		}
692
693	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
693	>	void SimSetup::makeElement(double x, double y, double z){
694		int k;
695		AtomStamp* current_atom;
696		DirectionalAtom* dAtom;
697		double rotMat[3][3];
698	+	double pos[3];
699
700	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
701	<
702	<	current_atom = comp_stamps[current_comp]->getAtom( k );
703	<	if( !current_atom->havePosition() ){
704	<	sprintf( painCave.errMsg,
705	<	"SimSetup:initFromBass error.\n"
706	<	"\tComponent %s, atom %s does not have a position specified.\n"
707	<	"\tThe initialization routine is unable to give a start"
708	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
700	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
701	>	current_atom = comp_stamps[current_comp]->getAtom(k);
702	>	if (!current_atom->havePosition()){
703	>	sprintf(painCave.errMsg,
704	>	"SimSetup:initFromBass error.\n"
705	>	"\tComponent %s, atom %s does not have a position specified.\n"
706	>	"\tThe initialization routine is unable to give a start"
707	>	" position.\n",
708	>	comp_stamps[current_comp]->getID(), current_atom->getType());
709		painCave.isFatal = 1;
710		simError();
711		}
712
713	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
714	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
715	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
713	>	pos[0] = x + current_atom->getPosX();
714	>	pos[1] = y + current_atom->getPosY();
715	>	pos[2] = z + current_atom->getPosZ();
716
717	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
717	>	info[0].atoms[current_atom_ndx]->setPos(pos);
718
719	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
719	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
720	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
721
722		rotMat[0][0] = 1.0;
723		rotMat[0][1] = 0.0;
#	Line 546 | Line 731 | void SimSetup::makeElement( double x, double y, double
731		rotMat[2][1] = 0.0;
732		rotMat[2][2] = 1.0;
733
734	<	dAtom->setA( rotMat );
734	>	dAtom->setA(rotMat);
735		}
736
737		current_atom_ndx++;
#	Line 555 | Line 740 | void SimSetup::makeElement( double x, double y, double
740		current_mol++;
741		current_comp_mol++;
742
743	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
743	>	if (current_comp_mol >= components_nmol[current_comp]){
744		current_comp_mol = 0;
745		current_comp++;
746		}
747		}
748
749
750	<	void SimSetup::gatherInfo( void ){
751	<	int i,j,k;
750	>	void SimSetup::gatherInfo(void){
751	>	int i;
752
753		ensembleCase = -1;
754		ffCase = -1;
755
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
756		// set the easy ones first
757	<	info->target_temp = globals->getTargetTemp();
758	<	info->dt = globals->getDt();
759	<	info->run_time = globals->getRunTime();
757	>
758	>	for (i = 0; i < nInfo; i++){
759	>	info[i].target_temp = globals->getTargetTemp();
760	>	info[i].dt = globals->getDt();
761	>	info[i].run_time = globals->getRunTime();
762	>	}
763		n_components = globals->getNComponents();
764
765
766		// get the forceField
767
768	<	strcpy( force_field, globals->getForceField() );
768	>	strcpy(force_field, globals->getForceField());
769
770	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
771	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
770	>	if (!strcasecmp(force_field, "DUFF")){
771	>	ffCase = FF_DUFF;
772	>	}
773	>	else if (!strcasecmp(force_field, "LJ")){
774	>	ffCase = FF_LJ;
775	>	}
776	>	else if (!strcasecmp(force_field, "EAM")){
777	>	ffCase = FF_EAM;
778	>	}
779	>	else if (!strcasecmp(force_field, "WATER")){
780	>	ffCase = FF_H2O;
781	>	}
782		else{
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup Error. Unrecognized force field -> %s\n",
785	<	force_field );
786	<	painCave.isFatal = 1;
594	<	simError();
783	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
784	>	force_field);
785	>	painCave.isFatal = 1;
786	>	simError();
787		}
788
789	<	// get the ensemble
789	>	// get the ensemble
790
791	<	strcpy( ensemble, globals->getEnsemble() );
791	>	strcpy(ensemble, globals->getEnsemble());
792
793	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
794	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
795	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
793	>	if (!strcasecmp(ensemble, "NVE")){
794	>	ensembleCase = NVE_ENS;
795	>	}
796	>	else if (!strcasecmp(ensemble, "NVT")){
797	>	ensembleCase = NVT_ENS;
798	>	}
799	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
800		ensembleCase = NPTi_ENS;
801	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
802	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
803	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
801	>	}
802	>	else if (!strcasecmp(ensemble, "NPTf")){
803	>	ensembleCase = NPTf_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NPTxyz")){
806	>	ensembleCase = NPTxyz_ENS;
807	>	}
808		else{
809	<	sprintf( painCave.errMsg,
810	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
811	<	"reverting to NVE for this simulation.\n",
812	<	ensemble );
813	<	painCave.isFatal = 0;
814	<	simError();
815	<	strcpy( ensemble, "NVE" );
816	<	ensembleCase = NVE_ENS;
809	>	sprintf(painCave.errMsg,
810	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
811	>	"\treverting to NVE for this simulation.\n",
812	>	ensemble);
813	>	painCave.isFatal = 0;
814	>	simError();
815	>	strcpy(ensemble, "NVE");
816	>	ensembleCase = NVE_ENS;
817		}
618	–	strcpy( info->ensemble, ensemble );
818
819	<	// get the mixing rule
819	>	for (i = 0; i < nInfo; i++){
820	>	strcpy(info[i].ensemble, ensemble);
821
822	<	strcpy( info->mixingRule, globals->getMixingRule() );
823	<	info->usePBC = globals->getPBC();
824	<
825	<
822	>	// get the mixing rule
823	>
824	>	strcpy(info[i].mixingRule, globals->getMixingRule());
825	>	info[i].usePBC = globals->getPBC();
826	>	}
827	>
828		// get the components and calculate the tot_nMol and indvidual n_mol
829	<
829	>
830		the_components = globals->getComponents();
831		components_nmol = new int[n_components];
832
833
834	<	if( !globals->haveNMol() ){
834	>	if (!globals->haveNMol()){
835		// we don't have the total number of molecules, so we assume it is
836		// given in each component
837
838		tot_nmol = 0;
839	<	for( i=0; i<n_components; i++ ){
840	<
841	<	if( !the_components[i]->haveNMol() ){
842	<	// we have a problem
843	<	sprintf( painCave.errMsg,
844	<	"SimSetup Error. No global NMol or component NMol"
845	<	" given. Cannot calculate the number of atoms.\n" );
846	<	painCave.isFatal = 1;
645	<	simError();
839	>	for (i = 0; i < n_components; i++){
840	>	if (!the_components[i]->haveNMol()){
841	>	// we have a problem
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup Error. No global NMol or component NMol given.\n"
844	>	"\tCannot calculate the number of atoms.\n");
845	>	painCave.isFatal = 1;
846	>	simError();
847		}
848
849		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 851 | void SimSetup::gatherInfo( void ){
851		}
852		}
853		else{
854	<	sprintf( painCave.errMsg,
855	<	"SimSetup error.\n"
856	<	"\tSorry, the ability to specify total"
857	<	" nMols and then give molfractions in the components\n"
858	<	"\tis not currently supported."
859	<	" Please give nMol in the components.\n" );
854	>	sprintf(painCave.errMsg,
855	>	"SimSetup error.\n"
856	>	"\tSorry, the ability to specify total"
857	>	" nMols and then give molfractions in the components\n"
858	>	"\tis not currently supported."
859	>	" Please give nMol in the components.\n");
860		painCave.isFatal = 1;
861		simError();
862		}
863
864	<	// set the status, sample, and thermal kick times
865	<
866	<	if( globals->haveSampleTime() ){
867	<	info->sampleTime = globals->getSampleTime();
868	<	info->statusTime = info->sampleTime;
869	<	info->thermalTime = info->sampleTime;
864	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
865	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
866	>	sprintf(painCave.errMsg,
867	>	"Sample time is not divisible by dt.\n"
868	>	"\tThis will result in samples that are not uniformly\n"
869	>	"\tdistributed in time.  If this is a problem, change\n"
870	>	"\tyour sampleTime variable.\n");
871	>	painCave.isFatal = 0;
872	>	simError();
873		}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
874
875	<	if( globals->haveStatusTime() ){
876	<	info->statusTime = globals->getStatusTime();
875	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
876	>	sprintf(painCave.errMsg,
877	>	"Status time is not divisible by dt.\n"
878	>	"\tThis will result in status reports that are not uniformly\n"
879	>	"\tdistributed in time.  If this is a problem, change \n"
880	>	"\tyour statusTime variable.\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883		}
884
885	<	if( globals->haveThermalTime() ){
886	<	info->thermalTime = globals->getThermalTime();
887	<	}
885	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
886	>	sprintf(painCave.errMsg,
887	>	"Thermal time is not divisible by dt.\n"
888	>	"\tThis will result in thermalizations that are not uniformly\n"
889	>	"\tdistributed in time.  If this is a problem, change \n"
890	>	"\tyour thermalTime variable.\n");
891	>	painCave.isFatal = 0;
892	>	simError();
893	>	}
894
895	<	// check for the temperature set flag
895	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
896	>	sprintf(painCave.errMsg,
897	>	"Reset time is not divisible by dt.\n"
898	>	"\tThis will result in integrator resets that are not uniformly\n"
899	>	"\tdistributed in time.  If this is a problem, change\n"
900	>	"\tyour resetTime variable.\n");
901	>	painCave.isFatal = 0;
902	>	simError();
903	>	}
904
905	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
905	>	// set the status, sample, and thermal kick times
906
907	<	// get some of the tricky things that may still be in the globals
907	>	for (i = 0; i < nInfo; i++){
908	>	if (globals->haveSampleTime()){
909	>	info[i].sampleTime = globals->getSampleTime();
910	>	info[i].statusTime = info[i].sampleTime;
911	>	}
912	>	else{
913	>	info[i].sampleTime = globals->getRunTime();
914	>	info[i].statusTime = info[i].sampleTime;
915	>	}
916
917	<	double boxVector[3];
918	<	if( globals->haveBox() ){
692	<	boxVector[0] = globals->getBox();
693	<	boxVector[1] = globals->getBox();
694	<	boxVector[2] = globals->getBox();
695	<
696	<	info->setBox( boxVector );
697	<	}
698	<	else if( globals->haveDensity() ){
699	<
700	<	double vol;
701	<	vol = (double)tot_nmol / globals->getDensity();
702	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	<	boxVector[1] = boxVector[0];
704	<	boxVector[2] = boxVector[0];
705	<
706	<	info->setBox( boxVector );
707	<	}
708	<	else{
709	<	if( !globals->haveBoxX() ){
710	<	sprintf( painCave.errMsg,
711	<	"SimSetup error, no periodic BoxX size given.\n" );
712	<	painCave.isFatal = 1;
713	<	simError();
917	>	if (globals->haveStatusTime()){
918	>	info[i].statusTime = globals->getStatusTime();
919		}
715	–	boxVector[0] = globals->getBoxX();
920
921	<	if( !globals->haveBoxY() ){
922	<	sprintf( painCave.errMsg,
923	<	"SimSetup error, no periodic BoxY size given.\n" );
924	<	painCave.isFatal = 1;
721	<	simError();
921	>	if (globals->haveThermalTime()){
922	>	info[i].thermalTime = globals->getThermalTime();
923	>	} else {
924	>	info[i].thermalTime = globals->getRunTime();
925		}
723	–	boxVector[1] = globals->getBoxY();
926
927	<	if( !globals->haveBoxZ() ){
928	<	sprintf( painCave.errMsg,
929	<	"SimSetup error, no periodic BoxZ size given.\n" );
930	<	painCave.isFatal = 1;
729	<	simError();
927	>	info[i].resetIntegrator = 0;
928	>	if( globals->haveResetTime() ){
929	>	info[i].resetTime = globals->getResetTime();
930	>	info[i].resetIntegrator = 1;
931		}
731	–	boxVector[2] = globals->getBoxZ();
932
933	<	info->setBox( boxVector );
933	>	// check for the temperature set flag
934	>
935	>	if (globals->haveTempSet())
936	>	info[i].setTemp = globals->getTempSet();
937	>
938	>	// check for the extended State init
939	>
940	>	info[i].useInitXSstate = globals->getUseInitXSstate();
941	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
942	>
943		}
944	+
945	+	//setup seed for random number generator
946	+	int seedValue;
947
948	+	if (globals->haveSeed()){
949	+	seedValue = globals->getSeed();
950
951	+	if(seedValue / 1E9 == 0){
952	+	sprintf(painCave.errMsg,
953	+	"Seed for sprng library should contain at least 9 digits\n"
954	+	"OOPSE will generate a seed for user\n");
955	+	painCave.isFatal = 0;
956	+	simError();
957	+
958	+	//using seed generated by system instead of invalid seed set by user
959	+	#ifndef IS_MPI
960	+	seedValue = make_sprng_seed();
961	+	#else
962	+	if (worldRank == 0){
963	+	seedValue = make_sprng_seed();
964	+	}
965	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
966	+	#endif
967	+	}
968	+	}//end of if branch of globals->haveSeed()
969	+	else{
970
971	+	#ifndef IS_MPI
972	+	seedValue = make_sprng_seed();
973	+	#else
974	+	if (worldRank == 0){
975	+	seedValue = make_sprng_seed();
976	+	}
977	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
978	+	#endif
979	+	}//end of globals->haveSeed()
980	+
981	+	for (int i = 0; i < nInfo; i++){
982	+	info[i].setSeed(seedValue);
983	+	}
984	+
985		#ifdef IS_MPI
986	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
986	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
987		MPIcheckPoint();
988		#endif // is_mpi
742	–
989		}
990
991
992	<	void SimSetup::finalInfoCheck( void ){
992	>	void SimSetup::finalInfoCheck(void){
993		int index;
994		int usesDipoles;
995	<
995	>	int usesCharges;
996	>	int i;
997
998	<	// check electrostatic parameters
999	<
1000	<	index = 0;
1001	<	usesDipoles = 0;
1002	<	while( (index < info->n_atoms) && !usesDipoles ){
1003	<	usesDipoles = ((info->atoms)[index])->hasDipole();
1004	<	index++;
1005	<	}
1006	<
998	>	for (i = 0; i < nInfo; i++){
999	>	// check electrostatic parameters
1000	>
1001	>	index = 0;
1002	>	usesDipoles = 0;
1003	>	while ((index < info[i].n_atoms) && !usesDipoles){
1004	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1005	>	index++;
1006	>	}
1007	>	index = 0;
1008	>	usesCharges = 0;
1009	>	while ((index < info[i].n_atoms) && !usesCharges){
1010	>	usesCharges= (info[i].atoms[index])->hasCharge();
1011	>	index++;
1012	>	}
1013		#ifdef IS_MPI
1014	<	int myUse = usesDipoles;
1015	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1014	>	int myUse = usesDipoles;
1015	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1016		#endif //is_mpi
1017
1018	<	double theEcr, theEst;
1018	>	double theRcut, theRsw;
1019
1020	<	if (globals->getUseRF() ) {
1021	<	info->useReactionField = 1;
769	<
770	<	if( !globals->haveECR() ){
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup Warning: using default value of 1/2 the smallest "
773	<	"box length for the electrostaticCutoffRadius.\n"
774	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
784	<	}
1020	>	if (globals->getUseRF()){
1021	>	info[i].useReactionField = 1;
1022
1023	<	if( !globals->haveEST() ){
1024	<	sprintf( painCave.errMsg,
1025	<	"SimSetup Warning: using default value of 0.05 * the "
1026	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1027	<	);
1028	<	painCave.isFatal = 0;
1029	<	simError();
1030	<	theEst = 0.05 * theEcr;
1031	<	} else {
1032	<	theEst= globals->getEST();
1033	<	}
1023	>	if (!globals->haveRcut()){
1024	>	sprintf(painCave.errMsg,
1025	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the cutoffRadius.\n");
1028	>	painCave.isFatal = 0;
1029	>	simError();
1030	>	theRcut = 15.0;
1031	>	}
1032	>	else{
1033	>	theRcut = globals->getRcut();
1034	>	}
1035
1036	<	info->setEcr( theEcr, theEst );
1037	<
1038	<	if(!globals->haveDielectric() ){
1039	<	sprintf( painCave.errMsg,
1040	<	"SimSetup Error: You are trying to use Reaction Field without"
1041	<	"setting a dielectric constant!\n"
1042	<	);
1043	<	painCave.isFatal = 1;
806	<	simError();
807	<	}
808	<	info->dielectric = globals->getDielectric();
809	<	}
810	<	else {
811	<	if (usesDipoles) {
812	<
813	<	if( !globals->haveECR() ){
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Warning: using default value of 1/2 the smallest "
816	<	"box length for the electrostaticCutoffRadius.\n"
817	<	"I hope you have a very fast processor!\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	double smallest;
821	<	smallest = info->boxL[0];
822	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
1036	>	if (!globals->haveRsw()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1039	>	"\tOOPSE will use a default value of\n"
1040	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1041	>	painCave.isFatal = 0;
1042	>	simError();
1043	>	theRsw = 0.95 * theRcut;
1044		}
1045	<
1046	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the "
833	<	"electrostaticSkinThickness\n"
834	<	);
835	<	painCave.isFatal = 0;
836	<	simError();
837	<	theEst = 0.05 * theEcr;
838	<	} else {
839	<	theEst= globals->getEST();
1045	>	else{
1046	>	theRsw = globals->getRsw();
1047		}
1048
1049	<	info->setEcr( theEcr, theEst );
1049	>	info[i].setDefaultRcut(theRcut, theRsw);
1050	>
1051	>	if (!globals->haveDielectric()){
1052	>	sprintf(painCave.errMsg,
1053	>	"SimSetup Error: No Dielectric constant was set.\n"
1054	>	"\tYou are trying to use Reaction Field without"
1055	>	"\tsetting a dielectric constant!\n");
1056	>	painCave.isFatal = 1;
1057	>	simError();
1058	>	}
1059	>	info[i].dielectric = globals->getDielectric();
1060		}
1061	<	}
1061	>	else{
1062	>	if (usesDipoles || usesCharges){
1063
1064	+	if (!globals->haveRcut()){
1065	+	sprintf(painCave.errMsg,
1066	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067	+	"\tOOPSE will use a default value of 15.0 angstroms"
1068	+	"\tfor the cutoffRadius.\n");
1069	+	painCave.isFatal = 0;
1070	+	simError();
1071	+	theRcut = 15.0;
1072	+	}
1073	+	else{
1074	+	theRcut = globals->getRcut();
1075	+	}
1076	+
1077	+	if (!globals->haveRsw()){
1078	+	sprintf(painCave.errMsg,
1079	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1080	+	"\tOOPSE will use a default value of\n"
1081	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082	+	painCave.isFatal = 0;
1083	+	simError();
1084	+	theRsw = 0.95 * theRcut;
1085	+	}
1086	+	else{
1087	+	theRsw = globals->getRsw();
1088	+	}
1089	+
1090	+	info[i].setDefaultRcut(theRcut, theRsw);
1091	+
1092	+	}
1093	+	}
1094	+	}
1095		#ifdef IS_MPI
1096	<	strcpy( checkPointMsg, "post processing checks out" );
1096	>	strcpy(checkPointMsg, "post processing checks out");
1097		MPIcheckPoint();
1098		#endif // is_mpi
850	–
1099		}
1100	+
1101	+	void SimSetup::initSystemCoords(void){
1102	+	int i;
1103
1104	<	void SimSetup::initSystemCoords( void ){
1104	>	char* inName;
1105
1106	<	if( globals->haveInitialConfig() ){
1107	<
1108	<	InitializeFromFile* fileInit;
1106	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1107	>
1108	>	for (i = 0; i < info[0].n_atoms; i++)
1109	>	info[0].atoms[i]->setCoords();
1110	>
1111	>	if (globals->haveInitialConfig()){
1112	>	InitializeFromFile* fileInit;
1113		#ifdef IS_MPI // is_mpi
1114	<	if( worldRank == 0 ){
1114	>	if (worldRank == 0){
1115		#endif //is_mpi
1116	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1116	>	inName = globals->getInitialConfig();
1117	>	fileInit = new InitializeFromFile(inName);
1118		#ifdef IS_MPI
1119	<	}else fileInit = new InitializeFromFile( NULL );
1119	>	}
1120	>	else
1121	>	fileInit = new InitializeFromFile(NULL);
1122		#endif
1123	<	fileInit->readInit( info ); // default velocities on
1123	>	fileInit->readInit(info); // default velocities on
1124
1125	<	delete fileInit;
1126	<	}
1127	<	else{
1125	>	delete fileInit;
1126	>	}
1127	>	else{
1128	>
1129	>	// no init from bass
1130	>
1131	>	sprintf(painCave.errMsg,
1132	>	"Cannot intialize a simulation without an initial configuration file.\n");
1133	>	painCave.isFatal = 1;;
1134	>	simError();
1135	>
1136	>	}
1137
871	–	#ifdef IS_MPI
872	–
873	–	// no init from bass
874	–
875	–	sprintf( painCave.errMsg,
876	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	–	painCave.isFatal;
878	–	simError();
879	–
880	–	#else
881	–
882	–	initFromBass();
883	–
884	–
885	–	#endif
886	–	}
887	–
1138		#ifdef IS_MPI
1139	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1139	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1140		MPIcheckPoint();
1141		#endif // is_mpi
892	–
1142		}
1143
1144
1145	<	void SimSetup::makeOutNames( void ){
1145	>	void SimSetup::makeOutNames(void){
1146	>	int k;
1147
1148	+
1149	+	for (k = 0; k < nInfo; k++){
1150		#ifdef IS_MPI
1151	<	if( worldRank == 0 ){
1151	>	if (worldRank == 0){
1152		#endif // is_mpi
1153	<
1154	<	if( globals->haveFinalConfig() ){
1155	<	strcpy( info->finalName, globals->getFinalConfig() );
904	<	}
905	<	else{
906	<	strcpy( info->finalName, inFileName );
907	<	char* endTest;
908	<	int nameLength = strlen( info->finalName );
909	<	endTest = &(info->finalName[nameLength - 5]);
910	<	if( !strcmp( endTest, ".bass" ) ){
911	<	strcpy( endTest, ".eor" );
1153	>
1154	>	if (globals->haveFinalConfig()){
1155	>	strcpy(info[k].finalName, globals->getFinalConfig());
1156		}
913	–	else if( !strcmp( endTest, ".BASS" ) ){
914	–	strcpy( endTest, ".eor" );
915	–	}
1157		else{
1158	<	endTest = &(info->finalName[nameLength - 4]);
1159	<	if( !strcmp( endTest, ".bss" ) ){
1160	<	strcpy( endTest, ".eor" );
1161	<	}
1162	<	else if( !strcmp( endTest, ".mdl" ) ){
1163	<	strcpy( endTest, ".eor" );
1164	<	}
1165	<	else{
1166	<	strcat( info->finalName, ".eor" );
1167	<	}
1158	>	strcpy(info[k].finalName, inFileName);
1159	>	char* endTest;
1160	>	int nameLength = strlen(info[k].finalName);
1161	>	endTest = &(info[k].finalName[nameLength - 5]);
1162	>	if (!strcmp(endTest, ".bass")){
1163	>	strcpy(endTest, ".eor");
1164	>	}
1165	>	else if (!strcmp(endTest, ".BASS")){
1166	>	strcpy(endTest, ".eor");
1167	>	}
1168	>	else{
1169	>	endTest = &(info[k].finalName[nameLength - 4]);
1170	>	if (!strcmp(endTest, ".bss")){
1171	>	strcpy(endTest, ".eor");
1172	>	}
1173	>	else if (!strcmp(endTest, ".mdl")){
1174	>	strcpy(endTest, ".eor");
1175	>	}
1176	>	else{
1177	>	strcat(info[k].finalName, ".eor");
1178	>	}
1179	>	}
1180		}
1181	<	}
1182	<
1183	<	// make the sample and status out names
1184	<
1185	<	strcpy( info->sampleName, inFileName );
1186	<	char* endTest;
1187	<	int nameLength = strlen( info->sampleName );
1188	<	endTest = &(info->sampleName[nameLength - 5]);
1189	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
945	<	strcpy( endTest, ".dump" );
1181	>
1182	>	// make the sample and status out names
1183	>
1184	>	strcpy(info[k].sampleName, inFileName);
1185	>	char* endTest;
1186	>	int nameLength = strlen(info[k].sampleName);
1187	>	endTest = &(info[k].sampleName[nameLength - 5]);
1188	>	if (!strcmp(endTest, ".bass")){
1189	>	strcpy(endTest, ".dump");
1190		}
1191	<	else if( !strcmp( endTest, ".mdl" ) ){
1192	<	strcpy( endTest, ".dump" );
1191	>	else if (!strcmp(endTest, ".BASS")){
1192	>	strcpy(endTest, ".dump");
1193		}
1194		else{
1195	<	strcat( info->sampleName, ".dump" );
1195	>	endTest = &(info[k].sampleName[nameLength - 4]);
1196	>	if (!strcmp(endTest, ".bss")){
1197	>	strcpy(endTest, ".dump");
1198	>	}
1199	>	else if (!strcmp(endTest, ".mdl")){
1200	>	strcpy(endTest, ".dump");
1201	>	}
1202	>	else{
1203	>	strcat(info[k].sampleName, ".dump");
1204	>	}
1205		}
1206	<	}
1207	<
1208	<	strcpy( info->statusName, inFileName );
1209	<	nameLength = strlen( info->statusName );
1210	<	endTest = &(info->statusName[nameLength - 5]);
1211	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".stat" );
1206	>
1207	>	strcpy(info[k].statusName, inFileName);
1208	>	nameLength = strlen(info[k].statusName);
1209	>	endTest = &(info[k].statusName[nameLength - 5]);
1210	>	if (!strcmp(endTest, ".bass")){
1211	>	strcpy(endTest, ".stat");
1212		}
1213	<	else if( !strcmp( endTest, ".mdl" ) ){
1214	<	strcpy( endTest, ".stat" );
1213	>	else if (!strcmp(endTest, ".BASS")){
1214	>	strcpy(endTest, ".stat");
1215		}
1216		else{
1217	<	strcat( info->statusName, ".stat" );
1217	>	endTest = &(info[k].statusName[nameLength - 4]);
1218	>	if (!strcmp(endTest, ".bss")){
1219	>	strcpy(endTest, ".stat");
1220	>	}
1221	>	else if (!strcmp(endTest, ".mdl")){
1222	>	strcpy(endTest, ".stat");
1223	>	}
1224	>	else{
1225	>	strcat(info[k].statusName, ".stat");
1226	>	}
1227		}
1228	<	}
976	<
1228	>
1229		#ifdef IS_MPI
978	–	}
979	–	#endif // is_mpi
1230
1231	+	}
1232	+	#endif // is_mpi
1233	+	}
1234		}
1235
1236
1237	<	void SimSetup::sysObjectsCreation( void ){
1237	>	void SimSetup::sysObjectsCreation(void){
1238	>	int i, k;
1239
986	–	int i;
987	–
1240		// create the forceField
1241
1242		createFF();
#	Line 999 | Line 1251 | void SimSetup::sysObjectsCreation( void ){
1251
1252		#ifdef IS_MPI
1253		// divide the molecules among the processors
1254	<
1254	>
1255		mpiMolDivide();
1256		#endif //is_mpi
1257	<
1257	>
1258		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1259	<
1259	>
1260		makeSysArrays();
1261
1262		// make and initialize the molecules (all but atomic coordinates)
1263	<
1263	>
1264		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1017	–
1265
1266	<
1266	>	for (k = 0; k < nInfo; k++){
1267	>	info[k].identArray = new int[info[k].n_atoms];
1268	>	for (i = 0; i < info[k].n_atoms; i++){
1269	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1270	>	}
1271	>	}
1272		}
1273
1274
1275	<	void SimSetup::createFF( void ){
1275	>	void SimSetup::createFF(void){
1276	>	switch (ffCase){
1277	>	case FF_DUFF:
1278	>	the_ff = new DUFF();
1279	>	break;
1280
1281	<	switch( ffCase ){
1281	>	case FF_LJ:
1282	>	the_ff = new LJFF();
1283	>	break;
1284
1285	<	case FF_DUFF:
1286	<	the_ff = new DUFF();
1287	<	break;
1285	>	case FF_EAM:
1286	>	the_ff = new EAM_FF();
1287	>	break;
1288
1289	<	case FF_LJ:
1290	<	the_ff = new LJFF();
1291	<	break;
1289	>	case FF_H2O:
1290	>	the_ff = new WATER();
1291	>	break;
1292
1293	<	default:
1294	<	sprintf( painCave.errMsg,
1295	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1296	<	painCave.isFatal = 1;
1297	<	simError();
1293	>	default:
1294	>	sprintf(painCave.errMsg,
1295	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1296	>	painCave.isFatal = 1;
1297	>	simError();
1298		}
1299
1300		#ifdef IS_MPI
1301	<	strcpy( checkPointMsg, "ForceField creation successful" );
1301	>	strcpy(checkPointMsg, "ForceField creation successful");
1302		MPIcheckPoint();
1303		#endif // is_mpi
1046	–
1304		}
1305
1306
1307	<	void SimSetup::compList( void ){
1051	<
1307	>	void SimSetup::compList(void){
1308		int i;
1309	+	char* id;
1310	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1311	+	LinkedMolStamp* currentStamp = NULL;
1312	+	comp_stamps = new MoleculeStamp * [n_components];
1313	+	bool haveCutoffGroups;
1314
1315	<	comp_stamps = new MoleculeStamp*[n_components];
1316	<
1315	>	haveCutoffGroups = false;
1316	>
1317		// make an array of molecule stamps that match the components used.
1318		// also extract the used stamps out into a separate linked list
1319
1320	<	info->nComponents = n_components;
1321	<	info->componentsNmol = components_nmol;
1322	<	info->compStamps = comp_stamps;
1323	<	info->headStamp = new LinkedMolStamp();
1324	<
1325	<	char* id;
1065	<	LinkedMolStamp* headStamp = info->headStamp;
1066	<	LinkedMolStamp* currentStamp = NULL;
1067	<	for( i=0; i<n_components; i++ ){
1320	>	for (i = 0; i < nInfo; i++){
1321	>	info[i].nComponents = n_components;
1322	>	info[i].componentsNmol = components_nmol;
1323	>	info[i].compStamps = comp_stamps;
1324	>	info[i].headStamp = headStamp;
1325	>	}
1326
1327	+
1328	+	for (i = 0; i < n_components; i++){
1329		id = the_components[i]->getType();
1330		comp_stamps[i] = NULL;
1331	<
1331	>
1332		// check to make sure the component isn't already in the list
1333
1334	<	comp_stamps[i] = headStamp->match( id );
1335	<	if( comp_stamps[i] == NULL ){
1076	<
1334	>	comp_stamps[i] = headStamp->match(id);
1335	>	if (comp_stamps[i] == NULL){
1336		// extract the component from the list;
1337	<
1338	<	currentStamp = stamps->extractMolStamp( id );
1339	<	if( currentStamp == NULL ){
1340	<	sprintf( painCave.errMsg,
1341	<	"SimSetup error: Component \"%s\" was not found in the "
1342	<	"list of declared molecules\n",
1343	<	id );
1344	<	painCave.isFatal = 1;
1345	<	simError();
1337	>
1338	>	currentStamp = stamps->extractMolStamp(id);
1339	>	if (currentStamp == NULL){
1340	>	sprintf(painCave.errMsg,
1341	>	"SimSetup error: Component \"%s\" was not found in the "
1342	>	"list of declared molecules\n",
1343	>	id);
1344	>	painCave.isFatal = 1;
1345	>	simError();
1346		}
1347	<
1348	<	headStamp->add( currentStamp );
1349	<	comp_stamps[i] = headStamp->match( id );
1347	>
1348	>	headStamp->add(currentStamp);
1349	>	comp_stamps[i] = headStamp->match(id);
1350		}
1351	+
1352	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1353	+	haveCutoffGroups = true;
1354		}
1355	+
1356	+	for (i = 0; i < nInfo; i++)
1357	+	info[i].haveCutoffGroups = haveCutoffGroups;
1358
1359		#ifdef IS_MPI
1360	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1360	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1361		MPIcheckPoint();
1362		#endif // is_mpi
1098	–
1099	–
1363		}
1364
1365	<	void SimSetup::calcSysValues( void ){
1366	<	int i, j, k;
1365	>	void SimSetup::calcSysValues(void){
1366	>	int i;
1367
1368	+	int* molMembershipArray;
1369
1370		tot_atoms = 0;
1371		tot_bonds = 0;
1372		tot_bends = 0;
1373		tot_torsions = 0;
1374	<	for( i=0; i<n_components; i++ ){
1375	<
1376	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1377	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1378	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1374	>	tot_rigid = 0;
1375	>	for (i = 0; i < n_components; i++){
1376	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1377	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1378	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1379		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1380	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1381		}
1382	<
1382	>
1383		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1384	+	molMembershipArray = new int[tot_atoms];
1385
1386	<	info->n_atoms = tot_atoms;
1387	<	info->n_bonds = tot_bonds;
1388	<	info->n_bends = tot_bends;
1389	<	info->n_torsions = tot_torsions;
1390	<	info->n_SRI = tot_SRI;
1391	<	info->n_mol = tot_nmol;
1392	<
1393	<	info->molMembershipArray = new int[tot_atoms];
1386	>	for (i = 0; i < nInfo; i++){
1387	>	info[i].n_atoms = tot_atoms;
1388	>	info[i].n_bonds = tot_bonds;
1389	>	info[i].n_bends = tot_bends;
1390	>	info[i].n_torsions = tot_torsions;
1391	>	info[i].n_SRI = tot_SRI;
1392	>	info[i].n_mol = tot_nmol;
1393	>
1394	>	info[i].molMembershipArray = molMembershipArray;
1395	>	}
1396		}
1397
1130	–
1398		#ifdef IS_MPI
1399
1400	<	void SimSetup::mpiMolDivide( void ){
1134	<
1400	>	void SimSetup::mpiMolDivide(void){
1401		int i, j, k;
1402		int localMol, allMol;
1403		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1404	+	int local_rigid;
1405	+	vector<int> globalMolIndex;
1406
1407	<	mpiSim = new mpiSimulation( info );
1140	<
1141	<	globalIndex = mpiSim->divideLabor();
1407	>	mpiSim = new mpiSimulation(info);
1408
1409	+	mpiSim->divideLabor();
1410	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1411	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1412	+
1413		// set up the local variables
1414	<
1414	>
1415		mol2proc = mpiSim->getMolToProcMap();
1416		molCompType = mpiSim->getMolComponentType();
1417	<
1417	>
1418		allMol = 0;
1419		localMol = 0;
1420		local_atoms = 0;
1421		local_bonds = 0;
1422		local_bends = 0;
1423		local_torsions = 0;
1424	<	globalAtomIndex = 0;
1424	>	local_rigid = 0;
1425	>	globalAtomCounter = 0;
1426
1427	<
1428	<	for( i=0; i<n_components; i++ ){
1429	<
1430	<	for( j=0; j<components_nmol[i]; j++ ){
1431	<
1432	<	if( mol2proc[allMol] == worldRank ){
1433	<
1434	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1435	<	local_bonds +=    comp_stamps[i]->getNBonds();
1165	<	local_bends +=    comp_stamps[i]->getNBends();
1166	<	local_torsions += comp_stamps[i]->getNTorsions();
1167	<	localMol++;
1427	>	for (i = 0; i < n_components; i++){
1428	>	for (j = 0; j < components_nmol[i]; j++){
1429	>	if (mol2proc[allMol] == worldRank){
1430	>	local_atoms += comp_stamps[i]->getNAtoms();
1431	>	local_bonds += comp_stamps[i]->getNBonds();
1432	>	local_bends += comp_stamps[i]->getNBends();
1433	>	local_torsions += comp_stamps[i]->getNTorsions();
1434	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1435	>	localMol++;
1436		}
1437	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1438	<	info->molMembershipArray[globalAtomIndex] = allMol;
1439	<	globalAtomIndex++;
1437	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1438	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1439	>	globalAtomCounter++;
1440		}
1441
1442	<	allMol++;
1442	>	allMol++;
1443		}
1444		}
1445		local_SRI = local_bonds + local_bends + local_torsions;
1446	<
1447	<	info->n_atoms = mpiSim->getMyNlocal();
1446	>
1447	>	info[0].n_atoms = mpiSim->getMyNlocal();
1448
1449	<	if( local_atoms != info->n_atoms ){
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1452	<	" localAtom (%d) are not equal.\n",
1453	<	info->n_atoms,
1454	<	local_atoms );
1449	>
1450	>	if (local_atoms != info[0].n_atoms){
1451	>	sprintf(painCave.errMsg,
1452	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1453	>	"\tlocalAtom (%d) are not equal.\n",
1454	>	info[0].n_atoms, local_atoms);
1455		painCave.isFatal = 1;
1456		simError();
1457		}
1458
1459	<	info->n_bonds = local_bonds;
1460	<	info->n_bends = local_bends;
1461	<	info->n_torsions = local_torsions;
1462	<	info->n_SRI = local_SRI;
1463	<	info->n_mol = localMol;
1459	>	info[0].n_bonds = local_bonds;
1460	>	info[0].n_bends = local_bends;
1461	>	info[0].n_torsions = local_torsions;
1462	>	info[0].n_SRI = local_SRI;
1463	>	info[0].n_mol = localMol;
1464
1465	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1465	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1466		MPIcheckPoint();
1467		}
1468	<
1468	>
1469		#endif // is_mpi
1470
1471
1472	<	void SimSetup::makeSysArrays( void ){
1473	<	int i, j, k;
1472	>	void SimSetup::makeSysArrays(void){
1473	>
1474	>	#ifndef IS_MPI
1475	>	int k, j;
1476	>	#endif // is_mpi
1477	>	int i, l;
1478
1479	+	Atom** the_atoms;
1480	+	Molecule* the_molecules;
1481
1482	<	// create the atom and short range interaction arrays
1482	>	for (l = 0; l < nInfo; l++){
1483	>	// create the atom and short range interaction arrays
1484
1485	<	Atom::createArrays(info->n_atoms);
1486	<	the_atoms = new Atom*[info->n_atoms];
1487	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1485	>	the_atoms = new Atom * [info[l].n_atoms];
1486	>	the_molecules = new Molecule[info[l].n_mol];
1487	>	int molIndex;
1488
1489	<	// initialize the molecule's stampID's
1489	>	// initialize the molecule's stampID's
1490
1491		#ifdef IS_MPI
1218	–
1492
1493	<	molIndex = 0;
1494	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1495	<
1496	<	if(mol2proc[i] == worldRank ){
1497	<	the_molecules[molIndex].setStampID( molCompType[i] );
1498	<	the_molecules[molIndex].setMyIndex( molIndex );
1499	<	the_molecules[molIndex].setGlobalIndex( i );
1500	<	molIndex++;
1493	>
1494	>	molIndex = 0;
1495	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1496	>	if (mol2proc[i] == worldRank){
1497	>	the_molecules[molIndex].setStampID(molCompType[i]);
1498	>	the_molecules[molIndex].setMyIndex(molIndex);
1499	>	the_molecules[molIndex].setGlobalIndex(i);
1500	>	molIndex++;
1501	>	}
1502		}
1229	–	}
1503
1504		#else // is_mpi
1505	<
1506	<	molIndex = 0;
1507	<	globalAtomIndex = 0;
1508	<	for(i=0; i<n_components; i++){
1509	<	for(j=0; j<components_nmol[i]; j++ ){
1510	<	the_molecules[molIndex].setStampID( i );
1511	<	the_molecules[molIndex].setMyIndex( molIndex );
1512	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1513	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1514	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1515	<	globalAtomIndex++;
1505	>
1506	>	molIndex = 0;
1507	>	globalAtomCounter = 0;
1508	>	for (i = 0; i < n_components; i++){
1509	>	for (j = 0; j < components_nmol[i]; j++){
1510	>	the_molecules[molIndex].setStampID(i);
1511	>	the_molecules[molIndex].setMyIndex(molIndex);
1512	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1513	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1514	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1515	>	globalAtomCounter++;
1516	>	}
1517	>	molIndex++;
1518		}
1244	–	molIndex++;
1519		}
1246	–	}
1247	–
1520
1521	+
1522		#endif // is_mpi
1523
1524	+	info[l].globalExcludes = new int;
1525	+	info[l].globalExcludes[0] = 0;
1526	+
1527	+	// set the arrays into the SimInfo object
1528
1529	<	if( info->n_SRI ){
1529	>	info[l].atoms = the_atoms;
1530	>	info[l].molecules = the_molecules;
1531	>	info[l].nGlobalExcludes = 0;
1532
1533	<	Exclude::createArray(info->n_SRI);
1255	<	the_excludes = new Exclude*[info->n_SRI];
1256	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1257	<	info->globalExcludes = new int;
1258	<	info->n_exclude = info->n_SRI;
1533	>	the_ff->setSimInfo(info);
1534		}
1535	<	else{
1261	<
1262	<	Exclude::createArray( 1 );
1263	<	the_excludes = new Exclude*;
1264	<	the_excludes[0] = new Exclude(0);
1265	<	the_excludes[0]->setPair( 0,0 );
1266	<	info->globalExcludes = new int;
1267	<	info->globalExcludes[0] = 0;
1268	<	info->n_exclude = 0;
1269	<	}
1535	>	}
1536
1537	<	// set the arrays into the SimInfo object
1537	>	void SimSetup::makeIntegrator(void){
1538	>	int k;
1539
1540	<	info->atoms = the_atoms;
1541	<	info->molecules = the_molecules;
1542	<	info->nGlobalExcludes = 0;
1543	<	info->excludes = the_excludes;
1540	>	NVE<RealIntegrator>* myNVE = NULL;
1541	>	NVT<RealIntegrator>* myNVT = NULL;
1542	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1543	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1544	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1545	>
1546	>	for (k = 0; k < nInfo; k++){
1547	>	switch (ensembleCase){
1548	>	case NVE_ENS:
1549	>	if (globals->haveZconstraints()){
1550	>	setupZConstraint(info[k]);
1551	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1552	>	}
1553	>	else{
1554	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1555	>	}
1556	>
1557	>	info->the_integrator = myNVE;
1558	>	break;
1559
1560	<	the_ff->setSimInfo( info );
1560	>	case NVT_ENS:
1561	>	if (globals->haveZconstraints()){
1562	>	setupZConstraint(info[k]);
1563	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1564	>	}
1565	>	else
1566	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1567
1568	<	}
1568	>	myNVT->setTargetTemp(globals->getTargetTemp());
1569
1570	<	void SimSetup::makeIntegrator( void ){
1570	>	if (globals->haveTauThermostat())
1571	>	myNVT->setTauThermostat(globals->getTauThermostat());
1572	>	else{
1573	>	sprintf(painCave.errMsg,
1574	>	"SimSetup error: If you use the NVT\n"
1575	>	"\tensemble, you must set tauThermostat.\n");
1576	>	painCave.isFatal = 1;
1577	>	simError();
1578	>	}
1579
1580	<	NVT*  myNVT = NULL;
1581	<	NPTi* myNPTi = NULL;
1286	<	NPTf* myNPTf = NULL;
1287	<	NPTim* myNPTim = NULL;
1288	<	NPTfm* myNPTfm = NULL;
1580	>	info->the_integrator = myNVT;
1581	>	break;
1582
1583	<	switch( ensembleCase ){
1583	>	case NPTi_ENS:
1584	>	if (globals->haveZconstraints()){
1585	>	setupZConstraint(info[k]);
1586	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1587	>	}
1588	>	else
1589	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1590
1591	<	case NVE_ENS:
1293	<	new NVE( info, the_ff );
1294	<	break;
1591	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1592
1593	<	case NVT_ENS:
1594	<	myNVT = new NVT( info, the_ff );
1595	<	myNVT->setTargetTemp(globals->getTargetTemp());
1593	>	if (globals->haveTargetPressure())
1594	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1595	>	else{
1596	>	sprintf(painCave.errMsg,
1597	>	"SimSetup error: If you use a constant pressure\n"
1598	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1599	>	painCave.isFatal = 1;
1600	>	simError();
1601	>	}
1602
1603	<	if (globals->haveTauThermostat())
1604	<	myNVT->setTauThermostat(globals->getTauThermostat());
1603	>	if (globals->haveTauThermostat())
1604	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1605	>	else{
1606	>	sprintf(painCave.errMsg,
1607	>	"SimSetup error: If you use an NPT\n"
1608	>	"\tensemble, you must set tauThermostat.\n");
1609	>	painCave.isFatal = 1;
1610	>	simError();
1611	>	}
1612
1613	<	else {
1614	<	sprintf( painCave.errMsg,
1615	<	"SimSetup error: If you use the NVT\n"
1616	<	"    ensemble, you must set tauThermostat.\n");
1617	<	painCave.isFatal = 1;
1618	<	simError();
1619	<	}
1620	<	break;
1613	>	if (globals->haveTauBarostat())
1614	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1615	>	else{
1616	>	sprintf(painCave.errMsg,
1617	>	"SimSetup error: If you use an NPT\n"
1618	>	"\tensemble, you must set tauBarostat.\n");
1619	>	painCave.isFatal = 1;
1620	>	simError();
1621	>	}
1622
1623	<	case NPTi_ENS:
1624	<	myNPTi = new NPTi( info, the_ff );
1314	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1623	>	info->the_integrator = myNPTi;
1624	>	break;
1625
1626	<	if (globals->haveTargetPressure())
1627	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1628	<	else {
1629	<	sprintf( painCave.errMsg,
1630	<	"SimSetup error: If you use a constant pressure\n"
1631	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1632	<	painCave.isFatal = 1;
1323	<	simError();
1324	<	}
1325	<
1326	<	if( globals->haveTauThermostat() )
1327	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	<	else{
1329	<	sprintf( painCave.errMsg,
1330	<	"SimSetup error: If you use an NPT\n"
1331	<	"    ensemble, you must set tauThermostat.\n");
1332	<	painCave.isFatal = 1;
1333	<	simError();
1334	<	}
1626	>	case NPTf_ENS:
1627	>	if (globals->haveZconstraints()){
1628	>	setupZConstraint(info[k]);
1629	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1630	>	}
1631	>	else
1632	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1633
1634	<	if( globals->haveTauBarostat() )
1337	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	<	else{
1339	<	sprintf( painCave.errMsg,
1340	<	"SimSetup error: If you use an NPT\n"
1341	<	"    ensemble, you must set tauBarostat.\n");
1342	<	painCave.isFatal = 1;
1343	<	simError();
1344	<	}
1345	<	break;
1634	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1635
1636	<	case NPTf_ENS:
1637	<	myNPTf = new NPTf( info, the_ff );
1638	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1636	>	if (globals->haveTargetPressure())
1637	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1638	>	else{
1639	>	sprintf(painCave.errMsg,
1640	>	"SimSetup error: If you use a constant pressure\n"
1641	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1642	>	painCave.isFatal = 1;
1643	>	simError();
1644	>	}
1645
1646	<	if (globals->haveTargetPressure())
1647	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	<	else {
1354	<	sprintf( painCave.errMsg,
1355	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	<	painCave.isFatal = 1;
1358	<	simError();
1359	<	}
1646	>	if (globals->haveTauThermostat())
1647	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1648
1649	<	if( globals->haveTauThermostat() )
1650	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1651	<	else{
1652	<	sprintf( painCave.errMsg,
1653	<	"SimSetup error: If you use an NPT\n"
1654	<	"    ensemble, you must set tauThermostat.\n");
1655	<	painCave.isFatal = 1;
1368	<	simError();
1369	<	}
1649	>	else{
1650	>	sprintf(painCave.errMsg,
1651	>	"SimSetup error: If you use an NPT\n"
1652	>	"\tensemble, you must set tauThermostat.\n");
1653	>	painCave.isFatal = 1;
1654	>	simError();
1655	>	}
1656
1657	<	if( globals->haveTauBarostat() )
1658	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	<	else{
1374	<	sprintf( painCave.errMsg,
1375	<	"SimSetup error: If you use an NPT\n"
1376	<	"    ensemble, you must set tauBarostat.\n");
1377	<	painCave.isFatal = 1;
1378	<	simError();
1379	<	}
1380	<	break;
1381	<
1382	<	case NPTim_ENS:
1383	<	myNPTim = new NPTim( info, the_ff );
1384	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1385	<
1386	<	if (globals->haveTargetPressure())
1387	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1388	<	else {
1389	<	sprintf( painCave.errMsg,
1390	<	"SimSetup error: If you use a constant pressure\n"
1391	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1392	<	painCave.isFatal = 1;
1393	<	simError();
1394	<	}
1395	<
1396	<	if( globals->haveTauThermostat() )
1397	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	<	else{
1399	<	sprintf( painCave.errMsg,
1400	<	"SimSetup error: If you use an NPT\n"
1401	<	"    ensemble, you must set tauThermostat.\n");
1402	<	painCave.isFatal = 1;
1403	<	simError();
1404	<	}
1657	>	if (globals->haveTauBarostat())
1658	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1659
1660	<	if( globals->haveTauBarostat() )
1661	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1662	<	else{
1663	<	sprintf( painCave.errMsg,
1664	<	"SimSetup error: If you use an NPT\n"
1665	<	"    ensemble, you must set tauBarostat.\n");
1666	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<	break;
1660	>	else{
1661	>	sprintf(painCave.errMsg,
1662	>	"SimSetup error: If you use an NPT\n"
1663	>	"\tensemble, you must set tauBarostat.\n");
1664	>	painCave.isFatal = 1;
1665	>	simError();
1666	>	}
1667
1668	<	case NPTfm_ENS:
1669	<	myNPTfm = new NPTfm( info, the_ff );
1419	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1668	>	info->the_integrator = myNPTf;
1669	>	break;
1670
1671	<	if (globals->haveTargetPressure())
1672	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1673	<	else {
1674	<	sprintf( painCave.errMsg,
1675	<	"SimSetup error: If you use a constant pressure\n"
1676	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1677	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1430	<
1431	<	if( globals->haveTauThermostat() )
1432	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	<	else{
1434	<	sprintf( painCave.errMsg,
1435	<	"SimSetup error: If you use an NPT\n"
1436	<	"    ensemble, you must set tauThermostat.\n");
1437	<	painCave.isFatal = 1;
1438	<	simError();
1439	<	}
1671	>	case NPTxyz_ENS:
1672	>	if (globals->haveZconstraints()){
1673	>	setupZConstraint(info[k]);
1674	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1675	>	}
1676	>	else
1677	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1678
1679	<	if( globals->haveTauBarostat() )
1442	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	<	else{
1444	<	sprintf( painCave.errMsg,
1445	<	"SimSetup error: If you use an NPT\n"
1446	<	"    ensemble, you must set tauBarostat.\n");
1447	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1450	<	break;
1679	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1680
1681	<	default:
1682	<	sprintf( painCave.errMsg,
1683	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1684	<	painCave.isFatal = 1;
1685	<	simError();
1686	<	}
1681	>	if (globals->haveTargetPressure())
1682	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1683	>	else{
1684	>	sprintf(painCave.errMsg,
1685	>	"SimSetup error: If you use a constant pressure\n"
1686	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1687	>	painCave.isFatal = 1;
1688	>	simError();
1689	>	}
1690
1691	+	if (globals->haveTauThermostat())
1692	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1693	+	else{
1694	+	sprintf(painCave.errMsg,
1695	+	"SimSetup error: If you use an NPT\n"
1696	+	"\tensemble, you must set tauThermostat.\n");
1697	+	painCave.isFatal = 1;
1698	+	simError();
1699	+	}
1700	+
1701	+	if (globals->haveTauBarostat())
1702	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1703	+	else{
1704	+	sprintf(painCave.errMsg,
1705	+	"SimSetup error: If you use an NPT\n"
1706	+	"\tensemble, you must set tauBarostat.\n");
1707	+	painCave.isFatal = 1;
1708	+	simError();
1709	+	}
1710	+
1711	+	info->the_integrator = myNPTxyz;
1712	+	break;
1713	+
1714	+	default:
1715	+	sprintf(painCave.errMsg,
1716	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1717	+	painCave.isFatal = 1;
1718	+	simError();
1719	+	}
1720	+	}
1721		}
1722
1723	<	void SimSetup::initFortran( void ){
1723	>	void SimSetup::initFortran(void){
1724	>	info[0].refreshSim();
1725
1726	<	info->refreshSim();
1727	<
1465	<	if( !strcmp( info->mixingRule, "standard") ){
1466	<	the_ff->initForceField( LB_MIXING_RULE );
1726	>	if (!strcmp(info[0].mixingRule, "standard")){
1727	>	the_ff->initForceField(LB_MIXING_RULE);
1728		}
1729	<	else if( !strcmp( info->mixingRule, "explicit") ){
1730	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1729	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1730	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1731		}
1732		else{
1733	<	sprintf( painCave.errMsg,
1734	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	<	info->mixingRule );
1733	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1734	>	info[0].mixingRule);
1735		painCave.isFatal = 1;
1736		simError();
1737		}
1738
1739
1740		#ifdef IS_MPI
1741	<	strcpy( checkPointMsg,
1482	<	"Successfully intialized the mixingRule for Fortran." );
1741	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1742		MPIcheckPoint();
1743		#endif // is_mpi
1744	+	}
1745
1746	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1747	+	int nZConstraints;
1748	+	ZconStamp** zconStamp;
1749	+
1750	+	if (globals->haveZconstraintTime()){
1751	+	//add sample time of z-constraint  into SimInfo's property list
1752	+	DoubleData* zconsTimeProp = new DoubleData();
1753	+	zconsTimeProp->setID(ZCONSTIME_ID);
1754	+	zconsTimeProp->setData(globals->getZconsTime());
1755	+	theInfo.addProperty(zconsTimeProp);
1756	+	}
1757	+	else{
1758	+	sprintf(painCave.errMsg,
1759	+	"ZConstraint error: If you use a ZConstraint,\n"
1760	+	"\tyou must set zconsTime.\n");
1761	+	painCave.isFatal = 1;
1762	+	simError();
1763	+	}
1764	+
1765	+	//push zconsTol into siminfo, if user does not specify
1766	+	//value for zconsTol, a default value will be used
1767	+	DoubleData* zconsTol = new DoubleData();
1768	+	zconsTol->setID(ZCONSTOL_ID);
1769	+	if (globals->haveZconsTol()){
1770	+	zconsTol->setData(globals->getZconsTol());
1771	+	}
1772	+	else{
1773	+	double defaultZConsTol = 0.01;
1774	+	sprintf(painCave.errMsg,
1775	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1776	+	"\tOOPSE will use a default value of %f.\n"
1777	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1778	+	defaultZConsTol);
1779	+	painCave.isFatal = 0;
1780	+	simError();
1781	+
1782	+	zconsTol->setData(defaultZConsTol);
1783	+	}
1784	+	theInfo.addProperty(zconsTol);
1785	+
1786	+	//set Force Subtraction Policy
1787	+	StringData* zconsForcePolicy = new StringData();
1788	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1789	+
1790	+	if (globals->haveZconsForcePolicy()){
1791	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1792	+	}
1793	+	else{
1794	+	sprintf(painCave.errMsg,
1795	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1796	+	"\tOOPSE will use PolicyByMass.\n"
1797	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1798	+	painCave.isFatal = 0;
1799	+	simError();
1800	+	zconsForcePolicy->setData("BYMASS");
1801	+	}
1802	+
1803	+	theInfo.addProperty(zconsForcePolicy);
1804	+
1805	+	//set zcons gap
1806	+	DoubleData* zconsGap = new DoubleData();
1807	+	zconsGap->setID(ZCONSGAP_ID);
1808	+
1809	+	if (globals->haveZConsGap()){
1810	+	zconsGap->setData(globals->getZconsGap());
1811	+	theInfo.addProperty(zconsGap);
1812	+	}
1813	+
1814	+	//set zcons fixtime
1815	+	DoubleData* zconsFixtime = new DoubleData();
1816	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1817	+
1818	+	if (globals->haveZConsFixTime()){
1819	+	zconsFixtime->setData(globals->getZconsFixtime());
1820	+	theInfo.addProperty(zconsFixtime);
1821	+	}
1822	+
1823	+	//set zconsUsingSMD
1824	+	IntData* zconsUsingSMD = new IntData();
1825	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1826	+
1827	+	if (globals->haveZConsUsingSMD()){
1828	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1829	+	theInfo.addProperty(zconsUsingSMD);
1830	+	}
1831	+
1832	+	//Determine the name of ouput file and add it into SimInfo's property list
1833	+	//Be careful, do not use inFileName, since it is a pointer which
1834	+	//point to a string at master node, and slave nodes do not contain that string
1835	+
1836	+	string zconsOutput(theInfo.finalName);
1837	+
1838	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1839	+
1840	+	StringData* zconsFilename = new StringData();
1841	+	zconsFilename->setID(ZCONSFILENAME_ID);
1842	+	zconsFilename->setData(zconsOutput);
1843	+
1844	+	theInfo.addProperty(zconsFilename);
1845	+
1846	+	//setup index, pos and other parameters of z-constraint molecules
1847	+	nZConstraints = globals->getNzConstraints();
1848	+	theInfo.nZconstraints = nZConstraints;
1849	+
1850	+	zconStamp = globals->getZconStamp();
1851	+	ZConsParaItem tempParaItem;
1852	+
1853	+	ZConsParaData* zconsParaData = new ZConsParaData();
1854	+	zconsParaData->setID(ZCONSPARADATA_ID);
1855	+
1856	+	for (int i = 0; i < nZConstraints; i++){
1857	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1858	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1859	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1860	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1861	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1862	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1863	+	zconsParaData->addItem(tempParaItem);
1864	+	}
1865	+
1866	+	//check the uniqueness of index
1867	+	if(!zconsParaData->isIndexUnique()){
1868	+	sprintf(painCave.errMsg,
1869	+	"ZConstraint Error: molIndex is not unique!\n");
1870	+	painCave.isFatal = 1;
1871	+	simError();
1872	+	}
1873	+
1874	+	//sort the parameters by index of molecules
1875	+	zconsParaData->sortByIndex();
1876	+
1877	+	//push data into siminfo, therefore, we can retrieve later
1878	+	theInfo.addProperty(zconsParaData);
1879		}
1880	+
1881	+	void SimSetup::makeMinimizer(){
1882	+
1883	+	OOPSEMinimizer* myOOPSEMinimizer;
1884	+	MinimizerParameterSet* param;
1885	+	char minimizerName[100];
1886	+
1887	+	for (int i = 0; i < nInfo; i++){
1888	+
1889	+	//prepare parameter set for minimizer
1890	+	param = new MinimizerParameterSet();
1891	+	param->setDefaultParameter();
1892	+
1893	+	if (globals->haveMinimizer()){
1894	+	param->setFTol(globals->getMinFTol());
1895	+	}
1896	+
1897	+	if (globals->haveMinGTol()){
1898	+	param->setGTol(globals->getMinGTol());
1899	+	}
1900	+
1901	+	if (globals->haveMinMaxIter()){
1902	+	param->setMaxIteration(globals->getMinMaxIter());
1903	+	}
1904	+
1905	+	if (globals->haveMinWriteFrq()){
1906	+	param->setMaxIteration(globals->getMinMaxIter());
1907	+	}
1908	+
1909	+	if (globals->haveMinWriteFrq()){
1910	+	param->setWriteFrq(globals->getMinWriteFrq());
1911	+	}
1912	+
1913	+	if (globals->haveMinStepSize()){
1914	+	param->setStepSize(globals->getMinStepSize());
1915	+	}
1916	+
1917	+	if (globals->haveMinLSMaxIter()){
1918	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1919	+	}
1920	+
1921	+	if (globals->haveMinLSTol()){
1922	+	param->setLineSearchTol(globals->getMinLSTol());
1923	+	}
1924	+
1925	+	strcpy(minimizerName, globals->getMinimizer());
1926	+
1927	+	if (!strcasecmp(minimizerName, "CG")){
1928	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1929	+	}
1930	+	else if (!strcasecmp(minimizerName, "SD")){
1931	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1932	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1933	+	}
1934	+	else{
1935	+	sprintf(painCave.errMsg,
1936	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1937	+	painCave.isFatal = 0;
1938	+	simError();
1939	+
1940	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1941	+	}
1942	+	info[i].the_integrator = myOOPSEMinimizer;
1943	+
1944	+	//store the minimizer into simInfo
1945	+	info[i].the_minimizer = myOOPSEMinimizer;
1946	+	info[i].has_minimizer = true;
1947	+	}
1948	+
1949	+	}

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