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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 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 20 | Line 24
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
27	>	#define NPTxyz_ENS     4
28
26	–	#define FF_DUFF 0
27	–	#define FF_LJ   1
28	–	#define FF_EAM  2
29
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 49 | 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;
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 ){
60	<
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();
88	<	mpiEventLoop();
89	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
96	–	int i, j, k, globalAtomIndex;
97	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 104 | 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	<	if( !isInfoArray ) initSystemCoords();
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();
117	–
118	–	// make the integrator
150
120	–	makeIntegrator();
121	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 127 | 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
131	–
166		}
167
168
169	<	void SimSetup::makeMolecules( void ){
170	<
171	<	int k,l;
172	<	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	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	<
195	>	set<int> skipList;
196	>
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200	>
201		//init the forceField paramters
202
203		the_ff->readParams();
204
157	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
161	<
162	<	for(k=0; k<nInfo; k++){
163	<
164	<	the_ff->setSimInfo( &(info[k]) );
207	>	int nMembers, nNew, rb1, rb2;
208
209	+	for (k = 0; k < nInfo; k++){
210	+	the_ff->setSimInfo(&(info[k]));
211	+
212		atomOffset = 0;
213	<	excludeOffset = 0;
214	<	for(i=0; i<info[k].n_mol; i++){
169	<
213	>
214	>	for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
219	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
220	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223	>
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	–	molInfo.myBends = new Bend*[molInfo.nBends];
182	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new Bend*[molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248	<
249	<	for(j=0; j<molInfo.nAtoms; j++){
250	<
251	<	currentAtom = comp_stamps[stampID]->getAtom( j );
252	<	if( currentAtom->haveOrientation() ){
253	<
254	<	dAtom = new DirectionalAtom( (j + atomOffset),
255	<	info[k].getConfiguration() );
256	<	info[k].n_oriented++;
257	<	molInfo.myAtoms[j] = dAtom;
258	<
259	<	ux = currentAtom->getOrntX();
260	<	uy = currentAtom->getOrntY();
261	<	uz = currentAtom->getOrntZ();
262	<
263	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
264	<
265	<	u = sqrt( uSqr );
266	<	ux = ux / u;
267	<	uy = uy / u;
268	<	uz = uz / u;
269	<
270	<	dAtom->setSUx( ux );
271	<	dAtom->setSUy( uy );
272	<	dAtom->setSUz( uz );
273	<	}
274	<	else{
275	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	<	info[k].getConfiguration() );
218	<	}
219	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	<
248	>
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251	>
252	>	if (currentAtom->haveOrientation()){
253	>	dAtom = new DirectionalAtom((j + atomOffset),
254	>	info[k].getConfiguration());
255	>	info[k].n_oriented++;
256	>	molInfo.myAtoms[j] = dAtom;
257	>
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261	>
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265	>
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270	>
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272	>
273	>	}
274	>
275	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277	<
278	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
279	<
277	>
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279	>
280		#endif // is_mpi
281		}
282	<
283	<	// make the bonds
284	<	for(j=0; j<molInfo.nBonds; j++){
285	<
286	<	currentBond = comp_stamps[stampID]->getBond( j );
287	<	theBonds[j].a = currentBond->getA() + atomOffset;
288	<	theBonds[j].b = currentBond->getB() + atomOffset;
289	<
290	<	exI = theBonds[j].a;
291	<	exJ = theBonds[j].b;
292	<
293	<	// exclude_I must always be the smaller of the pair
294	<	if( exI > exJ ){
295	<	tempEx = exI;
296	<	exI = exJ;
297	<	exJ = tempEx;
298	<	}
299	<	#ifdef IS_MPI
300	<	tempEx = exI;
246	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	<	tempEx = exJ;
248	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	<
250	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	<	#else  // isn't MPI
252	<
253	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	<	#endif  //is_mpi
282	>
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288	>
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291	>
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299	>
300	>	info[k].excludes->addPair(exI, exJ);
301		}
302	<	excludeOffset += molInfo.nBonds;
257	<
302	>
303		//make the bends
304	<	for(j=0; j<molInfo.nBends; j++){
305	<
306	<	currentBend = comp_stamps[stampID]->getBend( j );
307	<	theBends[j].a = currentBend->getA() + atomOffset;
308	<	theBends[j].b = currentBend->getB() + atomOffset;
309	<	theBends[j].c = currentBend->getC() + atomOffset;
310	<
311	<	if( currentBend->haveExtras() ){
312	<
313	<	extras = currentBend->getExtras();
314	<	current_extra = extras;
315	<
316	<	while( current_extra != NULL ){
317	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
318	<
319	<	switch( current_extra->getType() ){
320	<
321	<	case 0:
322	<	theBends[j].ghost =
323	<	current_extra->getInt() + atomOffset;
324	<	theBends[j].isGhost = 1;
325	<	break;
326	<
327	<	case 1:
328	<	theBends[j].ghost =
329	<	(int)current_extra->getDouble() + atomOffset;
330	<	theBends[j].isGhost = 1;
331	<	break;
332	<
333	<	default:
334	<	sprintf( painCave.errMsg,
335	<	"SimSetup Error: ghostVectorSource was neither a "
336	<	"double nor an int.\n"
337	<	"-->Bend[%d] in %s\n",
338	<	j, comp_stamps[stampID]->getID() );
339	<	painCave.isFatal = 1;
340	<	simError();
341	<	}
342	<	}
343	<
344	<	else{
345	<
346	<	sprintf( painCave.errMsg,
347	<	"SimSetup Error: unhandled bend assignment:\n"
348	<	"    -->%s in Bend[%d] in %s\n",
349	<	current_extra->getlhs(),
350	<	j, comp_stamps[stampID]->getID() );
351	<	painCave.isFatal = 1;
352	<	simError();
353	<	}
354	<
355	<	current_extra = current_extra->getNext();
311	<	}
312	<	}
313	<
314	<	if( !theBends[j].isGhost ){
315	<
316	<	exI = theBends[j].a;
317	<	exJ = theBends[j].c;
318	<	}
319	<	else{
320	<
321	<	exI = theBends[j].a;
322	<	exJ = theBends[j].b;
323	<	}
324	<
325	<	// exclude_I must always be the smaller of the pair
326	<	if( exI > exJ ){
327	<	tempEx = exI;
328	<	exI = exJ;
329	<	exJ = tempEx;
330	<	}
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309	>
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313	>
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321	>
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327	>
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346	>
347	>	current_extra = current_extra->getNext();
348	>	}
349	>	}
350	>
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
361	<
362	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
363	<	#else  // isn't MPI
364	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
365	<	#endif  //is_mpi
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364	>
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
386	<	excludeOffset += molInfo.nBends;
387	<
388	<	for(j=0; j<molInfo.nTorsions; j++){
389	<
390	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
391	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
392	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
393	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
394	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
395	<
396	<	exI = theTorsions[j].a;
397	<	exJ = theTorsions[j].d;
398	<
355	<	// exclude_I must always be the smaller of the pair
356	<	if( exI > exJ ){
357	<	tempEx = exI;
358	<	exI = exJ;
359	<	exJ = tempEx;
360	<	}
386	>
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393	>
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398	>
399		#ifdef IS_MPI
400	<	tempEx = exI;
401	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	<	tempEx = exJ;
403	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
404	<
405	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
406	<	#else  // isn't MPI
407	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
408	<	#endif  //is_mpi
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410	>
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417		}
418	<	excludeOffset += molInfo.nTorsions;
418	>
419
420	+	molInfo.myRigidBodies.clear();
421
422	<	// send the arrays off to the forceField for init.
423	<
424	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
425	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
426	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
427	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423	>
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487	>	}
488
489	+
490	+	//create cutoff group for molecule
491	+
492	+	cutoffAtomSet.clear();
493	+	molInfo.myCutoffGroups.clear();
494
495	<	info[k].molecules[i].initialize( molInfo );
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	+	nMembers = currentCutoffGroup->getNMembers();
499	+
500	+	myCutoffGroup = new CutoffGroup();
501	+
502	+	for (int cg = 0; cg < nMembers; cg++) {
503	+
504	+	// molI is atom numbering inside this molecule
505	+	molI = currentCutoffGroup->getMember(cg);
506	+
507	+	// tempI is atom numbering on local processor
508	+	tempI = molI + atomOffset;
509	+
510	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	+
512	+	cutoffAtomSet.insert(tempI);
513	+	}
514	+
515	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	+
518	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	+
520	+	for(j = 0; j < molInfo.nAtoms; j++){
521	+
522	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	+	myCutoffGroup = new CutoffGroup();
524	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	+	}
527	+
528	+	}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537
538	+
539	+	for (j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	#ifdef IS_MPI
542	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	+	#else
544	+	slJ = j+atomOffset;
545	+	#endif
546	+
547	+	// if they aren't on the skip list, then they can be integrated
548	+
549	+	if (skipList.find(slJ) == skipList.end()) {
550	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	+	info[k].integrableObjects.push_back(mySD);
552	+	molInfo.myIntegrableObjects.push_back(mySD);
553	+	}
554	+	}
555	+
556	+	// all rigid bodies are integrated:
557	+
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	+	theTorsions);
572	+
573	+	info[k].molecules[i].initialize(molInfo);
574	+
575	+
576		atomOffset += molInfo.nAtoms;
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582	<
582	>
583		#ifdef IS_MPI
584	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
397	–
398	–	// clean up the forcefield
587
400	–	the_ff->calcRcut();
401	–	the_ff->cleanMe();
402	–
588		}
589
590	<	void SimSetup::initFromBass( void ){
406	<
590	>	void SimSetup::initFromBass(void){
591		int i, j, k;
592		int n_cells;
593		double cellx, celly, cellz;
#	Line 417 | Line 601 | void SimSetup::initFromBass( void ){
601		vel[1] = 0.0;
602		vel[2] = 0.0;
603
604	<	temp1 = (double)tot_nmol / 4.0;
605	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
606	<	temp3 = ceil( temp2 );
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607
608	<	have_extra =0;
609	<	if( temp2 < temp3 ){ // we have a non-complete lattice
610	<	have_extra =1;
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612
613	<	n_cells = (int)temp3 - 1;
613	>	n_cells = (int) temp3 - 1;
614		cellx = info[0].boxL[0] / temp3;
615		celly = info[0].boxL[1] / temp3;
616		cellz = info[0].boxL[2] / temp3;
617	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
618	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
619	<	n_per_extra = (int)ceil( temp1 );
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620
621	<	if( n_per_extra > 4){
622	<	sprintf( painCave.errMsg,
623	<	"SimSetup error. There has been an error in constructing"
624	<	" the non-complete lattice.\n" );
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625		painCave.isFatal = 1;
626		simError();
627		}
628		}
629		else{
630	<	n_cells = (int)temp3;
630	>	n_cells = (int) temp3;
631		cellx = info[0].boxL[0] / temp3;
632		celly = info[0].boxL[1] / temp3;
633		cellz = info[0].boxL[2] / temp3;
#	Line 453 | Line 638 | void SimSetup::initFromBass( void ){
638		current_comp = 0;
639		current_atom_ndx = 0;
640
641	<	for( i=0; i < n_cells ; i++ ){
642	<	for( j=0; j < n_cells; j++ ){
643	<	for( k=0; k < n_cells; k++ ){
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645
646	<	makeElement( i * cellx,
461	<	j * celly,
462	<	k * cellz );
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	makeElement( i * cellx + 0.5 * cellx,
465	<	j * celly + 0.5 * celly,
466	<	k * cellz );
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	<	makeElement( i * cellx,
469	<	j * celly + 0.5 * celly,
470	<	k * cellz + 0.5 * cellz );
471	<
472	<	makeElement( i * cellx + 0.5 * cellx,
473	<	j * celly,
474	<	k * cellz + 0.5 * cellz );
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651		}
652		}
653		}
654
655	<	if( have_extra ){
655	>	if (have_extra){
656		done = 0;
657
658		int start_ndx;
659	<	for( i=0; i < (n_cells+1) && !done; i++ ){
660	<	for( j=0; j < (n_cells+1) && !done; j++ ){
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	if( i < n_cells ){
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	if( j < n_cells ){
676	<	start_ndx = n_cells;
677	<	}
678	<	else start_ndx = 0;
679	<	}
493	<	else start_ndx = 0;
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
682	<
683	<	makeElement( i * cellx,
684	<	j * celly,
685	<	k * cellz );
500	<	done = ( current_mol >= tot_nmol );
501	<
502	<	if( !done && n_per_extra > 1 ){
503	<	makeElement( i * cellx + 0.5 * cellx,
504	<	j * celly + 0.5 * celly,
505	<	k * cellz );
506	<	done = ( current_mol >= tot_nmol );
507	<	}
508	<
509	<	if( !done && n_per_extra > 2){
510	<	makeElement( i * cellx,
511	<	j * celly + 0.5 * celly,
512	<	k * cellz + 0.5 * cellz );
513	<	done = ( current_mol >= tot_nmol );
514	<	}
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	if( !done && n_per_extra > 3){
688	<	makeElement( i * cellx + 0.5 * cellx,
689	<	j * celly,
690	<	k * cellz + 0.5 * cellz );
691	<	done = ( current_mol >= tot_nmol );
692	<	}
522	<	}
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693		}
694		}
695		}
696
697	<	for( i=0; i<info[0].n_atoms; i++ ){
698	<	info[0].atoms[i]->setVel( vel );
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699		}
700		}
701
702	<	void SimSetup::makeElement( double x, double y, double z ){
533	<
702	>	void SimSetup::makeElement(double x, double y, double z){
703		int k;
704		AtomStamp* current_atom;
705		DirectionalAtom* dAtom;
706		double rotMat[3][3];
707		double pos[3];
708
709	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
710	<
711	<	current_atom = comp_stamps[current_comp]->getAtom( k );
712	<	if( !current_atom->havePosition() ){
713	<	sprintf( painCave.errMsg,
714	<	"SimSetup:initFromBass error.\n"
715	<	"\tComponent %s, atom %s does not have a position specified.\n"
716	<	"\tThe initialization routine is unable to give a start"
717	<	" position.\n",
549	<	comp_stamps[current_comp]->getID(),
550	<	current_atom->getType() );
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
721	<
721	>
722		pos[0] = x + current_atom->getPosX();
723		pos[1] = y + current_atom->getPosY();
724		pos[2] = z + current_atom->getPosZ();
558	–
559	–	info[0].atoms[current_atom_ndx]->setPos( pos );
725
726	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731		rotMat[0][0] = 1.0;
732		rotMat[0][1] = 0.0;
#	Line 574 | Line 740 | void SimSetup::makeElement( double x, double y, double
740		rotMat[2][1] = 0.0;
741		rotMat[2][2] = 1.0;
742
743	<	dAtom->setA( rotMat );
743	>	dAtom->setA(rotMat);
744		}
745
746		current_atom_ndx++;
#	Line 583 | Line 749 | void SimSetup::makeElement( double x, double y, double
749		current_mol++;
750		current_comp_mol++;
751
752	<	if( current_comp_mol >= components_nmol[current_comp] ){
587	<
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753		current_comp_mol = 0;
754		current_comp++;
755		}
756		}
757
758
759	<	void SimSetup::gatherInfo( void ){
760	<	int i,j,k;
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762		ensembleCase = -1;
763		ffCase = -1;
764
765		// set the easy ones first
766
767	<	for( i=0; i<nInfo; i++){
767	>	for (i = 0; i < nInfo; i++){
768		info[i].target_temp = globals->getTargetTemp();
769		info[i].dt = globals->getDt();
770		info[i].run_time = globals->getRunTime();
#	Line 609 | Line 774 | void SimSetup::gatherInfo( void ){
774
775		// get the forceField
776
777	<	strcpy( force_field, globals->getForceField() );
777	>	strcpy(force_field, globals->getForceField());
778
779	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
780	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
781	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791		else{
792	<	sprintf( painCave.errMsg,
793	<	"SimSetup Error. Unrecognized force field -> %s\n",
794	<	force_field );
795	<	painCave.isFatal = 1;
622	<	simError();
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796		}
797
798	<	// get the ensemble
798	>	// get the ensemble
799
800	<	strcpy( ensemble, globals->getEnsemble() );
800	>	strcpy(ensemble, globals->getEnsemble());
801
802	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
803	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
804	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809		ensembleCase = NPTi_ENS;
810	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
811	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
812	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817		else{
818	<	sprintf( painCave.errMsg,
819	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
820	<	"reverting to NVE for this simulation.\n",
821	<	ensemble );
822	<	painCave.isFatal = 0;
823	<	simError();
824	<	strcpy( ensemble, "NVE" );
825	<	ensembleCase = NVE_ENS;
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826		}
646	–
647	–	for(i=0; i<nInfo; i++){
648	–
649	–	strcpy( info[i].ensemble, ensemble );
827
828	+	for (i = 0; i < nInfo; i++){
829	+	strcpy(info[i].ensemble, ensemble);
830	+
831		// get the mixing rule
832
833	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834		info[i].usePBC = globals->getPBC();
835		}
836	<
836	>
837		// get the components and calculate the tot_nMol and indvidual n_mol
838	<
838	>
839		the_components = globals->getComponents();
840		components_nmol = new int[n_components];
841
842
843	<	if( !globals->haveNMol() ){
843	>	if (!globals->haveNMol()){
844		// we don't have the total number of molecules, so we assume it is
845		// given in each component
846
847		tot_nmol = 0;
848	<	for( i=0; i<n_components; i++ ){
849	<
850	<	if( !the_components[i]->haveNMol() ){
851	<	// we have a problem
852	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error. No global NMol or component NMol"
854	<	" given. Cannot calculate the number of atoms.\n" );
855	<	painCave.isFatal = 1;
676	<	simError();
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856		}
857
858		tot_nmol += the_components[i]->getNMol();
#	Line 681 | Line 860 | void SimSetup::gatherInfo( void ){
860		}
861		}
862		else{
863	<	sprintf( painCave.errMsg,
864	<	"SimSetup error.\n"
865	<	"\tSorry, the ability to specify total"
866	<	" nMols and then give molfractions in the components\n"
867	<	"\tis not currently supported."
868	<	" Please give nMol in the components.\n" );
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869		painCave.isFatal = 1;
870		simError();
871		}
872
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903	+
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914		// set the status, sample, and thermal kick times
695	–
696	–	for(i=0; i<nInfo; i++){
915
916	<	if( globals->haveSampleTime() ){
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
701	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
706	–	info[i].thermalTime = info[i].sampleTime;
924		}
925	<
926	<	if( globals->haveStatusTime() ){
925	>
926	>	if (globals->haveStatusTime()){
927		info[i].statusTime = globals->getStatusTime();
928		}
712	–
713	–	if( globals->haveThermalTime() ){
714	–	info[i].thermalTime = globals->getThermalTime();
715	–	}
929
930	<	// check for the temperature set flag
930	>	if (globals->haveThermalTime()){
931	>	info[i].thermalTime = globals->getThermalTime();
932	>	} else {
933	>	info[i].thermalTime = globals->getRunTime();
934	>	}
935
936	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
937	<
938	<	// get some of the tricky things that may still be in the globals
939	<
723	<	double boxVector[3];
724	<	if( globals->haveBox() ){
725	<	boxVector[0] = globals->getBox();
726	<	boxVector[1] = globals->getBox();
727	<	boxVector[2] = globals->getBox();
728	<
729	<	info[i].setBox( boxVector );
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940		}
941	<	else if( globals->haveDensity() ){
942	<
943	<	double vol;
944	<	vol = (double)tot_nmol / globals->getDensity();
945	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
946	<	boxVector[1] = boxVector[0];
947	<	boxVector[2] = boxVector[0];
948	<
949	<	info[i].setBox( boxVector );
950	<	}
951	<	else{
952	<	if( !globals->haveBoxX() ){
953	<	sprintf( painCave.errMsg,
954	<	"SimSetup error, no periodic BoxX size given.\n" );
955	<	painCave.isFatal = 1;
956	<	simError();
941	>
942	>	// check for the temperature set flag
943	>
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952	>	// check for thermodynamic integration
953	>	if (globals->getUseThermInt()) {
954	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	>	info[i].useThermInt = globals->getUseThermInt();
956	>	info[i].thermIntLambda = globals->getThermIntLambda();
957	>	info[i].thermIntK = globals->getThermIntK();
958	>
959	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	>	info[i].restraint = myRestraint;
961		}
962	<	boxVector[0] = globals->getBoxX();
963	<
964	<	if( !globals->haveBoxY() ){
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup error, no periodic BoxY size given.\n" );
962	>	else {
963	>	sprintf(painCave.errMsg,
964	>	"SimSetup Error:\n"
965	>	"\tKeyword useThermInt was set to 'true' but\n"
966	>	"\tthermodynamicIntegrationLambda (and/or\n"
967	>	"\tthermodynamicIntegrationK) was not specified.\n"
968	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
969		painCave.isFatal = 1;
970	<	simError();
970	>	simError();
971		}
972	<	boxVector[1] = globals->getBoxY();
973	<
974	<	if( !globals->haveBoxZ() ){
975	<	sprintf( painCave.errMsg,
976	<	"SimSetup error, no periodic BoxZ size given.\n" );
977	<	painCave.isFatal = 1;
978	<	simError();
972	>	}
973	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974	>	sprintf(painCave.errMsg,
975	>	"SimSetup Warning: If you want to use Thermodynamic\n"
976	>	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	>	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	>	"\tlambda and/or k values are being ignored.\n");
979	>	painCave.isFatal = 0;
980	>	simError();
981	>	}
982	>	}
983	>
984	>	//setup seed for random number generator
985	>	int seedValue;
986	>
987	>	if (globals->haveSeed()){
988	>	seedValue = globals->getSeed();
989	>
990	>	if(seedValue / 1E9 == 0){
991	>	sprintf(painCave.errMsg,
992	>	"Seed for sprng library should contain at least 9 digits\n"
993	>	"OOPSE will generate a seed for user\n");
994	>	painCave.isFatal = 0;
995	>	simError();
996	>
997	>	//using seed generated by system instead of invalid seed set by user
998	>	#ifndef IS_MPI
999	>	seedValue = make_sprng_seed();
1000	>	#else
1001	>	if (worldRank == 0){
1002	>	seedValue = make_sprng_seed();
1003		}
1004	<	boxVector[2] = globals->getBoxZ();
1005	<
766	<	info[i].setBox( boxVector );
1004	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1005	>	#endif
1006		}
1007	+	}//end of if branch of globals->haveSeed()
1008	+	else{
1009	+
1010	+	#ifndef IS_MPI
1011	+	seedValue = make_sprng_seed();
1012	+	#else
1013	+	if (worldRank == 0){
1014	+	seedValue = make_sprng_seed();
1015	+	}
1016	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1017	+	#endif
1018	+	}//end of globals->haveSeed()
1019
1020	+	for (int i = 0; i < nInfo; i++){
1021	+	info[i].setSeed(seedValue);
1022		}
1023	<
1023	>
1024		#ifdef IS_MPI
1025	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1025	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026		MPIcheckPoint();
1027		#endif // is_mpi
775	–
1028		}
1029
1030
1031	<	void SimSetup::finalInfoCheck( void ){
1031	>	void SimSetup::finalInfoCheck(void){
1032		int index;
1033		int usesDipoles;
1034	+	int usesCharges;
1035		int i;
1036
1037	<	for(i=0; i<nInfo; i++){
1037	>	for (i = 0; i < nInfo; i++){
1038		// check electrostatic parameters
1039	<
1039	>
1040		index = 0;
1041		usesDipoles = 0;
1042	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1042	>	while ((index < info[i].n_atoms) && !usesDipoles){
1043		usesDipoles = (info[i].atoms[index])->hasDipole();
1044		index++;
1045		}
1046	<
1046	>	index = 0;
1047	>	usesCharges = 0;
1048	>	while ((index < info[i].n_atoms) && !usesCharges){
1049	>	usesCharges= (info[i].atoms[index])->hasCharge();
1050	>	index++;
1051	>	}
1052		#ifdef IS_MPI
1053		int myUse = usesDipoles;
1054	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1054	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055		#endif //is_mpi
1056	<
1057	<	double theEcr, theEst;
1058	<
1059	<	if (globals->getUseRF() ) {
1060	<	info[i].useReactionField = 1;
1056	>
1057	>	double theRcut, theRsw;
1058	>
1059	>	if (globals->haveRcut()) {
1060	>	theRcut = globals->getRcut();
1061	>
1062	>	if (globals->haveRsw())
1063	>	theRsw = globals->getRsw();
1064	>	else
1065	>	theRsw = theRcut;
1066
1067	<	if( !globals->haveECR() ){
1068	<	sprintf( painCave.errMsg,
1069	<	"SimSetup Warning: using default value of 1/2 the smallest "
807	<	"box length for the electrostaticCutoffRadius.\n"
808	<	"I hope you have a very fast processor!\n");
809	<	painCave.isFatal = 0;
810	<	simError();
811	<	double smallest;
812	<	smallest = info[i].boxL[0];
813	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	<	theEcr = 0.5 * smallest;
816	<	} else {
817	<	theEcr = globals->getECR();
818	<	}
1067	>	info[i].setDefaultRcut(theRcut, theRsw);
1068	>
1069	>	} else {
1070
1071	<	if( !globals->haveEST() ){
1072	<	sprintf( painCave.errMsg,
1073	<	"SimSetup Warning: using default value of 0.05 * the "
1074	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1075	<	);
1076	<	painCave.isFatal = 0;
1077	<	simError();
827	<	theEst = 0.05 * theEcr;
828	<	} else {
829	<	theEst= globals->getEST();
830	<	}
1071	>	the_ff->calcRcut();
1072	>	theRcut = info[i].getRcut();
1073	>
1074	>	if (globals->haveRsw())
1075	>	theRsw = globals->getRsw();
1076	>	else
1077	>	theRsw = theRcut;
1078
1079	<	info[i].setEcr( theEcr, theEst );
1079	>	info[i].setDefaultRcut(theRcut, theRsw);
1080	>	}
1081	>
1082	>	if (globals->getUseRF()){
1083	>	info[i].useReactionField = 1;
1084
1085	<	if(!globals->haveDielectric() ){
1086	<	sprintf( painCave.errMsg,
1087	<	"SimSetup Error: You are trying to use Reaction Field without"
1088	<	"setting a dielectric constant!\n"
1089	<	);
1090	<	painCave.isFatal = 1;
1091	<	simError();
1092	<	}
1093	<	info[i].dielectric = globals->getDielectric();
1094	<	}
1095	<	else {
1096	<	if (usesDipoles) {
1085	>	if (!globals->haveRcut()){
1086	>	sprintf(painCave.errMsg,
1087	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088	>	"\tOOPSE will use a default value of 15.0 angstroms"
1089	>	"\tfor the cutoffRadius.\n");
1090	>	painCave.isFatal = 0;
1091	>	simError();
1092	>	theRcut = 15.0;
1093	>	}
1094	>	else{
1095	>	theRcut = globals->getRcut();
1096	>	}
1097	>
1098	>	if (!globals->haveRsw()){
1099	>	sprintf(painCave.errMsg,
1100	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1101	>	"\tOOPSE will use a default value of\n"
1102	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103	>	painCave.isFatal = 0;
1104	>	simError();
1105	>	theRsw = 0.95 * theRcut;
1106	>	}
1107	>	else{
1108	>	theRsw = globals->getRsw();
1109	>	}
1110	>
1111	>	info[i].setDefaultRcut(theRcut, theRsw);
1112	>
1113	>	if (!globals->haveDielectric()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error: No Dielectric constant was set.\n"
1116	>	"\tYou are trying to use Reaction Field without"
1117	>	"\tsetting a dielectric constant!\n");
1118	>	painCave.isFatal = 1;
1119	>	simError();
1120	>	}
1121	>	info[i].dielectric = globals->getDielectric();
1122	>	}
1123	>	else{
1124	>	if (usesDipoles || usesCharges){
1125	>
1126	>	if (!globals->haveRcut()){
1127	>	sprintf(painCave.errMsg,
1128	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129	>	"\tOOPSE will use a default value of 15.0 angstroms"
1130	>	"\tfor the cutoffRadius.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	theRcut = 15.0;
1134	>	}
1135	>	else{
1136	>	theRcut = globals->getRcut();
1137	>	}
1138	>
1139	>	if (!globals->haveRsw()){
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1142	>	"\tOOPSE will use a default value of\n"
1143	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144	>	painCave.isFatal = 0;
1145	>	simError();
1146	>	theRsw = 0.95 * theRcut;
1147	>	}
1148	>	else{
1149	>	theRsw = globals->getRsw();
1150	>	}
1151	>
1152	>	info[i].setDefaultRcut(theRcut, theRsw);
1153
847	–	if( !globals->haveECR() ){
848	–	sprintf( painCave.errMsg,
849	–	"SimSetup Warning: using default value of 1/2 the smallest "
850	–	"box length for the electrostaticCutoffRadius.\n"
851	–	"I hope you have a very fast processor!\n");
852	–	painCave.isFatal = 0;
853	–	simError();
854	–	double smallest;
855	–	smallest = info[i].boxL[0];
856	–	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	–	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	–	theEcr = 0.5 * smallest;
859	–	} else {
860	–	theEcr = globals->getECR();
861	–	}
862	–
863	–	if( !globals->haveEST() ){
864	–	sprintf( painCave.errMsg,
865	–	"SimSetup Warning: using default value of 0.05 * the "
866	–	"electrostaticCutoffRadius for the "
867	–	"electrostaticSkinThickness\n"
868	–	);
869	–	painCave.isFatal = 0;
870	–	simError();
871	–	theEst = 0.05 * theEcr;
872	–	} else {
873	–	theEst= globals->getEST();
874	–	}
875	–
876	–	info[i].setEcr( theEcr, theEst );
1154		}
1155	<	}
1155	>	}
1156		}
880	–
1157		#ifdef IS_MPI
1158	<	strcpy( checkPointMsg, "post processing checks out" );
1158	>	strcpy(checkPointMsg, "post processing checks out");
1159		MPIcheckPoint();
1160		#endif // is_mpi
1161
1162	+	// clean up the forcefield
1163	+	the_ff->cleanMe();
1164		}
887	–
888	–	void SimSetup::initSystemCoords( void ){
889	–	int i;
1165
1166	<	std::cerr << "Setting atom Coords\n";
1166	>	void SimSetup::initSystemCoords(void){
1167	>	int i;
1168
1169	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1170	<
1171	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1172	<
1173	<	if( globals->haveInitialConfig() ){
1174	<
1169	>	char* inName;
1170	>
1171	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1172	>
1173	>	for (i = 0; i < info[0].n_atoms; i++)
1174	>	info[0].atoms[i]->setCoords();
1175	>
1176	>	if (globals->haveInitialConfig()){
1177		InitializeFromFile* fileInit;
1178		#ifdef IS_MPI // is_mpi
1179	<	if( worldRank == 0 ){
1179	>	if (worldRank == 0){
1180		#endif //is_mpi
1181	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1181	>	inName = globals->getInitialConfig();
1182	>	fileInit = new InitializeFromFile(inName);
1183		#ifdef IS_MPI
1184	<	}else fileInit = new InitializeFromFile( NULL );
1184	>	}
1185	>	else
1186	>	fileInit = new InitializeFromFile(NULL);
1187		#endif
1188	<	fileInit->readInit( info ); // default velocities on
1189	<
1188	>	fileInit->readInit(info); // default velocities on
1189	>
1190		delete fileInit;
1191		}
1192		else{
1193
913	–	#ifdef IS_MPI
914	–
1194		// no init from bass
1195
1196	<	sprintf( painCave.errMsg,
1197	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1198	<	painCave.isFatal;
1196	>	sprintf(painCave.errMsg,
1197	>	"Cannot intialize a simulation without an initial configuration file.\n");
1198	>	painCave.isFatal = 1;;
1199		simError();
1200
922	–	#else
923	–
924	–	initFromBass();
925	–
926	–
927	–	#endif
1201		}
1202	<
1202	>
1203		#ifdef IS_MPI
1204	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1204	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1205		MPIcheckPoint();
1206		#endif // is_mpi
934	–
1207		}
1208
1209
1210	<	void SimSetup::makeOutNames( void ){
939	<
1210	>	void SimSetup::makeOutNames(void){
1211		int k;
1212
942	–
943	–	for(k=0; k<nInfo; k++){
1213
1214	+	for (k = 0; k < nInfo; k++){
1215		#ifdef IS_MPI
1216	<	if( worldRank == 0 ){
1216	>	if (worldRank == 0){
1217		#endif // is_mpi
1218	<
1219	<	if( globals->haveFinalConfig() ){
1220	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1218	>
1219	>	if (globals->haveFinalConfig()){
1220	>	strcpy(info[k].finalName, globals->getFinalConfig());
1221		}
1222		else{
1223	<	strcpy( info[k].finalName, inFileName );
1224	<	char* endTest;
1225	<	int nameLength = strlen( info[k].finalName );
1226	<	endTest = &(info[k].finalName[nameLength - 5]);
1227	<	if( !strcmp( endTest, ".bass" ) ){
1228	<	strcpy( endTest, ".eor" );
1229	<	}
1230	<	else if( !strcmp( endTest, ".BASS" ) ){
1231	<	strcpy( endTest, ".eor" );
1232	<	}
1233	<	else{
1234	<	endTest = &(info[k].finalName[nameLength - 4]);
1235	<	if( !strcmp( endTest, ".bss" ) ){
1236	<	strcpy( endTest, ".eor" );
1237	<	}
1238	<	else if( !strcmp( endTest, ".mdl" ) ){
1239	<	strcpy( endTest, ".eor" );
1240	<	}
1241	<	else{
1242	<	strcat( info[k].finalName, ".eor" );
1243	<	}
1244	<	}
1245	<	}
1246	<
1247	<	// make the sample and status out names
1248	<
1249	<	strcpy( info[k].sampleName, inFileName );
1223	>	strcpy(info[k].finalName, inFileName);
1224	>	char* endTest;
1225	>	int nameLength = strlen(info[k].finalName);
1226	>	endTest = &(info[k].finalName[nameLength - 5]);
1227	>	if (!strcmp(endTest, ".bass")){
1228	>	strcpy(endTest, ".eor");
1229	>	}
1230	>	else if (!strcmp(endTest, ".BASS")){
1231	>	strcpy(endTest, ".eor");
1232	>	}
1233	>	else{
1234	>	endTest = &(info[k].finalName[nameLength - 4]);
1235	>	if (!strcmp(endTest, ".bss")){
1236	>	strcpy(endTest, ".eor");
1237	>	}
1238	>	else if (!strcmp(endTest, ".mdl")){
1239	>	strcpy(endTest, ".eor");
1240	>	}
1241	>	else{
1242	>	strcat(info[k].finalName, ".eor");
1243	>	}
1244	>	}
1245	>	}
1246	>
1247	>	// make the sample and status out names
1248	>
1249	>	strcpy(info[k].sampleName, inFileName);
1250		char* endTest;
1251	<	int nameLength = strlen( info[k].sampleName );
1251	>	int nameLength = strlen(info[k].sampleName);
1252		endTest = &(info[k].sampleName[nameLength - 5]);
1253	<	if( !strcmp( endTest, ".bass" ) ){
1254	<	strcpy( endTest, ".dump" );
1253	>	if (!strcmp(endTest, ".bass")){
1254	>	strcpy(endTest, ".dump");
1255		}
1256	<	else if( !strcmp( endTest, ".BASS" ) ){
1257	<	strcpy( endTest, ".dump" );
1256	>	else if (!strcmp(endTest, ".BASS")){
1257	>	strcpy(endTest, ".dump");
1258		}
1259		else{
1260	<	endTest = &(info[k].sampleName[nameLength - 4]);
1261	<	if( !strcmp( endTest, ".bss" ) ){
1262	<	strcpy( endTest, ".dump" );
1263	<	}
1264	<	else if( !strcmp( endTest, ".mdl" ) ){
1265	<	strcpy( endTest, ".dump" );
1266	<	}
1267	<	else{
1268	<	strcat( info[k].sampleName, ".dump" );
1269	<	}
1260	>	endTest = &(info[k].sampleName[nameLength - 4]);
1261	>	if (!strcmp(endTest, ".bss")){
1262	>	strcpy(endTest, ".dump");
1263	>	}
1264	>	else if (!strcmp(endTest, ".mdl")){
1265	>	strcpy(endTest, ".dump");
1266	>	}
1267	>	else{
1268	>	strcat(info[k].sampleName, ".dump");
1269	>	}
1270		}
1271	<
1272	<	strcpy( info[k].statusName, inFileName );
1273	<	nameLength = strlen( info[k].statusName );
1271	>
1272	>	strcpy(info[k].statusName, inFileName);
1273	>	nameLength = strlen(info[k].statusName);
1274		endTest = &(info[k].statusName[nameLength - 5]);
1275	<	if( !strcmp( endTest, ".bass" ) ){
1276	<	strcpy( endTest, ".stat" );
1275	>	if (!strcmp(endTest, ".bass")){
1276	>	strcpy(endTest, ".stat");
1277		}
1278	<	else if( !strcmp( endTest, ".BASS" ) ){
1279	<	strcpy( endTest, ".stat" );
1278	>	else if (!strcmp(endTest, ".BASS")){
1279	>	strcpy(endTest, ".stat");
1280		}
1281		else{
1282	<	endTest = &(info[k].statusName[nameLength - 4]);
1283	<	if( !strcmp( endTest, ".bss" ) ){
1284	<	strcpy( endTest, ".stat" );
1285	<	}
1286	<	else if( !strcmp( endTest, ".mdl" ) ){
1287	<	strcpy( endTest, ".stat" );
1288	<	}
1289	<	else{
1290	<	strcat( info[k].statusName, ".stat" );
1291	<	}
1282	>	endTest = &(info[k].statusName[nameLength - 4]);
1283	>	if (!strcmp(endTest, ".bss")){
1284	>	strcpy(endTest, ".stat");
1285	>	}
1286	>	else if (!strcmp(endTest, ".mdl")){
1287	>	strcpy(endTest, ".stat");
1288	>	}
1289	>	else{
1290	>	strcat(info[k].statusName, ".stat");
1291	>	}
1292		}
1293	<
1293	>
1294	>	strcpy(info[k].rawPotName, inFileName);
1295	>	nameLength = strlen(info[k].rawPotName);
1296	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	>	if (!strcmp(endTest, ".bass")){
1298	>	strcpy(endTest, ".raw");
1299	>	}
1300	>	else if (!strcmp(endTest, ".BASS")){
1301	>	strcpy(endTest, ".raw");
1302	>	}
1303	>	else{
1304	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	>	if (!strcmp(endTest, ".bss")){
1306	>	strcpy(endTest, ".raw");
1307	>	}
1308	>	else if (!strcmp(endTest, ".mdl")){
1309	>	strcpy(endTest, ".raw");
1310	>	}
1311	>	else{
1312	>	strcat(info[k].rawPotName, ".raw");
1313	>	}
1314	>	}
1315	>
1316		#ifdef IS_MPI
1317	+
1318		}
1319		#endif // is_mpi
1320		}
1321		}
1322
1323
1324	<	void SimSetup::sysObjectsCreation( void ){
1325	<
1326	<	int i,k;
1034	<
1324	>	void SimSetup::sysObjectsCreation(void){
1325	>	int i, k;
1326	>
1327		// create the forceField
1328	<
1328	>
1329		createFF();
1330
1331		// extract componentList
#	Line 1046 | Line 1338 | void SimSetup::sysObjectsCreation( void ){
1338
1339		#ifdef IS_MPI
1340		// divide the molecules among the processors
1341	<
1341	>
1342		mpiMolDivide();
1343		#endif //is_mpi
1344	<
1344	>
1345		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1346	<
1346	>
1347		makeSysArrays();
1348
1349		// make and initialize the molecules (all but atomic coordinates)
1350	<
1350	>
1351		makeMolecules();
1352	<
1353	<	for(k=0; k<nInfo; k++){
1352	>
1353	>	for (k = 0; k < nInfo; k++){
1354		info[k].identArray = new int[info[k].n_atoms];
1355	<	for(i=0; i<info[k].n_atoms; i++){
1355	>	for (i = 0; i < info[k].n_atoms; i++){
1356		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1357		}
1358		}
1359		}
1360
1361
1362	<	void SimSetup::createFF( void ){
1362	>	void SimSetup::createFF(void){
1363	>	switch (ffCase){
1364	>	case FF_DUFF:
1365	>	the_ff = new DUFF();
1366	>	break;
1367
1368	<	switch( ffCase ){
1368	>	case FF_LJ:
1369	>	the_ff = new LJFF();
1370	>	break;
1371
1372	<	case FF_DUFF:
1373	<	the_ff = new DUFF();
1374	<	break;
1372	>	case FF_EAM:
1373	>	the_ff = new EAM_FF();
1374	>	break;
1375
1376	<	case FF_LJ:
1377	<	the_ff = new LJFF();
1378	<	break;
1376	>	case FF_H2O:
1377	>	the_ff = new WATER();
1378	>	break;
1379
1380	<	case FF_EAM:
1381	<	the_ff = new EAM_FF();
1382	<	break;
1383	<
1384	<	default:
1087	<	sprintf( painCave.errMsg,
1088	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	<	painCave.isFatal = 1;
1090	<	simError();
1380	>	default:
1381	>	sprintf(painCave.errMsg,
1382	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1383	>	painCave.isFatal = 1;
1384	>	simError();
1385		}
1386
1387		#ifdef IS_MPI
1388	<	strcpy( checkPointMsg, "ForceField creation successful" );
1388	>	strcpy(checkPointMsg, "ForceField creation successful");
1389		MPIcheckPoint();
1390		#endif // is_mpi
1097	–
1391		}
1392
1393
1394	<	void SimSetup::compList( void ){
1102	<
1394	>	void SimSetup::compList(void){
1395		int i;
1396		char* id;
1397		LinkedMolStamp* headStamp = new LinkedMolStamp();
1398		LinkedMolStamp* currentStamp = NULL;
1399	<	comp_stamps = new MoleculeStamp*[n_components];
1399	>	comp_stamps = new MoleculeStamp * [n_components];
1400	>	bool haveCutoffGroups;
1401	>
1402	>	haveCutoffGroups = false;
1403
1404		// make an array of molecule stamps that match the components used.
1405		// also extract the used stamps out into a separate linked list
1406	<
1407	<	for(i=0; i<nInfo; i++){
1406	>
1407	>	for (i = 0; i < nInfo; i++){
1408		info[i].nComponents = n_components;
1409		info[i].componentsNmol = components_nmol;
1410		info[i].compStamps = comp_stamps;
1411		info[i].headStamp = headStamp;
1412		}
1118	–
1413
1120	–	for( i=0; i<n_components; i++ ){
1414
1415	+	for (i = 0; i < n_components; i++){
1416		id = the_components[i]->getType();
1417		comp_stamps[i] = NULL;
1418	<
1418	>
1419		// check to make sure the component isn't already in the list
1420
1421	<	comp_stamps[i] = headStamp->match( id );
1422	<	if( comp_stamps[i] == NULL ){
1129	<
1421	>	comp_stamps[i] = headStamp->match(id);
1422	>	if (comp_stamps[i] == NULL){
1423		// extract the component from the list;
1424	<
1425	<	currentStamp = stamps->extractMolStamp( id );
1426	<	if( currentStamp == NULL ){
1427	<	sprintf( painCave.errMsg,
1428	<	"SimSetup error: Component \"%s\" was not found in the "
1429	<	"list of declared molecules\n",
1430	<	id );
1431	<	painCave.isFatal = 1;
1432	<	simError();
1424	>
1425	>	currentStamp = stamps->extractMolStamp(id);
1426	>	if (currentStamp == NULL){
1427	>	sprintf(painCave.errMsg,
1428	>	"SimSetup error: Component \"%s\" was not found in the "
1429	>	"list of declared molecules\n",
1430	>	id);
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433		}
1434	<
1435	<	headStamp->add( currentStamp );
1436	<	comp_stamps[i] = headStamp->match( id );
1434	>
1435	>	headStamp->add(currentStamp);
1436	>	comp_stamps[i] = headStamp->match(id);
1437		}
1438	+
1439	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	+	haveCutoffGroups = true;
1441		}
1442	+
1443	+	for (i = 0; i < nInfo; i++)
1444	+	info[i].haveCutoffGroups = haveCutoffGroups;
1445
1446		#ifdef IS_MPI
1447	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1447	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1448		MPIcheckPoint();
1449		#endif // is_mpi
1450	+	}
1451
1452	+	void SimSetup::calcSysValues(void){
1453	+	int i, j;
1454	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1455
1456	<	}
1456	>	int* molMembershipArray;
1457	>	CutoffGroupStamp* cg;
1458
1155	–	void SimSetup::calcSysValues( void ){
1156	–	int i, j, k;
1157	–
1158	–	int *molMembershipArray;
1159	–
1459		tot_atoms = 0;
1460		tot_bonds = 0;
1461		tot_bends = 0;
1462		tot_torsions = 0;
1463	<	for( i=0; i<n_components; i++ ){
1464	<
1465	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1466	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1467	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1463	>	tot_rigid = 0;
1464	>	tot_groups = 0;
1465	>	for (i = 0; i < n_components; i++){
1466	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1467	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1468	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1469		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1470	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1471	+
1472	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1473	+	atomsingroups = 0;
1474	+	for (j=0; j < ncutgroups; j++) {
1475	+	cg = comp_stamps[i]->getCutoffGroup(j);
1476	+	atomsingroups += cg->getNMembers();
1477	+	}
1478	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1479	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1480		}
1481
1482		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1483		molMembershipArray = new int[tot_atoms];
1484	<
1485	<	for(i=0; i<nInfo; i++){
1484	>
1485	>	for (i = 0; i < nInfo; i++){
1486		info[i].n_atoms = tot_atoms;
1487		info[i].n_bonds = tot_bonds;
1488		info[i].n_bends = tot_bends;
1489		info[i].n_torsions = tot_torsions;
1490		info[i].n_SRI = tot_SRI;
1491		info[i].n_mol = tot_nmol;
1492	<
1492	>	info[i].ngroup = tot_groups;
1493		info[i].molMembershipArray = molMembershipArray;
1494	<	}
1494	>	}
1495		}
1496
1497		#ifdef IS_MPI
1498
1499	<	void SimSetup::mpiMolDivide( void ){
1190	<
1499	>	void SimSetup::mpiMolDivide(void){
1500		int i, j, k;
1501		int localMol, allMol;
1502		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1503	+	int local_rigid;
1504	+	vector<int> globalMolIndex;
1505
1506	<	mpiSim = new mpiSimulation( info );
1196	<
1197	<	globalIndex = mpiSim->divideLabor();
1506	>	mpiSim = new mpiSimulation(info);
1507
1508	+	mpiSim->divideLabor();
1509	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1510	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1511	+
1512		// set up the local variables
1513	<
1513	>
1514		mol2proc = mpiSim->getMolToProcMap();
1515		molCompType = mpiSim->getMolComponentType();
1516	<
1516	>
1517		allMol = 0;
1518		localMol = 0;
1519		local_atoms = 0;
1520		local_bonds = 0;
1521		local_bends = 0;
1522		local_torsions = 0;
1523	<	globalAtomIndex = 0;
1523	>	local_rigid = 0;
1524	>	globalAtomCounter = 0;
1525
1526	<
1527	<	for( i=0; i<n_components; i++ ){
1528	<
1529	<	for( j=0; j<components_nmol[i]; j++ ){
1530	<
1531	<	if( mol2proc[allMol] == worldRank ){
1532	<
1533	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1534	<	local_bonds +=    comp_stamps[i]->getNBonds();
1221	<	local_bends +=    comp_stamps[i]->getNBends();
1222	<	local_torsions += comp_stamps[i]->getNTorsions();
1223	<	localMol++;
1526	>	for (i = 0; i < n_components; i++){
1527	>	for (j = 0; j < components_nmol[i]; j++){
1528	>	if (mol2proc[allMol] == worldRank){
1529	>	local_atoms += comp_stamps[i]->getNAtoms();
1530	>	local_bonds += comp_stamps[i]->getNBonds();
1531	>	local_bends += comp_stamps[i]->getNBends();
1532	>	local_torsions += comp_stamps[i]->getNTorsions();
1533	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1534	>	localMol++;
1535		}
1536	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1537	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1538	<	globalAtomIndex++;
1536	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1537	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1538	>	globalAtomCounter++;
1539		}
1540
1541	<	allMol++;
1541	>	allMol++;
1542		}
1543		}
1544		local_SRI = local_bonds + local_bends + local_torsions;
1545	+
1546	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1547
1548	<	info[0].n_atoms = mpiSim->getMyNlocal();
1549	<
1550	<	if( local_atoms != info[0].n_atoms ){
1551	<	sprintf( painCave.errMsg,
1552	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1553	<	" localAtom (%d) are not equal.\n",
1241	<	info[0].n_atoms,
1242	<	local_atoms );
1548	>
1549	>	if (local_atoms != info[0].n_atoms){
1550	>	sprintf(painCave.errMsg,
1551	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1552	>	"\tlocalAtom (%d) are not equal.\n",
1553	>	info[0].n_atoms, local_atoms);
1554		painCave.isFatal = 1;
1555		simError();
1556		}
#	Line 1250 | Line 1561 | void SimSetup::mpiMolDivide( void ){
1561		info[0].n_SRI = local_SRI;
1562		info[0].n_mol = localMol;
1563
1564	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1564	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1565		MPIcheckPoint();
1566		}
1567	<
1567	>
1568		#endif // is_mpi
1569
1570
1571	<	void SimSetup::makeSysArrays( void ){
1572	<	int i, j, k, l;
1571	>	void SimSetup::makeSysArrays(void){
1572	>
1573	>	#ifndef IS_MPI
1574	>	int k, j;
1575	>	#endif // is_mpi
1576	>	int i, l;
1577
1578		Atom** the_atoms;
1579		Molecule* the_molecules;
1265	–	Exclude** the_excludes;
1580
1581	<
1268	<	for(l=0; l<nInfo; l++){
1269	<
1581	>	for (l = 0; l < nInfo; l++){
1582		// create the atom and short range interaction arrays
1583	<
1584	<	the_atoms = new Atom*[info[l].n_atoms];
1583	>
1584	>	the_atoms = new Atom * [info[l].n_atoms];
1585		the_molecules = new Molecule[info[l].n_mol];
1586		int molIndex;
1587
1588		// initialize the molecule's stampID's
1589	<
1589	>
1590		#ifdef IS_MPI
1591	<
1592	<
1591	>
1592	>
1593		molIndex = 0;
1594	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1595	<
1596	<	if(mol2proc[i] == worldRank ){
1597	<	the_molecules[molIndex].setStampID( molCompType[i] );
1598	<	the_molecules[molIndex].setMyIndex( molIndex );
1599	<	the_molecules[molIndex].setGlobalIndex( i );
1288	<	molIndex++;
1594	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1595	>	if (mol2proc[i] == worldRank){
1596	>	the_molecules[molIndex].setStampID(molCompType[i]);
1597	>	the_molecules[molIndex].setMyIndex(molIndex);
1598	>	the_molecules[molIndex].setGlobalIndex(i);
1599	>	molIndex++;
1600		}
1601		}
1602	<
1602	>
1603		#else // is_mpi
1604	<
1604	>
1605		molIndex = 0;
1606	<	globalAtomIndex = 0;
1607	<	for(i=0; i<n_components; i++){
1608	<	for(j=0; j<components_nmol[i]; j++ ){
1609	<	the_molecules[molIndex].setStampID( i );
1610	<	the_molecules[molIndex].setMyIndex( molIndex );
1611	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1612	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1613	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1614	<	globalAtomIndex++;
1615	<	}
1616	<	molIndex++;
1606	>	globalAtomCounter = 0;
1607	>	for (i = 0; i < n_components; i++){
1608	>	for (j = 0; j < components_nmol[i]; j++){
1609	>	the_molecules[molIndex].setStampID(i);
1610	>	the_molecules[molIndex].setMyIndex(molIndex);
1611	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1612	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1613	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1614	>	globalAtomCounter++;
1615	>	}
1616	>	molIndex++;
1617		}
1618		}
1308	–
1309	–
1310	–	#endif // is_mpi
1619
1620
1621	<	if( info[l].n_SRI ){
1314	<
1315	<	Exclude::createArray(info[l].n_SRI);
1316	<	the_excludes = new Exclude*[info[l].n_SRI];
1317	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	<	the_excludes[ex] = new Exclude(ex);
1319	<	}
1320	<	info[l].globalExcludes = new int;
1321	<	info[l].n_exclude = info[l].n_SRI;
1322	<	}
1323	<	else{
1324	<
1325	<	Exclude::createArray( 1 );
1326	<	the_excludes = new Exclude*;
1327	<	the_excludes[0] = new Exclude(0);
1328	<	the_excludes[0]->setPair( 0,0 );
1329	<	info[l].globalExcludes = new int;
1330	<	info[l].globalExcludes[0] = 0;
1331	<	info[l].n_exclude = 0;
1332	<	}
1621	>	#endif // is_mpi
1622
1623	+	info[l].globalExcludes = new int;
1624	+	info[l].globalExcludes[0] = 0;
1625	+
1626		// set the arrays into the SimInfo object
1627
1628		info[l].atoms = the_atoms;
1629		info[l].molecules = the_molecules;
1630		info[l].nGlobalExcludes = 0;
1339	–	info[l].excludes = the_excludes;
1340	–
1341	–	the_ff->setSimInfo( info );
1631
1632	+	the_ff->setSimInfo(info);
1633		}
1634		}
1635
1636	<	void SimSetup::makeIntegrator( void ){
1347	<
1636	>	void SimSetup::makeIntegrator(void){
1637		int k;
1638
1639	<	NVT<RealIntegrator>*  myNVT = NULL;
1640	<	NPTi<RealIntegrator>* myNPTi = NULL;
1641	<	NPTf<RealIntegrator>* myNPTf = NULL;
1642	<	NPTim<RealIntegrator>* myNPTim = NULL;
1643	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1644	<
1645	<	for(k=0; k<nInfo; k++){
1646	<
1647	<	switch( ensembleCase ){
1648	<
1649	<	case NVE_ENS:
1650	<	if (haveZConstraint){
1651	<	setupZConstraint();
1652	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1639	>	NVE<RealIntegrator>* myNVE = NULL;
1640	>	NVT<RealIntegrator>* myNVT = NULL;
1641	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1642	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1643	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1644	>
1645	>	for (k = 0; k < nInfo; k++){
1646	>	switch (ensembleCase){
1647	>	case NVE_ENS:
1648	>	if (globals->haveZconstraints()){
1649	>	setupZConstraint(info[k]);
1650	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1651	>	}
1652	>	else{
1653	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1654		}
1655	+
1656	+	info->the_integrator = myNVE;
1657	+	break;
1658
1659	<	else
1660	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1661	<	break;
1662	<
1663	<	case NVT_ENS:
1664	<	if (haveZConstraint){
1665	<	setupZConstraint();
1373	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	<	}
1375	<	else
1376	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1659	>	case NVT_ENS:
1660	>	if (globals->haveZconstraints()){
1661	>	setupZConstraint(info[k]);
1662	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1663	>	}
1664	>	else
1665	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1666
1667	<	myNVT->setTargetTemp(globals->getTargetTemp());
1379	<
1380	<	if (globals->haveTauThermostat())
1381	<	myNVT->setTauThermostat(globals->getTauThermostat());
1382	<
1383	<	else {
1384	<	sprintf( painCave.errMsg,
1385	<	"SimSetup error: If you use the NVT\n"
1386	<	"    ensemble, you must set tauThermostat.\n");
1387	<	painCave.isFatal = 1;
1388	<	simError();
1389	<	}
1390	<	break;
1391	<
1392	<	case NPTi_ENS:
1393	<	if (haveZConstraint){
1394	<	setupZConstraint();
1395	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	<	}
1397	<	else
1398	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1667	>	myNVT->setTargetTemp(globals->getTargetTemp());
1668
1669	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1670	<
1671	<	if (globals->haveTargetPressure())
1672	<	myNPTi->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;
1409	<	simError();
1410	<	}
1411	<
1412	<	if( globals->haveTauThermostat() )
1413	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	<	else{
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use an NPT\n"
1417	<	"    ensemble, you must set tauThermostat.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<
1422	<	if( globals->haveTauBarostat() )
1423	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	<	else{
1425	<	sprintf( painCave.errMsg,
1426	<	"SimSetup error: If you use an NPT\n"
1427	<	"    ensemble, you must set tauBarostat.\n");
1428	<	painCave.isFatal = 1;
1429	<	simError();
1430	<	}
1431	<	break;
1432	<
1433	<	case NPTf_ENS:
1434	<	if (haveZConstraint){
1435	<	setupZConstraint();
1436	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	<	}
1438	<	else
1439	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1669	>	if (globals->haveTauThermostat())
1670	>	myNVT->setTauThermostat(globals->getTauThermostat());
1671	>	else{
1672	>	sprintf(painCave.errMsg,
1673	>	"SimSetup error: If you use the NVT\n"
1674	>	"\tensemble, you must set tauThermostat.\n");
1675	>	painCave.isFatal = 1;
1676	>	simError();
1677	>	}
1678
1679	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1680	<
1443	<	if (globals->haveTargetPressure())
1444	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	<	else {
1446	<	sprintf( painCave.errMsg,
1447	<	"SimSetup error: If you use a constant pressure\n"
1448	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	<	painCave.isFatal = 1;
1450	<	simError();
1451	<	}
1452	<
1453	<	if( globals->haveTauThermostat() )
1454	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	<	else{
1456	<	sprintf( painCave.errMsg,
1457	<	"SimSetup error: If you use an NPT\n"
1458	<	"    ensemble, you must set tauThermostat.\n");
1459	<	painCave.isFatal = 1;
1460	<	simError();
1461	<	}
1462	<
1463	<	if( globals->haveTauBarostat() )
1464	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	<	else{
1466	<	sprintf( painCave.errMsg,
1467	<	"SimSetup error: If you use an NPT\n"
1468	<	"    ensemble, you must set tauBarostat.\n");
1469	<	painCave.isFatal = 1;
1470	<	simError();
1471	<	}
1472	<	break;
1473	<
1474	<	case NPTim_ENS:
1475	<	if (haveZConstraint){
1476	<	setupZConstraint();
1477	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	<	}
1479	<	else
1480	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1679	>	info->the_integrator = myNVT;
1680	>	break;
1681
1682	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1683	<
1684	<	if (globals->haveTargetPressure())
1685	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1686	<	else {
1687	<	sprintf( painCave.errMsg,
1688	<	"SimSetup error: If you use a constant pressure\n"
1489	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<
1494	<	if( globals->haveTauThermostat() )
1495	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	<	else{
1497	<	sprintf( painCave.errMsg,
1498	<	"SimSetup error: If you use an NPT\n"
1499	<	"    ensemble, you must set tauThermostat.\n");
1500	<	painCave.isFatal = 1;
1501	<	simError();
1502	<	}
1503	<
1504	<	if( globals->haveTauBarostat() )
1505	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	<	else{
1507	<	sprintf( painCave.errMsg,
1508	<	"SimSetup error: If you use an NPT\n"
1509	<	"    ensemble, you must set tauBarostat.\n");
1510	<	painCave.isFatal = 1;
1511	<	simError();
1512	<	}
1513	<	break;
1514	<
1515	<	case NPTfm_ENS:
1516	<	if (haveZConstraint){
1517	<	setupZConstraint();
1518	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	<	}
1520	<	else
1521	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1682	>	case NPTi_ENS:
1683	>	if (globals->haveZconstraints()){
1684	>	setupZConstraint(info[k]);
1685	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1686	>	}
1687	>	else
1688	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1689
1690	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1691	<
1692	<	if (globals->haveTargetPressure())
1693	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1694	<	else {
1695	<	sprintf( painCave.errMsg,
1696	<	"SimSetup error: If you use a constant pressure\n"
1697	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1698	<	painCave.isFatal = 1;
1699	<	simError();
1700	<	}
1701	<
1702	<	if( globals->haveTauThermostat() )
1703	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1704	<	else{
1705	<	sprintf( painCave.errMsg,
1706	<	"SimSetup error: If you use an NPT\n"
1707	<	"    ensemble, you must set tauThermostat.\n");
1708	<	painCave.isFatal = 1;
1709	<	simError();
1710	<	}
1711	<
1712	<	if( globals->haveTauBarostat() )
1713	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1714	<	else{
1715	<	sprintf( painCave.errMsg,
1716	<	"SimSetup error: If you use an NPT\n"
1717	<	"    ensemble, you must set tauBarostat.\n");
1718	<	painCave.isFatal = 1;
1719	<	simError();
1720	<	}
1721	<	break;
1722	<
1723	<	default:
1724	<	sprintf( painCave.errMsg,
1725	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1726	<	painCave.isFatal = 1;
1727	<	simError();
1690	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1691	>
1692	>	if (globals->haveTargetPressure())
1693	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1694	>	else{
1695	>	sprintf(painCave.errMsg,
1696	>	"SimSetup error: If you use a constant pressure\n"
1697	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1698	>	painCave.isFatal = 1;
1699	>	simError();
1700	>	}
1701	>
1702	>	if (globals->haveTauThermostat())
1703	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1704	>	else{
1705	>	sprintf(painCave.errMsg,
1706	>	"SimSetup error: If you use an NPT\n"
1707	>	"\tensemble, you must set tauThermostat.\n");
1708	>	painCave.isFatal = 1;
1709	>	simError();
1710	>	}
1711	>
1712	>	if (globals->haveTauBarostat())
1713	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1714	>	else{
1715	>	sprintf(painCave.errMsg,
1716	>	"SimSetup error: If you use an NPT\n"
1717	>	"\tensemble, you must set tauBarostat.\n");
1718	>	painCave.isFatal = 1;
1719	>	simError();
1720	>	}
1721	>
1722	>	info->the_integrator = myNPTi;
1723	>	break;
1724	>
1725	>	case NPTf_ENS:
1726	>	if (globals->haveZconstraints()){
1727	>	setupZConstraint(info[k]);
1728	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1729	>	}
1730	>	else
1731	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1732	>
1733	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1734	>
1735	>	if (globals->haveTargetPressure())
1736	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1737	>	else{
1738	>	sprintf(painCave.errMsg,
1739	>	"SimSetup error: If you use a constant pressure\n"
1740	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1741	>	painCave.isFatal = 1;
1742	>	simError();
1743	>	}
1744	>
1745	>	if (globals->haveTauThermostat())
1746	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1747	>
1748	>	else{
1749	>	sprintf(painCave.errMsg,
1750	>	"SimSetup error: If you use an NPT\n"
1751	>	"\tensemble, you must set tauThermostat.\n");
1752	>	painCave.isFatal = 1;
1753	>	simError();
1754	>	}
1755	>
1756	>	if (globals->haveTauBarostat())
1757	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1758	>
1759	>	else{
1760	>	sprintf(painCave.errMsg,
1761	>	"SimSetup error: If you use an NPT\n"
1762	>	"\tensemble, you must set tauBarostat.\n");
1763	>	painCave.isFatal = 1;
1764	>	simError();
1765	>	}
1766	>
1767	>	info->the_integrator = myNPTf;
1768	>	break;
1769	>
1770	>	case NPTxyz_ENS:
1771	>	if (globals->haveZconstraints()){
1772	>	setupZConstraint(info[k]);
1773	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1774	>	}
1775	>	else
1776	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1777	>
1778	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1779	>
1780	>	if (globals->haveTargetPressure())
1781	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1782	>	else{
1783	>	sprintf(painCave.errMsg,
1784	>	"SimSetup error: If you use a constant pressure\n"
1785	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1786	>	painCave.isFatal = 1;
1787	>	simError();
1788	>	}
1789	>
1790	>	if (globals->haveTauThermostat())
1791	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1792	>	else{
1793	>	sprintf(painCave.errMsg,
1794	>	"SimSetup error: If you use an NPT\n"
1795	>	"\tensemble, you must set tauThermostat.\n");
1796	>	painCave.isFatal = 1;
1797	>	simError();
1798	>	}
1799	>
1800	>	if (globals->haveTauBarostat())
1801	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1802	>	else{
1803	>	sprintf(painCave.errMsg,
1804	>	"SimSetup error: If you use an NPT\n"
1805	>	"\tensemble, you must set tauBarostat.\n");
1806	>	painCave.isFatal = 1;
1807	>	simError();
1808	>	}
1809	>
1810	>	info->the_integrator = myNPTxyz;
1811	>	break;
1812	>
1813	>	default:
1814	>	sprintf(painCave.errMsg,
1815	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1816	>	painCave.isFatal = 1;
1817	>	simError();
1818		}
1819		}
1820		}
1821
1822	<	void SimSetup::initFortran( void ){
1566	<
1822	>	void SimSetup::initFortran(void){
1823		info[0].refreshSim();
1824	<
1825	<	if( !strcmp( info[0].mixingRule, "standard") ){
1826	<	the_ff->initForceField( LB_MIXING_RULE );
1824	>
1825	>	if (!strcmp(info[0].mixingRule, "standard")){
1826	>	the_ff->initForceField(LB_MIXING_RULE);
1827		}
1828	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1829	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1828	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1829	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1830		}
1831		else{
1832	<	sprintf( painCave.errMsg,
1833	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	<	info[0].mixingRule );
1832	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1833	>	info[0].mixingRule);
1834		painCave.isFatal = 1;
1835		simError();
1836		}
1837
1838
1839		#ifdef IS_MPI
1840	<	strcpy( checkPointMsg,
1586	<	"Successfully intialized the mixingRule for Fortran." );
1840	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1841		MPIcheckPoint();
1842		#endif // is_mpi
1843	+	}
1844
1845	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1846	+	int nZConstraints;
1847	+	ZconStamp** zconStamp;
1848	+
1849	+	if (globals->haveZconstraintTime()){
1850	+	//add sample time of z-constraint  into SimInfo's property list
1851	+	DoubleData* zconsTimeProp = new DoubleData();
1852	+	zconsTimeProp->setID(ZCONSTIME_ID);
1853	+	zconsTimeProp->setData(globals->getZconsTime());
1854	+	theInfo.addProperty(zconsTimeProp);
1855	+	}
1856	+	else{
1857	+	sprintf(painCave.errMsg,
1858	+	"ZConstraint error: If you use a ZConstraint,\n"
1859	+	"\tyou must set zconsTime.\n");
1860	+	painCave.isFatal = 1;
1861	+	simError();
1862	+	}
1863	+
1864	+	//push zconsTol into siminfo, if user does not specify
1865	+	//value for zconsTol, a default value will be used
1866	+	DoubleData* zconsTol = new DoubleData();
1867	+	zconsTol->setID(ZCONSTOL_ID);
1868	+	if (globals->haveZconsTol()){
1869	+	zconsTol->setData(globals->getZconsTol());
1870	+	}
1871	+	else{
1872	+	double defaultZConsTol = 0.01;
1873	+	sprintf(painCave.errMsg,
1874	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1875	+	"\tOOPSE will use a default value of %f.\n"
1876	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1877	+	defaultZConsTol);
1878	+	painCave.isFatal = 0;
1879	+	simError();
1880	+
1881	+	zconsTol->setData(defaultZConsTol);
1882	+	}
1883	+	theInfo.addProperty(zconsTol);
1884	+
1885	+	//set Force Subtraction Policy
1886	+	StringData* zconsForcePolicy = new StringData();
1887	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1888	+
1889	+	if (globals->haveZconsForcePolicy()){
1890	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1891	+	}
1892	+	else{
1893	+	sprintf(painCave.errMsg,
1894	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1895	+	"\tOOPSE will use PolicyByMass.\n"
1896	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1897	+	painCave.isFatal = 0;
1898	+	simError();
1899	+	zconsForcePolicy->setData("BYMASS");
1900	+	}
1901	+
1902	+	theInfo.addProperty(zconsForcePolicy);
1903	+
1904	+	//set zcons gap
1905	+	DoubleData* zconsGap = new DoubleData();
1906	+	zconsGap->setID(ZCONSGAP_ID);
1907	+
1908	+	if (globals->haveZConsGap()){
1909	+	zconsGap->setData(globals->getZconsGap());
1910	+	theInfo.addProperty(zconsGap);
1911	+	}
1912	+
1913	+	//set zcons fixtime
1914	+	DoubleData* zconsFixtime = new DoubleData();
1915	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1916	+
1917	+	if (globals->haveZConsFixTime()){
1918	+	zconsFixtime->setData(globals->getZconsFixtime());
1919	+	theInfo.addProperty(zconsFixtime);
1920	+	}
1921	+
1922	+	//set zconsUsingSMD
1923	+	IntData* zconsUsingSMD = new IntData();
1924	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1925	+
1926	+	if (globals->haveZConsUsingSMD()){
1927	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1928	+	theInfo.addProperty(zconsUsingSMD);
1929	+	}
1930	+
1931	+	//Determine the name of ouput file and add it into SimInfo's property list
1932	+	//Be careful, do not use inFileName, since it is a pointer which
1933	+	//point to a string at master node, and slave nodes do not contain that string
1934	+
1935	+	string zconsOutput(theInfo.finalName);
1936	+
1937	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1938	+
1939	+	StringData* zconsFilename = new StringData();
1940	+	zconsFilename->setID(ZCONSFILENAME_ID);
1941	+	zconsFilename->setData(zconsOutput);
1942	+
1943	+	theInfo.addProperty(zconsFilename);
1944	+
1945	+	//setup index, pos and other parameters of z-constraint molecules
1946	+	nZConstraints = globals->getNzConstraints();
1947	+	theInfo.nZconstraints = nZConstraints;
1948	+
1949	+	zconStamp = globals->getZconStamp();
1950	+	ZConsParaItem tempParaItem;
1951	+
1952	+	ZConsParaData* zconsParaData = new ZConsParaData();
1953	+	zconsParaData->setID(ZCONSPARADATA_ID);
1954	+
1955	+	for (int i = 0; i < nZConstraints; i++){
1956	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1957	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1958	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1959	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1960	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1961	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1962	+	zconsParaData->addItem(tempParaItem);
1963	+	}
1964	+
1965	+	//check the uniqueness of index
1966	+	if(!zconsParaData->isIndexUnique()){
1967	+	sprintf(painCave.errMsg,
1968	+	"ZConstraint Error: molIndex is not unique!\n");
1969	+	painCave.isFatal = 1;
1970	+	simError();
1971	+	}
1972	+
1973	+	//sort the parameters by index of molecules
1974	+	zconsParaData->sortByIndex();
1975	+
1976	+	//push data into siminfo, therefore, we can retrieve later
1977	+	theInfo.addProperty(zconsParaData);
1978		}
1979
1980	<	void SimSetup::setupZConstraint()
1593	<	{
1594	<	int k;
1980	>	void SimSetup::makeMinimizer(){
1981
1982	<	for(k=0; k<nInfo; k++){
1982	>	OOPSEMinimizer* myOOPSEMinimizer;
1983	>	MinimizerParameterSet* param;
1984	>	char minimizerName[100];
1985	>
1986	>	for (int i = 0; i < nInfo; i++){
1987
1988	<	if(globals->haveZConsTime()){
1989	<
1990	<	//add sample time of z-constraint  into SimInfo's property list
1991	<	DoubleData* zconsTimeProp = new DoubleData();
1992	<	zconsTimeProp->setID("zconstime");
1993	<	zconsTimeProp->setData(globals->getZConsTime());
1604	<	info[k].addProperty(zconsTimeProp);
1988	>	//prepare parameter set for minimizer
1989	>	param = new MinimizerParameterSet();
1990	>	param->setDefaultParameter();
1991	>
1992	>	if (globals->haveMinimizer()){
1993	>	param->setFTol(globals->getMinFTol());
1994		}
1995	<	else{
1996	<	sprintf( painCave.errMsg,
1997	<	"ZConstraint error: If you use an ZConstraint\n"
1609	<	" , you must set sample time.\n");
1610	<	painCave.isFatal = 1;
1611	<	simError();
1995	>
1996	>	if (globals->haveMinGTol()){
1997	>	param->setGTol(globals->getMinGTol());
1998		}
1999	+
2000	+	if (globals->haveMinMaxIter()){
2001	+	param->setMaxIteration(globals->getMinMaxIter());
2002	+	}
2003	+
2004	+	if (globals->haveMinWriteFrq()){
2005	+	param->setMaxIteration(globals->getMinMaxIter());
2006	+	}
2007	+
2008	+	if (globals->haveMinWriteFrq()){
2009	+	param->setWriteFrq(globals->getMinWriteFrq());
2010	+	}
2011
2012	<	if(globals->haveIndexOfAllZConsMols()){
2013	<
1616	<	//add index of z-constraint molecules into SimInfo's property list
1617	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618	<
1619	<	//sort the index
1620	<	sort(tempIndex.begin(), tempIndex.end());
1621	<
1622	<	IndexData* zconsIndex = new IndexData();
1623	<	zconsIndex->setID("zconsindex");
1624	<	zconsIndex->setIndexData(tempIndex);
1625	<	info[k].addProperty(zconsIndex);
2012	>	if (globals->haveMinStepSize()){
2013	>	param->setStepSize(globals->getMinStepSize());
2014		}
2015	+
2016	+	if (globals->haveMinLSMaxIter()){
2017	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2018	+	}
2019	+
2020	+	if (globals->haveMinLSTol()){
2021	+	param->setLineSearchTol(globals->getMinLSTol());
2022	+	}
2023	+
2024	+	strcpy(minimizerName, globals->getMinimizer());
2025	+
2026	+	if (!strcasecmp(minimizerName, "CG")){
2027	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2028	+	}
2029	+	else if (!strcasecmp(minimizerName, "SD")){
2030	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2031	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2032	+	}
2033		else{
2034	<	sprintf( painCave.errMsg,
2035	<	"SimSetup error: If you use an ZConstraint\n"
2036	<	" , you must set index of z-constraint molecules.\n");
2037	<	painCave.isFatal = 1;
2038	<	simError();
2039	<
2034	>	sprintf(painCave.errMsg,
2035	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2036	>	painCave.isFatal = 0;
2037	>	simError();
2038	>
2039	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2040		}
2041	<
2042	<	//Determine the name of ouput file and add it into SimInfo's property list
2043	<	//Be careful, do not use inFileName, since it is a pointer which
2044	<	//point to a string at master node, and slave nodes do not contain that string
2045	<
1640	<	string zconsOutput(info[k].finalName);
1641	<
1642	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	<
1644	<	StringData* zconsFilename = new StringData();
1645	<	zconsFilename->setID("zconsfilename");
1646	<	zconsFilename->setData(zconsOutput);
1647	<
1648	<	info[k].addProperty(zconsFilename);
2041	>	info[i].the_integrator = myOOPSEMinimizer;
2042	>
2043	>	//store the minimizer into simInfo
2044	>	info[i].the_minimizer = myOOPSEMinimizer;
2045	>	info[i].has_minimizer = true;
2046		}
2047	+
2048		}

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