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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 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 21 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#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 50 | 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 ){
61	<
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();
89	<	mpiEventLoop();
90	<
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
97	–	int i, j, k, globalAtomIndex;
98	–
126		// gather all of the information from the Bass file
127
128		gatherInfo();
#	Line 110 | Line 137 | void SimSetup::createSim(void){
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();
118	–
119	–	// make the integrator
150
121	–	makeIntegrator();
122	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 128 | 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
132	–
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	<
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
158	–
203		// init the atoms
204
205	<	double ux, uy, uz, u, uSqr;
162	<
163	<	for(k=0; k<nInfo; k++){
164	<
165	<	the_ff->setSimInfo( &(info[k]) );
205	>	int nMembers, nNew, rb1, rb2;
206
207	+	for (k = 0; k < nInfo; k++){
208	+	the_ff->setSimInfo(&(info[k]));
209	+
210		atomOffset = 0;
211	<	excludeOffset = 0;
212	<	for(i=0; i<info[k].n_mol; i++){
170	<
211	>
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();
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.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222
223		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	–	molInfo.myBends = new Bend*[molInfo.nBends];
183	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
224
225	+	if (molInfo.nBonds > 0)
226	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	+	else
228	+	molInfo.myBonds = NULL;
229	+
230	+	if (molInfo.nBends > 0)
231	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	+	else
233	+	molInfo.myBends = NULL;
234	+
235	+	if (molInfo.nTorsions > 0)
236	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	+	else
238	+	molInfo.myTorsions = NULL;
239	+
240		theBonds = new bond_pair[molInfo.nBonds];
241		theBends = new bend_set[molInfo.nBends];
242		theTorsions = new torsion_set[molInfo.nTorsions];
243	<
243	>
244		// make the Atoms
245	<
246	<	for(j=0; j<molInfo.nAtoms; j++){
247	<
248	<	currentAtom = comp_stamps[stampID]->getAtom( j );
249	<	if( currentAtom->haveOrientation() ){
250	<
251	<	dAtom = new DirectionalAtom( (j + atomOffset),
252	<	info[k].getConfiguration() );
253	<	info[k].n_oriented++;
254	<	molInfo.myAtoms[j] = dAtom;
255	<
256	<	ux = currentAtom->getOrntX();
257	<	uy = currentAtom->getOrntY();
258	<	uz = currentAtom->getOrntZ();
259	<
260	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
261	<
262	<	u = sqrt( uSqr );
263	<	ux = ux / u;
264	<	uy = uy / u;
265	<	uz = uz / u;
266	<
267	<	dAtom->setSUx( ux );
268	<	dAtom->setSUy( uy );
269	<	dAtom->setSUz( uz );
270	<	}
271	<	else{
272	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
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( globalIndex[j+atomOffset] );
276	<
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	<
283	<	currentBond = comp_stamps[stampID]->getBond( j );
284	<	theBonds[j].a = currentBond->getA() + atomOffset;
285	<	theBonds[j].b = currentBond->getB() + atomOffset;
286	<
287	<	exI = theBonds[j].a;
288	<	exJ = theBonds[j].b;
289	<
290	<	// exclude_I must always be the smaller of the pair
291	<	if( exI > exJ ){
292	<	tempEx = exI;
293	<	exI = exJ;
294	<	exJ = tempEx;
295	<	}
296	<	#ifdef IS_MPI
297	<	tempEx = exI;
298	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	<	tempEx = exJ;
249	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	<	#else  // isn't MPI
253	<
254	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	<	#endif  //is_mpi
256	<	}
257	<	excludeOffset += molInfo.nBonds;
258	<
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		//make the bends
301	<	for(j=0; j<molInfo.nBends; j++){
302	<
303	<	currentBend = comp_stamps[stampID]->getBend( j );
304	<	theBends[j].a = currentBend->getA() + atomOffset;
305	<	theBends[j].b = currentBend->getB() + atomOffset;
306	<	theBends[j].c = currentBend->getC() + atomOffset;
307	<
308	<	if( currentBend->haveExtras() ){
309	<
310	<	extras = currentBend->getExtras();
311	<	current_extra = extras;
312	<
313	<	while( current_extra != NULL ){
314	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
315	<
316	<	switch( current_extra->getType() ){
317	<
318	<	case 0:
319	<	theBends[j].ghost =
320	<	current_extra->getInt() + atomOffset;
321	<	theBends[j].isGhost = 1;
322	<	break;
323	<
324	<	case 1:
325	<	theBends[j].ghost =
326	<	(int)current_extra->getDouble() + atomOffset;
327	<	theBends[j].isGhost = 1;
328	<	break;
329	<
330	<	default:
331	<	sprintf( painCave.errMsg,
332	<	"SimSetup Error: ghostVectorSource was neither a "
333	<	"double nor an int.\n"
334	<	"-->Bend[%d] in %s\n",
335	<	j, comp_stamps[stampID]->getID() );
336	<	painCave.isFatal = 1;
337	<	simError();
338	<	}
339	<	}
340	<
341	<	else{
342	<
343	<	sprintf( painCave.errMsg,
344	<	"SimSetup Error: unhandled bend assignment:\n"
345	<	"    -->%s in Bend[%d] in %s\n",
346	<	current_extra->getlhs(),
347	<	j, comp_stamps[stampID]->getID() );
348	<	painCave.isFatal = 1;
349	<	simError();
350	<	}
351	<
352	<	current_extra = current_extra->getNext();
312	<	}
313	<	}
314	<
315	<	if( !theBends[j].isGhost ){
316	<
317	<	exI = theBends[j].a;
318	<	exJ = theBends[j].c;
319	<	}
320	<	else{
321	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].b;
324	<	}
325	<
326	<	// exclude_I must always be the smaller of the pair
327	<	if( exI > exJ ){
328	<	tempEx = exI;
329	<	exI = exJ;
330	<	exJ = tempEx;
331	<	}
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 = info[k].atoms[tempEx]->getGlobalIndex() + 1;
356	<	tempEx = exJ;
357	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
358	<
359	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
360	<	#else  // isn't MPI
361	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
362	<	#endif  //is_mpi
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	>	} else {
363	>
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	<	excludeOffset += molInfo.nBends;
384	<
385	<	for(j=0; j<molInfo.nTorsions; j++){
386	<
387	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
388	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
389	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
390	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
391	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
392	<
393	<	exI = theTorsions[j].a;
394	<	exJ = theTorsions[j].d;
395	<
356	<	// exclude_I must always be the smaller of the pair
357	<	if( exI > exJ ){
358	<	tempEx = exI;
359	<	exI = exJ;
360	<	exJ = tempEx;
361	<	}
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 = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	<	tempEx = exJ;
400	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
401	<
402	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
403	<	#else  // isn't MPI
404	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
405	<	#endif  //is_mpi
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	>	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	<	excludeOffset += molInfo.nTorsions;
415	>
416
417	+	molInfo.myRigidBodies.clear();
418
419	<	// send the arrays off to the forceField for init.
420	<
421	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
422	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
423	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
424	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420	>
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423	>
424	>	// Create the Rigid Body:
425	>
426	>	myRB = new RigidBody();
427	>
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
384	–	info[k].molecules[i].initialize( molInfo );
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	<	}
559	>	}
560		}
561	<
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	<
566	>
567		// clean up the forcefield
568
569	<	the_ff->calcRcut();
569	>	if (!globals->haveRcut()){
570	>
571	>	the_ff->calcRcut();
572	>
573	>	} else {
574	>
575	>	the_ff->setRcut( globals->getRcut() );
576	>	}
577	>
578		the_ff->cleanMe();
403	–
579		}
580
581	<	void SimSetup::initFromBass( void ){
407	<
581	>	void SimSetup::initFromBass(void){
582		int i, j, k;
583		int n_cells;
584		double cellx, celly, cellz;
#	Line 418 | Line 592 | void SimSetup::initFromBass( void ){
592		vel[1] = 0.0;
593		vel[2] = 0.0;
594
595	<	temp1 = (double)tot_nmol / 4.0;
596	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
597	<	temp3 = ceil( temp2 );
595	>	temp1 = (double) tot_nmol / 4.0;
596	>	temp2 = pow(temp1, (1.0 / 3.0));
597	>	temp3 = ceil(temp2);
598
599	<	have_extra =0;
600	<	if( temp2 < temp3 ){ // we have a non-complete lattice
601	<	have_extra =1;
599	>	have_extra = 0;
600	>	if (temp2 < temp3){
601	>	// we have a non-complete lattice
602	>	have_extra = 1;
603
604	<	n_cells = (int)temp3 - 1;
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 );
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" );
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;
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;
#	Line 454 | 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,
462	<	j * celly,
463	<	k * cellz );
637	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
638
639	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
639	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
640
641	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
472	<
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	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	<	}
494	<	else start_ndx = 0;
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	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
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	<	makeElement( i * cellx,
679	<	j * celly,
680	<	k * cellz );
681	<	done = ( current_mol >= tot_nmol );
682	<
683	<	if( !done && n_per_extra > 1 ){
504	<	makeElement( i * cellx + 0.5 * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
509	<
510	<	if( !done && n_per_extra > 2){
511	<	makeElement( i * cellx,
512	<	j * celly + 0.5 * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
516	<
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
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	<	for( i=0; i<info[0].n_atoms; i++ ){
689	<	info[0].atoms[i]->setVel( vel );
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 ){
534	<
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",
550	<	comp_stamps[current_comp]->getID(),
551	<	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	<
712	>
713		pos[0] = x + current_atom->getPosX();
714		pos[1] = y + current_atom->getPosY();
715		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
716
717	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
717	>	info[0].atoms[current_atom_ndx]->setPos(pos);
718
719	<	dAtom = (DirectionalAtom *)info[0].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 575 | 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 584 | 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] ){
588	<
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
756		// set the easy ones first
757
758	<	for( i=0; i<nInfo; i++){
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();
#	Line 610 | Line 765 | void SimSetup::gatherInfo( void ){
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;
772	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
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;
623	<	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		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
818
819	+	for (i = 0; i < nInfo; i++){
820	+	strcpy(info[i].ensemble, ensemble);
821	+
822		// get the mixing rule
823
824	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
824	>	strcpy(info[i].mixingRule, globals->getMixingRule());
825		info[i].usePBC = globals->getPBC();
826		}
827	<
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;
677	<	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 682 | 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	+	//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	+	}
874	+
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() && !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	+	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		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
906
907	<	if( globals->haveSampleTime() ){
907	>	for (i = 0; i < nInfo; i++){
908	>	if (globals->haveSampleTime()){
909		info[i].sampleTime = globals->getSampleTime();
910		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
911		}
912		else{
913		info[i].sampleTime = globals->getRunTime();
914		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
915		}
916	<
917	<	if( globals->haveStatusTime() ){
916	>
917	>	if (globals->haveStatusTime()){
918		info[i].statusTime = globals->getStatusTime();
919		}
920	<
921	<	if( globals->haveThermalTime() ){
920	>
921	>	if (globals->haveThermalTime()){
922		info[i].thermalTime = globals->getThermalTime();
923	+	} else {
924	+	info[i].thermalTime = globals->getRunTime();
925		}
926
927	+	info[i].resetIntegrator = 0;
928	+	if( globals->haveResetTime() ){
929	+	info[i].resetTime = globals->getResetTime();
930	+	info[i].resetIntegrator = 1;
931	+	}
932	+
933		// check for the temperature set flag
934	+
935	+	if (globals->haveTempSet())
936	+	info[i].setTemp = globals->getTempSet();
937
938	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
938	>	// check for the extended State init
939	>
940	>	info[i].useInitXSstate = globals->getUseInitXSstate();
941	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
942
722	–	// get some of the tricky things that may still be in the globals
723	–
724	–	double boxVector[3];
725	–	if( globals->haveBox() ){
726	–	boxVector[0] = globals->getBox();
727	–	boxVector[1] = globals->getBox();
728	–	boxVector[2] = globals->getBox();
729	–
730	–	info[i].setBox( boxVector );
731	–	}
732	–	else if( globals->haveDensity() ){
733	–
734	–	double vol;
735	–	vol = (double)tot_nmol / globals->getDensity();
736	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	–	boxVector[1] = boxVector[0];
738	–	boxVector[2] = boxVector[0];
739	–
740	–	info[i].setBox( boxVector );
943		}
944	<	else{
945	<	if( !globals->haveBoxX() ){
946	<	sprintf( painCave.errMsg,
947	<	"SimSetup error, no periodic BoxX size given.\n" );
948	<	painCave.isFatal = 1;
949	<	simError();
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	<	boxVector[0] = globals->getBoxX();
966	<
751	<	if( !globals->haveBoxY() ){
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error, no periodic BoxY size given.\n" );
754	<	painCave.isFatal = 1;
755	<	simError();
756	<	}
757	<	boxVector[1] = globals->getBoxY();
758	<
759	<	if( !globals->haveBoxZ() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxZ size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
765	<	boxVector[2] = globals->getBoxZ();
766	<
767	<	info[i].setBox( boxVector );
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	<
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
776	–
989		}
990
991
992	<	void SimSetup::finalInfoCheck( void ){
992	>	void SimSetup::finalInfoCheck(void){
993		int index;
994		int usesDipoles;
995	+	int usesCharges;
996		int i;
997
998	<	for(i=0; i<nInfo; i++){
998	>	for (i = 0; i < nInfo; i++){
999		// check electrostatic parameters
1000	<
1000	>
1001		index = 0;
1002		usesDipoles = 0;
1003	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1003	>	while ((index < info[i].n_atoms) && !usesDipoles){
1004		usesDipoles = (info[i].atoms[index])->hasDipole();
1005		index++;
1006		}
1007	<
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 );
1015	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1016		#endif //is_mpi
1017	<
1018	<	double theEcr, theEst;
1019	<
1020	<	if (globals->getUseRF() ) {
1017	>
1018	>	double theRcut, theRsw;
1019	>
1020	>	if (globals->getUseRF()){
1021		info[i].useReactionField = 1;
1022	<
1023	<	if( !globals->haveECR() ){
1024	<	sprintf( painCave.errMsg,
1025	<	"SimSetup Warning: using default value of 1/2 the smallest "
1026	<	"box length for the electrostaticCutoffRadius.\n"
1027	<	"I hope you have a very fast processor!\n");
1028	<	painCave.isFatal = 0;
1029	<	simError();
1030	<	double smallest;
813	<	smallest = info[i].boxL[0];
814	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	<	theEcr = 0.5 * smallest;
817	<	} else {
818	<	theEcr = globals->getECR();
1022	>
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	<
1033	<	if( !globals->haveEST() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	<	);
826	<	painCave.isFatal = 0;
827	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
1032	>	else{
1033	>	theRcut = globals->getRcut();
1034		}
1035	<
1036	<	info[i].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;
841	<	simError();
1035	>
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	<	info[i].dielectric = globals->getDielectric();
1046	<	}
845	<	else {
846	<	if (usesDipoles) {
847	<
848	<	if( !globals->haveECR() ){
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup Warning: using default value of 1/2 the smallest "
851	<	"box length for the electrostaticCutoffRadius.\n"
852	<	"I hope you have a very fast processor!\n");
853	<	painCave.isFatal = 0;
854	<	simError();
855	<	double smallest;
856	<	smallest = info[i].boxL[0];
857	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	<	theEcr = 0.5 * smallest;
860	<	} else {
861	<	theEcr = globals->getECR();
862	<	}
863	<
864	<	if( !globals->haveEST() ){
865	<	sprintf( painCave.errMsg,
866	<	"SimSetup Warning: using default value of 0.05 * the "
867	<	"electrostaticCutoffRadius for the "
868	<	"electrostaticSkinThickness\n"
869	<	);
870	<	painCave.isFatal = 0;
871	<	simError();
872	<	theEst = 0.05 * theEcr;
873	<	} else {
874	<	theEst= globals->getEST();
875	<	}
876	<
877	<	info[i].setEcr( theEcr, theEst );
1045	>	else{
1046	>	theRsw = globals->getRsw();
1047		}
1048	<	}
1049	<	}
1048	>
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	>	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
886	–
1099		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
1100
1101	+	void SimSetup::initSystemCoords(void){
1102	+	int i;
1103	+
1104		char* inName;
1105
1106	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1107
1108	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1109	<
1110	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1111	<
899	<	if( globals->haveInitialConfig() ){
900	<
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		inName = globals->getInitialConfig();
1117	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
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
1124	<
1123	>	fileInit->readInit(info); // default velocities on
1124	>
1125		delete fileInit;
1126		}
1127		else{
1128
917	–	#ifdef IS_MPI
918	–
1129		// no init from bass
1130
1131	<	sprintf( painCave.errMsg,
1132	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1133	<	painCave.isFatal;
1131	>	sprintf(painCave.errMsg,
1132	>	"Cannot intialize a simulation without an initial configuration file.\n");
1133	>	painCave.isFatal = 1;;
1134		simError();
1135
926	–	#else
927	–
928	–	initFromBass();
929	–
930	–
931	–	#endif
1136		}
1137	<
1137	>
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
938	–
1142		}
1143
1144
1145	<	void SimSetup::makeOutNames( void ){
943	<
1145	>	void SimSetup::makeOutNames(void){
1146		int k;
1147
946	–
947	–	for(k=0; k<nInfo; k++){
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[k].finalName, globals->getFinalConfig() );
1153	>
1154	>	if (globals->haveFinalConfig()){
1155	>	strcpy(info[k].finalName, globals->getFinalConfig());
1156		}
1157		else{
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	<	}
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	<
1181	>
1182		// make the sample and status out names
1183	<
1184	<	strcpy( info[k].sampleName, inFileName );
1183	>
1184	>	strcpy(info[k].sampleName, inFileName);
1185		char* endTest;
1186	<	int nameLength = strlen( info[k].sampleName );
1186	>	int nameLength = strlen(info[k].sampleName);
1187		endTest = &(info[k].sampleName[nameLength - 5]);
1188	<	if( !strcmp( endTest, ".bass" ) ){
1189	<	strcpy( endTest, ".dump" );
1188	>	if (!strcmp(endTest, ".bass")){
1189	>	strcpy(endTest, ".dump");
1190		}
1191	<	else if( !strcmp( endTest, ".BASS" ) ){
1192	<	strcpy( endTest, ".dump" );
1191	>	else if (!strcmp(endTest, ".BASS")){
1192	>	strcpy(endTest, ".dump");
1193		}
1194		else{
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	<	strcpy( info[k].statusName, inFileName );
1208	<	nameLength = strlen( info[k].statusName );
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	>	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" );
1210	>	if (!strcmp(endTest, ".bass")){
1211	>	strcpy(endTest, ".stat");
1212		}
1213	<	else if( !strcmp( endTest, ".BASS" ) ){
1214	<	strcpy( endTest, ".stat" );
1213	>	else if (!strcmp(endTest, ".BASS")){
1214	>	strcpy(endTest, ".stat");
1215		}
1216		else{
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	<	}
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	<
1228	>
1229		#ifdef IS_MPI
1230	+
1231		}
1232		#endif // is_mpi
1233		}
1234		}
1235
1236
1237	<	void SimSetup::sysObjectsCreation( void ){
1238	<
1239	<	int i,k;
1038	<
1237	>	void SimSetup::sysObjectsCreation(void){
1238	>	int i, k;
1239	>
1240		// create the forceField
1241
1242		createFF();
#	Line 1050 | 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();
1265	<
1266	<	for(k=0; k<nInfo; k++){
1265	>
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++){
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	<	case FF_EAM:
1294	<	the_ff = new EAM_FF();
1295	<	break;
1296	<
1297	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	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
1101	–
1304		}
1305
1306
1307	<	void SimSetup::compList( void ){
1106	<
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];
1312	>	comp_stamps = new MoleculeStamp * [n_components];
1313	>	bool haveCutoffGroups;
1314	>
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	<	for(i=0; i<nInfo; i++){
1319	>
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		}
1122	–
1326
1124	–	for( i=0; i<n_components; i++ ){
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 ){
1133	<
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
1363	+	}
1364
1365	+	void SimSetup::calcSysValues(void){
1366	+	int i;
1367
1368	<	}
1368	>	int* molMembershipArray;
1369
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
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
1383		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1384		molMembershipArray = new int[tot_atoms];
1385	<
1386	<	for(i=0; i<nInfo; i++){
1385	>
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	<
1393	>
1394		info[i].molMembershipArray = molMembershipArray;
1395	<	}
1395	>	}
1396		}
1397
1398		#ifdef IS_MPI
1399
1400	<	void SimSetup::mpiMolDivide( void ){
1194	<
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 );
1200	<
1201	<	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();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	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[0].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	<
1446	>
1447		info[0].n_atoms = mpiSim->getMyNlocal();
1448
1449	<	if( local_atoms != info[0].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[0].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		}
#	Line 1254 | Line 1462 | void SimSetup::mpiMolDivide( void ){
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, l;
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;
1269	–	Exclude** the_excludes;
1481
1482	<
1272	<	for(l=0; l<nInfo; l++){
1273	<
1482	>	for (l = 0; l < nInfo; l++){
1483		// create the atom and short range interaction arrays
1484	<
1485	<	the_atoms = new Atom*[info[l].n_atoms];
1484	>
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
1490	<
1490	>
1491		#ifdef IS_MPI
1492	<
1493	<
1492	>
1493	>
1494		molIndex = 0;
1495	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1496	<
1497	<	if(mol2proc[i] == worldRank ){
1498	<	the_molecules[molIndex].setStampID( molCompType[i] );
1499	<	the_molecules[molIndex].setMyIndex( molIndex );
1500	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
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		}
1503	<
1503	>
1504		#else // is_mpi
1505	<
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[l].molMembershipArray[globalAtomIndex] = molIndex;
1515	<	globalAtomIndex++;
1516	<	}
1517	<	molIndex++;
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		}
1519		}
1312	–
1313	–
1314	–	#endif // is_mpi
1520
1521
1522	<	if( info[l].n_SRI ){
1318	<
1319	<	Exclude::createArray(info[l].n_SRI);
1320	<	the_excludes = new Exclude*[info[l].n_SRI];
1321	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	<	the_excludes[ex] = new Exclude(ex);
1323	<	}
1324	<	info[l].globalExcludes = new int;
1325	<	info[l].n_exclude = info[l].n_SRI;
1326	<	}
1327	<	else{
1328	<
1329	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1331	<	the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair( 0,0 );
1333	<	info[l].globalExcludes = new int;
1334	<	info[l].globalExcludes[0] = 0;
1335	<	info[l].n_exclude = 0;
1336	<	}
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		info[l].atoms = the_atoms;
1530		info[l].molecules = the_molecules;
1531		info[l].nGlobalExcludes = 0;
1343	–	info[l].excludes = the_excludes;
1344	–
1345	–	the_ff->setSimInfo( info );
1532
1533	+	the_ff->setSimInfo(info);
1534		}
1535		}
1536
1537	<	void SimSetup::makeIntegrator( void ){
1351	<
1537	>	void SimSetup::makeIntegrator(void){
1538		int k;
1539
1540	<	NVT<RealIntegrator>*  myNVT = NULL;
1541	<	NPTi<RealIntegrator>* myNPTi = NULL;
1542	<	NPTf<RealIntegrator>* myNPTf = NULL;
1543	<	NPTim<RealIntegrator>* myNPTim = NULL;
1544	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1545	<
1546	<	for(k=0; k<nInfo; k++){
1547	<
1548	<	switch( ensembleCase ){
1549	<
1550	<	case NVE_ENS:
1551	<	if (globals->haveZconstraints()){
1552	<	setupZConstraint(info[k]);
1553	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
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	<	else
1561	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1562	<	break;
1563	<
1564	<	case NVT_ENS:
1565	<	if (globals->haveZconstraints()){
1566	<	setupZConstraint(info[k]);
1377	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	<	}
1379	<	else
1380	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
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	<	myNVT->setTargetTemp(globals->getTargetTemp());
1383	<
1384	<	if (globals->haveTauThermostat())
1385	<	myNVT->setTauThermostat(globals->getTauThermostat());
1386	<
1387	<	else {
1388	<	sprintf( painCave.errMsg,
1389	<	"SimSetup error: If you use the NVT\n"
1390	<	"    ensemble, you must set tauThermostat.\n");
1391	<	painCave.isFatal = 1;
1392	<	simError();
1393	<	}
1394	<	break;
1395	<
1396	<	case NPTi_ENS:
1397	<	if (globals->haveZconstraints()){
1398	<	setupZConstraint(info[k]);
1399	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	<	}
1401	<	else
1402	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1568	>	myNVT->setTargetTemp(globals->getTargetTemp());
1569
1570	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1571	<
1572	<	if (globals->haveTargetPressure())
1573	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1574	<	else {
1575	<	sprintf( painCave.errMsg,
1576	<	"SimSetup error: If you use a constant pressure\n"
1577	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1578	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<
1416	<	if( globals->haveTauThermostat() )
1417	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	<	else{
1419	<	sprintf( painCave.errMsg,
1420	<	"SimSetup error: If you use an NPT\n"
1421	<	"    ensemble, you must set tauThermostat.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauBarostat() )
1427	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauBarostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<	break;
1436	<
1437	<	case NPTf_ENS:
1438	<	if (globals->haveZconstraints()){
1439	<	setupZConstraint(info[k]);
1440	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	<	}
1442	<	else
1443	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
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	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1581	<
1447	<	if (globals->haveTargetPressure())
1448	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	<	else {
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use a constant pressure\n"
1452	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1466	<
1467	<	if( globals->haveTauBarostat() )
1468	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NPTim_ENS:
1479	<	if (globals->haveZconstraints()){
1480	<	setupZConstraint(info[k]);
1481	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	<	}
1483	<	else
1484	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1580	>	info->the_integrator = myNVT;
1581	>	break;
1582
1583	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1584	<
1585	<	if (globals->haveTargetPressure())
1586	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1587	<	else {
1588	<	sprintf( painCave.errMsg,
1589	<	"SimSetup error: If you use a constant pressure\n"
1493	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	<	painCave.isFatal = 1;
1495	<	simError();
1496	<	}
1497	<
1498	<	if( globals->haveTauThermostat() )
1499	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	<	else{
1501	<	sprintf( painCave.errMsg,
1502	<	"SimSetup error: If you use an NPT\n"
1503	<	"    ensemble, you must set tauThermostat.\n");
1504	<	painCave.isFatal = 1;
1505	<	simError();
1506	<	}
1507	<
1508	<	if( globals->haveTauBarostat() )
1509	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	<	else{
1511	<	sprintf( painCave.errMsg,
1512	<	"SimSetup error: If you use an NPT\n"
1513	<	"    ensemble, you must set tauBarostat.\n");
1514	<	painCave.isFatal = 1;
1515	<	simError();
1516	<	}
1517	<	break;
1518	<
1519	<	case NPTfm_ENS:
1520	<	if (globals->haveZconstraints()){
1521	<	setupZConstraint(info[k]);
1522	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	<	}
1524	<	else
1525	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
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	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1592	<
1593	<	if (globals->haveTargetPressure())
1594	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1595	<	else {
1596	<	sprintf( painCave.errMsg,
1597	<	"SimSetup error: If you use a constant pressure\n"
1598	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1599	<	painCave.isFatal = 1;
1600	<	simError();
1601	<	}
1602	<
1603	<	if( globals->haveTauThermostat() )
1604	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1605	<	else{
1606	<	sprintf( painCave.errMsg,
1607	<	"SimSetup error: If you use an NPT\n"
1608	<	"    ensemble, you must set tauThermostat.\n");
1609	<	painCave.isFatal = 1;
1610	<	simError();
1611	<	}
1612	<
1613	<	if( globals->haveTauBarostat() )
1614	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1615	<	else{
1616	<	sprintf( painCave.errMsg,
1617	<	"SimSetup error: If you use an NPT\n"
1618	<	"    ensemble, you must set tauBarostat.\n");
1619	<	painCave.isFatal = 1;
1620	<	simError();
1621	<	}
1622	<	break;
1623	<
1624	<	default:
1625	<	sprintf( painCave.errMsg,
1626	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1627	<	painCave.isFatal = 1;
1628	<	simError();
1591	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1592	>
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	>	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	>	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	>	info->the_integrator = myNPTi;
1624	>	break;
1625	>
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	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1635	>
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->haveTauThermostat())
1647	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1648	>
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());
1659	>
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	>	info->the_integrator = myNPTf;
1669	>	break;
1670	>
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	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1680	>
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 ){
1570	<
1723	>	void SimSetup::initFortran(void){
1724		info[0].refreshSim();
1725	<
1726	<	if( !strcmp( info[0].mixingRule, "standard") ){
1727	<	the_ff->initForceField( LB_MIXING_RULE );
1725	>
1726	>	if (!strcmp(info[0].mixingRule, "standard")){
1727	>	the_ff->initForceField(LB_MIXING_RULE);
1728		}
1729	<	else if( !strcmp( info[0].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",
1582	<	info[0].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,
1590	<	"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::setupZConstraint(SimInfo& theInfo)
1882	<	{
1883	<	int nZConstraints;
1884	<	ZconStamp** zconStamp;
1885	<
1886	<	if(globals->haveZconstraintTime()){
1887	<
1888	<	//add sample time of z-constraint  into SimInfo's property list
1889	<	DoubleData* zconsTimeProp = new DoubleData();
1890	<	zconsTimeProp->setID(ZCONSTIME_ID);
1891	<	zconsTimeProp->setData(globals->getZconsTime());
1892	<	theInfo.addProperty(zconsTimeProp);
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	<	else{
1897	<	sprintf( painCave.errMsg,
1898	<	"ZConstraint error: If you use an ZConstraint\n"
1612	<	" , you must set sample time.\n");
1613	<	painCave.isFatal = 1;
1614	<	simError();
1896	>
1897	>	if (globals->haveMinGTol()){
1898	>	param->setGTol(globals->getMinGTol());
1899		}
1900
1901	<	//push zconsTol into siminfo, if user does not specify
1902	<	//value for zconsTol, a default value will be used
1619	<	DoubleData* zconsTol = new DoubleData();
1620	<	zconsTol->setID(ZCONSTOL_ID);
1621	<	if(globals->haveZconsTol()){
1622	<	zconsTol->setData(globals->getZconsTol());
1901	>	if (globals->haveMinMaxIter()){
1902	>	param->setMaxIteration(globals->getMinMaxIter());
1903		}
1624	–	else{
1625	–	double defaultZConsTol = 0.01;
1626	–	sprintf( painCave.errMsg,
1627	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	–	" , default value %f is used.\n", defaultZConsTol);
1629	–	painCave.isFatal = 0;
1630	–	simError();
1904
1905	<	zconsTol->setData(defaultZConsTol);
1906	<	}
1907	<	theInfo.addProperty(zconsTol);
1905	>	if (globals->haveMinWriteFrq()){
1906	>	param->setMaxIteration(globals->getMinMaxIter());
1907	>	}
1908
1909	<	//set Force Substraction Policy
1910	<	StringData* zconsForcePolicy =  new StringData();
1911	<	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	<
1640	<	if(globals->haveZconsForcePolicy()){
1641	<	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	<	}
1643	<	else{
1644	<	sprintf( painCave.errMsg,
1645	<	"ZConstraint Warning: User does not set force substraction policy, "
1646	<	"average force substraction policy is used\n");
1647	<	painCave.isFatal = 0;
1648	<	simError();
1649	<	zconsForcePolicy->setData("BYNUMBER");
1650	<	}
1651	<
1652	<	theInfo.addProperty(zconsForcePolicy);
1653	<
1654	<	//Determine the name of ouput file and add it into SimInfo's property list
1655	<	//Be careful, do not use inFileName, since it is a pointer which
1656	<	//point to a string at master node, and slave nodes do not contain that string
1909	>	if (globals->haveMinWriteFrq()){
1910	>	param->setWriteFrq(globals->getMinWriteFrq());
1911	>	}
1912
1913	<	string zconsOutput(theInfo.finalName);
1914	<
1915	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	<
1662	<	StringData* zconsFilename = new StringData();
1663	<	zconsFilename->setID(ZCONSFILENAME_ID);
1664	<	zconsFilename->setData(zconsOutput);
1665	<
1666	<	theInfo.addProperty(zconsFilename);
1667	<
1668	<	//setup index, pos and other parameters of z-constraint molecules
1669	<	nZConstraints = globals->getNzConstraints();
1670	<	theInfo.nZconstraints = nZConstraints;
1671	<
1672	<	zconStamp = globals->getZconStamp();
1673	<	ZConsParaItem tempParaItem;
1913	>	if (globals->haveMinStepSize()){
1914	>	param->setStepSize(globals->getMinStepSize());
1915	>	}
1916
1917	<	ZConsParaData* zconsParaData = new ZConsParaData();
1918	<	zconsParaData->setID(ZCONSPARADATA_ID);
1919	<
1678	<	for(int i = 0; i < nZConstraints; i++){
1679	<	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	<	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	<	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	<	tempParaItem.kRatio = zconStamp[i]->getKratio();
1917	>	if (globals->haveMinLSMaxIter()){
1918	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1919	>	}
1920
1921	<	zconsParaData->addItem(tempParaItem);
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	<	//sort the parameters by index of molecules
1941	<	zconsParaData->sortByIndex();
1942	<
1943	<	//push data into siminfo, therefore, we can retrieve later
1944	<	theInfo.addProperty(zconsParaData);
1945	<
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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