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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 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 "OOPSEMinimizer.hpp"
14	+	#include "ConstraintElement.hpp"
15	+	#include "ConstraintPair.hpp"
16	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
#	Line 21 | Line 26
26		#define NVT_ENS        1
27		#define NPTi_ENS       2
28		#define NPTf_ENS       3
29	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
29	>	#define NPTxyz_ENS     4
30
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#define FF_EAM  2
31
32	+	#define FF_DUFF  0
33	+	#define FF_LJ    1
34	+	#define FF_EAM   2
35	+	#define FF_H2O   3
36	+
37		using namespace std;
38
39	+	/**
40	+	* Check whether dividend is divisble by divisor or not
41	+	*/
42	+	bool isDivisible(double dividend, double divisor){
43	+	double tolerance = 0.000001;
44	+	double quotient;
45	+	double diff;
46	+	int intQuotient;
47	+
48	+	quotient = dividend / divisor;
49	+
50	+	if (quotient < 0)
51	+	quotient = -quotient;
52	+
53	+	intQuotient = int (quotient + tolerance);
54	+
55	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
56	+
57	+	if (diff <= tolerance)
58	+	return true;
59	+	else
60	+	return false;
61	+	}
62	+
63		SimSetup::SimSetup(){
64
65	+	initSuspend = false;
66		isInfoArray = 0;
67		nInfo = 1;
68	<
68	>
69		stamps = new MakeStamps();
70		globals = new Globals();
71	<
72	<
71	>
72	>
73		#ifdef IS_MPI
74	<	strcpy( checkPointMsg, "SimSetup creation successful" );
74	>	strcpy(checkPointMsg, "SimSetup creation successful");
75		MPIcheckPoint();
76		#endif // IS_MPI
77		}
#	Line 50 | Line 81 | SimSetup::~SimSetup(){
81		delete globals;
82		}
83
84	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
85	<	info = the_info;
86	<	nInfo = theNinfo;
87	<	isInfoArray = 1;
84	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
85	>	info = the_info;
86	>	nInfo = theNinfo;
87	>	isInfoArray = 1;
88	>	initSuspend = true;
89		}
90
91
92	<	void SimSetup::parseFile( char* fileName ){
61	<
92	>	void SimSetup::parseFile(char* fileName){
93		#ifdef IS_MPI
94	<	if( worldRank == 0 ){
94	>	if (worldRank == 0){
95		#endif // is_mpi
96	<
96	>
97		inFileName = fileName;
98	<	set_interface_stamps( stamps, globals );
99	<
98	>	set_interface_stamps(stamps, globals);
99	>
100		#ifdef IS_MPI
101		mpiEventInit();
102		#endif
103
104	<	yacc_BASS( fileName );
104	>	yacc_BASS(fileName);
105
106		#ifdef IS_MPI
107		throwMPIEvent(NULL);
108		}
109	<	else receiveParse();
109	>	else{
110	>	receiveParse();
111	>	}
112		#endif
113
114		}
115
116		#ifdef IS_MPI
117		void SimSetup::receiveParse(void){
118	<
119	<	set_interface_stamps( stamps, globals );
120	<	mpiEventInit();
121	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
118	>	set_interface_stamps(stamps, globals);
119	>	mpiEventInit();
120	>	MPIcheckPoint();
121	>	mpiEventLoop();
122		}
123
124		#endif // is_mpi
125
126		void SimSetup::createSim(void){
127
97	–	int i, j, k, globalAtomIndex;
98	–
128		// gather all of the information from the Bass file
129
130		gatherInfo();
#	Line 110 | Line 139 | void SimSetup::createSim(void){
139
140		// initialize the system coordinates
141
142	<	if( !isInfoArray ) initSystemCoords();
142	>	if ( !initSuspend ){
143	>	initSystemCoords();
144
145	+	if( !(globals->getUseInitTime()) )
146	+	info[0].currentTime = 0.0;
147	+	}
148	+
149		// make the output filenames
150
151		makeOutNames();
118	–
119	–	// make the integrator
152
121	–	makeIntegrator();
122	–
153		#ifdef IS_MPI
154		mpiSim->mpiRefresh();
155		#endif
#	Line 128 | Line 158 | void SimSetup::createSim(void){
158
159		initFortran();
160
161	+	//creat constraint manager
162	+	for(int i = 0; i < nInfo; i++)
163	+	info[i].consMan = new ConstraintManager(&info[i]);
164
165	+	if (globals->haveMinimizer())
166	+	// make minimizer
167	+	makeMinimizer();
168	+	else
169	+	// make the integrator
170	+	makeIntegrator();
171
172		}
173
174
175	<	void SimSetup::makeMolecules( void ){
176	<
177	<	int k,l;
178	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
175	>	void SimSetup::makeMolecules(void){
176	>	int i, j, k;
177	>	int exI, exJ, exK, exL, slI, slJ;
178	>	int tempI, tempJ, tempK, tempL;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181		molInit molInfo;
182		DirectionalAtom* dAtom;
183	+	RigidBody* myRB;
184	+	StuntDouble* mySD;
185		LinkedAssign* extras;
186		LinkedAssign* current_extra;
187		AtomStamp* currentAtom;
188		BondStamp* currentBond;
189		BendStamp* currentBend;
190		TorsionStamp* currentTorsion;
191	+	RigidBodyStamp* currentRigidBody;
192	+	CutoffGroupStamp* currentCutoffGroup;
193	+	CutoffGroup* myCutoffGroup;
194	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196
197		bond_pair* theBonds;
198		bend_set* theBends;
199		torsion_set* theTorsions;
200
201	<
201	>	set<int> skipList;
202	>
203	>	double phi, theta, psi;
204	>	char* molName;
205	>	char rbName[100];
206	>
207	>	ConstraintPair* consPair; //constraint pair
208	>	ConstraintElement* consElement1;  //first element of constraint pair
209	>	ConstraintElement* consElement2;  //second element of constraint pair
210	>	int whichRigidBody;
211	>	int consAtomIndex;  //index of constraint atom in rigid body's atom array
212	>	vector<pair<int, int> > jointAtoms;
213	>	double bondLength2;
214		//init the forceField paramters
215
216		the_ff->readParams();
217
158	–
218		// init the atoms
219
220	<	double ux, uy, uz, u, uSqr;
162	<
163	<	for(k=0; k<nInfo; k++){
164	<
165	<	the_ff->setSimInfo( &(info[k]) );
220	>	int nMembers, nNew, rb1, rb2;
221
222	+	for (k = 0; k < nInfo; k++){
223	+	the_ff->setSimInfo(&(info[k]));
224	+
225	+	#ifdef IS_MPI
226	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	+	info[k].globalGroupMembership[i] = 0;
229	+	#else
230	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	+	for (i = 0; i < info[k].n_atoms; i++)
232	+	info[k].globalGroupMembership[i] = 0;
233	+	#endif
234	+
235		atomOffset = 0;
236	<	excludeOffset = 0;
237	<	for(i=0; i<info[k].n_mol; i++){
238	<
236	>	groupOffset = 0;
237	>
238	>	for (i = 0; i < info[k].n_mol; i++){
239		stampID = info[k].molecules[i].getStampID();
240	+	molName = comp_stamps[stampID]->getID();
241
242	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
243	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
244	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
242	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
245		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
246	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247	>
248	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249
250		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];
251
252	+	if (molInfo.nBonds > 0)
253	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	+	else
255	+	molInfo.myBonds = NULL;
256	+
257	+	if (molInfo.nBends > 0)
258	+	molInfo.myBends = new Bend*[molInfo.nBends];
259	+	else
260	+	molInfo.myBends = NULL;
261	+
262	+	if (molInfo.nTorsions > 0)
263	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	+	else
265	+	molInfo.myTorsions = NULL;
266	+
267		theBonds = new bond_pair[molInfo.nBonds];
268		theBends = new bend_set[molInfo.nBends];
269		theTorsions = new torsion_set[molInfo.nTorsions];
270	<
270	>
271		// make the Atoms
272	<
273	<	for(j=0; j<molInfo.nAtoms; j++){
274	<
275	<	currentAtom = comp_stamps[stampID]->getAtom( j );
276	<	if( currentAtom->haveOrientation() ){
277	<
278	<	dAtom = new DirectionalAtom( (j + atomOffset),
279	<	info[k].getConfiguration() );
280	<	info[k].n_oriented++;
281	<	molInfo.myAtoms[j] = dAtom;
282	<
283	<	ux = currentAtom->getOrntX();
284	<	uy = currentAtom->getOrntY();
285	<	uz = currentAtom->getOrntZ();
286	<
287	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
288	<
289	<	u = sqrt( uSqr );
290	<	ux = ux / u;
291	<	uy = uy / u;
292	<	uz = uz / u;
293	<
294	<	dAtom->setSUx( ux );
295	<	dAtom->setSUy( uy );
296	<	dAtom->setSUz( uz );
297	<	}
298	<	else{
299	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
272	>
273	>	for (j = 0; j < molInfo.nAtoms; j++){
274	>	currentAtom = comp_stamps[stampID]->getAtom(j);
275	>
276	>	if (currentAtom->haveOrientation()){
277	>	dAtom = new DirectionalAtom((j + atomOffset),
278	>	info[k].getConfiguration());
279	>	info[k].n_oriented++;
280	>	molInfo.myAtoms[j] = dAtom;
281	>
282	>	// Directional Atoms have standard unit vectors which are oriented
283	>	// in space using the three Euler angles.  We assume the standard
284	>	// unit vector was originally along the z axis below.
285	>
286	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
287	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
288	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
289	>
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292	>	}
293	>	else{
294	>
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296	>
297	>	}
298	>
299	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
300		#ifdef IS_MPI
301	<
224	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	<
301	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302		#endif // is_mpi
303		}
304	<
305	<	// make the bonds
306	<	for(j=0; j<molInfo.nBonds; j++){
307	<
308	<	currentBond = comp_stamps[stampID]->getBond( j );
309	<	theBonds[j].a = currentBond->getA() + atomOffset;
310	<	theBonds[j].b = currentBond->getB() + atomOffset;
311	<
312	<	exI = theBonds[j].a;
313	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
304	>
305	>	// make the bonds
306	>	for (j = 0; j < molInfo.nBonds; j++){
307	>	currentBond = comp_stamps[stampID]->getBond(j);
308	>	theBonds[j].a = currentBond->getA() + atomOffset;
309	>	theBonds[j].b = currentBond->getB() + atomOffset;
310	>
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313	>
314		#ifdef IS_MPI
315	<	tempEx = exI;
316	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	<	tempEx = exJ;
318	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
319	<
320	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
321	<	#else  // isn't MPI
322	<
254	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	<	#endif  //is_mpi
315	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
316	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
317	>	#else
318	>	exI = tempI + 1;
319	>	exJ = tempJ + 1;
320	>	#endif
321	>
322	>	info[k].excludes->addPair(exI, exJ);
323		}
324	<	excludeOffset += molInfo.nBonds;
258	<
324	>
325		//make the bends
326	<	for(j=0; j<molInfo.nBends; j++){
327	<
328	<	currentBend = comp_stamps[stampID]->getBend( j );
329	<	theBends[j].a = currentBend->getA() + atomOffset;
330	<	theBends[j].b = currentBend->getB() + atomOffset;
331	<	theBends[j].c = currentBend->getC() + atomOffset;
332	<
333	<	if( currentBend->haveExtras() ){
334	<
335	<	extras = currentBend->getExtras();
336	<	current_extra = extras;
337	<
338	<	while( current_extra != NULL ){
339	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
340	<
341	<	switch( current_extra->getType() ){
342	<
343	<	case 0:
344	<	theBends[j].ghost =
345	<	current_extra->getInt() + atomOffset;
346	<	theBends[j].isGhost = 1;
347	<	break;
348	<
349	<	case 1:
350	<	theBends[j].ghost =
351	<	(int)current_extra->getDouble() + atomOffset;
352	<	theBends[j].isGhost = 1;
353	<	break;
354	<
355	<	default:
356	<	sprintf( painCave.errMsg,
357	<	"SimSetup Error: ghostVectorSource was neither a "
358	<	"double nor an int.\n"
359	<	"-->Bend[%d] in %s\n",
360	<	j, comp_stamps[stampID]->getID() );
361	<	painCave.isFatal = 1;
362	<	simError();
363	<	}
364	<	}
365	<
366	<	else{
367	<
368	<	sprintf( painCave.errMsg,
369	<	"SimSetup Error: unhandled bend assignment:\n"
370	<	"    -->%s in Bend[%d] in %s\n",
371	<	current_extra->getlhs(),
372	<	j, comp_stamps[stampID]->getID() );
373	<	painCave.isFatal = 1;
374	<	simError();
375	<	}
376	<
377	<	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	<	}
326	>	for (j = 0; j < molInfo.nBends; j++){
327	>	currentBend = comp_stamps[stampID]->getBend(j);
328	>	theBends[j].a = currentBend->getA() + atomOffset;
329	>	theBends[j].b = currentBend->getB() + atomOffset;
330	>	theBends[j].c = currentBend->getC() + atomOffset;
331	>
332	>	if (currentBend->haveExtras()){
333	>	extras = currentBend->getExtras();
334	>	current_extra = extras;
335	>
336	>	while (current_extra != NULL){
337	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
338	>	switch (current_extra->getType()){
339	>	case 0:
340	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343	>
344	>	case 1:
345	>	theBends[j].ghost = (int) current_extra->getDouble() +
346	>	atomOffset;
347	>	theBends[j].isGhost = 1;
348	>	break;
349	>
350	>	default:
351	>	sprintf(painCave.errMsg,
352	>	"SimSetup Error: ghostVectorSource was neither a "
353	>	"double nor an int.\n"
354	>	"-->Bend[%d] in %s\n",
355	>	j, comp_stamps[stampID]->getID());
356	>	painCave.isFatal = 1;
357	>	simError();
358	>	}
359	>	}
360	>	else{
361	>	sprintf(painCave.errMsg,
362	>	"SimSetup Error: unhandled bend assignment:\n"
363	>	"    -->%s in Bend[%d] in %s\n",
364	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
365	>	painCave.isFatal = 1;
366	>	simError();
367	>	}
368	>
369	>	current_extra = current_extra->getNext();
370	>	}
371	>	}
372	>
373	>	if (theBends[j].isGhost) {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>
378		#ifdef IS_MPI
379	<	tempEx = exI;
380	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
381	<	tempEx = exJ;
382	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
383	<
384	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
385	<	#else  // isn't MPI
386	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
387	<	#endif  //is_mpi
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386	>
387	>	} else {
388	>
389	>	tempI = theBends[j].a;
390	>	tempJ = theBends[j].b;
391	>	tempK = theBends[j].c;
392	>
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	#endif
402	>
403	>	info[k].excludes->addPair(exI, exK);
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exJ, exK);
406	>	}
407		}
408	<	excludeOffset += molInfo.nBends;
409	<
410	<	for(j=0; j<molInfo.nTorsions; j++){
411	<
412	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
413	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
414	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
415	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
416	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
417	<
418	<	exI = theTorsions[j].a;
419	<	exJ = theTorsions[j].d;
420	<
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	<	}
408	>
409	>	for (j = 0; j < molInfo.nTorsions; j++){
410	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
411	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
412	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
413	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
414	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
415	>
416	>	tempI = theTorsions[j].a;
417	>	tempJ = theTorsions[j].b;
418	>	tempK = theTorsions[j].c;
419	>	tempL = theTorsions[j].d;
420	>
421		#ifdef IS_MPI
422	<	tempEx = exI;
423	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
424	<	tempEx = exJ;
425	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
426	<
427	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
428	<	#else  // isn't MPI
429	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
430	<	#endif  //is_mpi
422	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
423	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
424	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
425	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
426	>	#else
427	>	exI = tempI + 1;
428	>	exJ = tempJ + 1;
429	>	exK = tempK + 1;
430	>	exL = tempL + 1;
431	>	#endif
432	>
433	>	info[k].excludes->addPair(exI, exJ);
434	>	info[k].excludes->addPair(exI, exK);
435	>	info[k].excludes->addPair(exI, exL);
436	>	info[k].excludes->addPair(exJ, exK);
437	>	info[k].excludes->addPair(exJ, exL);
438	>	info[k].excludes->addPair(exK, exL);
439		}
440	<	excludeOffset += molInfo.nTorsions;
440	>
441
442	+	molInfo.myRigidBodies.clear();
443
444	+	for (j = 0; j < molInfo.nRigidBodies; j++){
445	+
446	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
447	+	nMembers = currentRigidBody->getNMembers();
448	+
449	+	// Create the Rigid Body:
450	+
451	+	myRB = new RigidBody();
452	+
453	+	sprintf(rbName,"%s_RB_%d", molName, j);
454	+	myRB->setType(rbName);
455	+
456	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
457	+
458	+	// molI is atom numbering inside this molecule
459	+	molI = currentRigidBody->getMember(rb1);
460	+
461	+	// tempI is atom numbering on local processor
462	+	tempI = molI + atomOffset;
463	+
464	+	// currentAtom is the AtomStamp (which we need for
465	+	// rigid body reference positions)
466	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
467	+
468	+	// When we add to the rigid body, add the atom itself and
469	+	// the stamp info:
470	+
471	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
472	+
473	+	// Add this atom to the Skip List for the integrators
474	+	#ifdef IS_MPI
475	+	slI = info[k].atoms[tempI]->getGlobalIndex();
476	+	#else
477	+	slI = tempI;
478	+	#endif
479	+	skipList.insert(slI);
480	+
481	+	}
482	+
483	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
484	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
485	+
486	+	tempI = currentRigidBody->getMember(rb1);
487	+	tempJ = currentRigidBody->getMember(rb2);
488	+
489	+	// Some explanation is required here.
490	+	// Fortran indexing starts at 1, while c indexing starts at 0
491	+	// Also, in parallel computations, the GlobalIndex is
492	+	// used for the exclude list:
493	+
494	+	#ifdef IS_MPI
495	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497	+	#else
498	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500	+	#endif
501	+
502	+	info[k].excludes->addPair(exI, exJ);
503	+
504	+	}
505	+	}
506	+
507	+	molInfo.myRigidBodies.push_back(myRB);
508	+	info[k].rigidBodies.push_back(myRB);
509	+	}
510	+
511	+
512	+	//create cutoff group for molecule
513	+
514	+	cutoffAtomSet.clear();
515	+	molInfo.myCutoffGroups.clear();
516	+
517	+	for (j = 0; j < nCutoffGroups; j++){
518	+
519	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	+	nMembers = currentCutoffGroup->getNMembers();
521	+
522	+	myCutoffGroup = new CutoffGroup();
523	+
524	+	#ifdef IS_MPI
525	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	+	#else
527	+	myCutoffGroup->setGlobalIndex(groupOffset);
528	+	#endif
529	+
530	+	for (int cg = 0; cg < nMembers; cg++) {
531	+
532	+	// molI is atom numbering inside this molecule
533	+	molI = currentCutoffGroup->getMember(cg);
534	+
535	+	// tempI is atom numbering on local processor
536	+	tempI = molI + atomOffset;
537	+
538	+	#ifdef IS_MPI
539	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	+	#else
542	+	globalID = info[k].atoms[tempI]->getIndex();
543	+	info[k].globalGroupMembership[globalID] = groupOffset;
544	+	#endif
545	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	+	cutoffAtomSet.insert(tempI);
547	+	}
548	+
549	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	+	groupOffset++;
551	+
552	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553	+
554	+
555	+	// create a cutoff group for every atom in current molecule which
556	+	// does not belong to cutoffgroup defined at mdl file
557	+
558	+	for(j = 0; j < molInfo.nAtoms; j++){
559	+
560	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	+	myCutoffGroup = new CutoffGroup();
562	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	+
564	+	#ifdef IS_MPI
565	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	+	#else
569	+	myCutoffGroup->setGlobalIndex(groupOffset);
570	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	+	info[k].globalGroupMembership[globalID] = groupOffset;
572	+	#endif
573	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	+	groupOffset++;
575	+	}
576	+	}
577	+
578	+	// After this is all set up, scan through the atoms to
579	+	// see if they can be added to the integrableObjects:
580	+
581	+	molInfo.myIntegrableObjects.clear();
582	+
583	+
584	+	for (j = 0; j < molInfo.nAtoms; j++){
585	+
586	+	#ifdef IS_MPI
587	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	+	#else
589	+	slJ = j+atomOffset;
590	+	#endif
591	+
592	+	// if they aren't on the skip list, then they can be integrated
593	+
594	+	if (skipList.find(slJ) == skipList.end()) {
595	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	+	info[k].integrableObjects.push_back(mySD);
597	+	molInfo.myIntegrableObjects.push_back(mySD);
598	+	}
599	+	}
600	+
601	+	// all rigid bodies are integrated:
602	+
603	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	+	info[k].integrableObjects.push_back(mySD);
606	+	molInfo.myIntegrableObjects.push_back(mySD);
607	+	}
608	+
609		// send the arrays off to the forceField for init.
610
611	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
612	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
613	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
614	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
611	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
612	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
613	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
614	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615	>	theTorsions);
616	>
617	>
618	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620
621	+	for (j = 0; j < molInfo.nBonds; j++){
622	+
623	+	//if bond is constrained bond, add it into constraint pair
624	+	if(molInfo.myBonds[j]->is_constrained()){
625	+
626	+	//if both atoms are in the same rigid body, just skip it
627	+	currentBond = comp_stamps[stampID]->getBond(j);
628	+
629	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630	+
631	+	tempI = currentBond->getA() + atomOffset;
632	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	+	else
635	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636	+
637	+	tempJ =  currentBond->getB() + atomOffset;
638	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	+	else
641	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642	+
643	+	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	+	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645	+
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648	+	}//end if(molInfo.myBonds[j]->is_constrained())
649	+	}
650
651	<	info[k].molecules[i].initialize( molInfo );
651	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	>
655	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656
657	+	for(size_t m = 0; m < jointAtoms.size(); m++){
658	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660	+
661	+	consPair = new JointConstraintPair(consElement1, consElement2);
662	+	molInfo.myConstraintPairs.push_back(consPair);
663	+	}
664	+
665	+	}
666	+	}
667
668	+
669	+	info[k].molecules[i].initialize(molInfo);
670	+
671	+
672		atomOffset += molInfo.nAtoms;
673		delete[] theBonds;
674		delete[] theBends;
675		delete[] theTorsions;
676		}
677	+
678	+
679	+
680	+	#ifdef IS_MPI
681	+	// Since the globalGroupMembership has been zero filled and we've only
682	+	// poked values into the atoms we know, we can do an Allreduce
683	+	// to get the full globalGroupMembership array (We think).
684	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	+	// docs said we could.
686	+
687	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688	+
689	+	MPI_Allreduce(info[k].globalGroupMembership,
690	+	ggMjunk,
691	+	mpiSim->getNAtomsGlobal(),
692	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693	+
694	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	+	info[k].globalGroupMembership[i] = ggMjunk[i];
696	+
697	+	delete[] ggMjunk;
698	+
699	+	#endif
700	+
701	+
702	+
703		}
704	<
704	>
705		#ifdef IS_MPI
706	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
706	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
707		MPIcheckPoint();
708		#endif // is_mpi
398	–
399	–	// clean up the forcefield
709
401	–	the_ff->calcRcut();
402	–	the_ff->cleanMe();
403	–
710		}
711
712	<	void SimSetup::initFromBass( void ){
407	<
712	>	void SimSetup::initFromBass(void){
713		int i, j, k;
714		int n_cells;
715		double cellx, celly, cellz;
#	Line 418 | Line 723 | void SimSetup::initFromBass( void ){
723		vel[1] = 0.0;
724		vel[2] = 0.0;
725
726	<	temp1 = (double)tot_nmol / 4.0;
727	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
728	<	temp3 = ceil( temp2 );
726	>	temp1 = (double) tot_nmol / 4.0;
727	>	temp2 = pow(temp1, (1.0 / 3.0));
728	>	temp3 = ceil(temp2);
729
730	<	have_extra =0;
731	<	if( temp2 < temp3 ){ // we have a non-complete lattice
732	<	have_extra =1;
730	>	have_extra = 0;
731	>	if (temp2 < temp3){
732	>	// we have a non-complete lattice
733	>	have_extra = 1;
734
735	<	n_cells = (int)temp3 - 1;
735	>	n_cells = (int) temp3 - 1;
736		cellx = info[0].boxL[0] / temp3;
737		celly = info[0].boxL[1] / temp3;
738		cellz = info[0].boxL[2] / temp3;
739	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
740	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
741	<	n_per_extra = (int)ceil( temp1 );
739	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
740	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
741	>	n_per_extra = (int) ceil(temp1);
742
743	<	if( n_per_extra > 4){
744	<	sprintf( painCave.errMsg,
745	<	"SimSetup error. There has been an error in constructing"
746	<	" the non-complete lattice.\n" );
743	>	if (n_per_extra > 4){
744	>	sprintf(painCave.errMsg,
745	>	"SimSetup error. There has been an error in constructing"
746	>	" the non-complete lattice.\n");
747		painCave.isFatal = 1;
748		simError();
749		}
750		}
751		else{
752	<	n_cells = (int)temp3;
752	>	n_cells = (int) temp3;
753		cellx = info[0].boxL[0] / temp3;
754		celly = info[0].boxL[1] / temp3;
755		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 760 | void SimSetup::initFromBass( void ){
760		current_comp = 0;
761		current_atom_ndx = 0;
762
763	<	for( i=0; i < n_cells ; i++ ){
764	<	for( j=0; j < n_cells; j++ ){
765	<	for( k=0; k < n_cells; k++ ){
763	>	for (i = 0; i < n_cells ; i++){
764	>	for (j = 0; j < n_cells; j++){
765	>	for (k = 0; k < n_cells; k++){
766	>	makeElement(i * cellx, j * celly, k * cellz);
767
768	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
768	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
769
770	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
770	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
771
772	<	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 );
772	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
773		}
774		}
775		}
776
777	<	if( have_extra ){
777	>	if (have_extra){
778		done = 0;
779
780		int start_ndx;
781	<	for( i=0; i < (n_cells+1) && !done; i++ ){
782	<	for( j=0; j < (n_cells+1) && !done; j++ ){
781	>	for (i = 0; i < (n_cells + 1) && !done; i++){
782	>	for (j = 0; j < (n_cells + 1) && !done; j++){
783	>	if (i < n_cells){
784	>	if (j < n_cells){
785	>	start_ndx = n_cells;
786	>	}
787	>	else
788	>	start_ndx = 0;
789	>	}
790	>	else
791	>	start_ndx = 0;
792
793	<	if( i < n_cells ){
793	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
794	>	makeElement(i * cellx, j * celly, k * cellz);
795	>	done = (current_mol >= tot_nmol);
796
797	<	if( j < n_cells ){
798	<	start_ndx = n_cells;
799	<	}
800	<	else start_ndx = 0;
801	<	}
494	<	else start_ndx = 0;
797	>	if (!done && n_per_extra > 1){
798	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
799	>	k * cellz);
800	>	done = (current_mol >= tot_nmol);
801	>	}
802
803	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
803	>	if (!done && n_per_extra > 2){
804	>	makeElement(i * cellx, j * celly + 0.5 * celly,
805	>	k * cellz + 0.5 * cellz);
806	>	done = (current_mol >= tot_nmol);
807	>	}
808
809	<	makeElement( i * cellx,
810	<	j * celly,
811	<	k * cellz );
812	<	done = ( current_mol >= tot_nmol );
813	<
814	<	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	<	}
809	>	if (!done && n_per_extra > 3){
810	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
811	>	k * cellz + 0.5 * cellz);
812	>	done = (current_mol >= tot_nmol);
813	>	}
814	>	}
815		}
816		}
817		}
818
819	<	for( i=0; i<info[0].n_atoms; i++ ){
820	<	info[0].atoms[i]->setVel( vel );
819	>	for (i = 0; i < info[0].n_atoms; i++){
820	>	info[0].atoms[i]->setVel(vel);
821		}
822		}
823
824	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
824	>	void SimSetup::makeElement(double x, double y, double z){
825		int k;
826		AtomStamp* current_atom;
827		DirectionalAtom* dAtom;
828		double rotMat[3][3];
829		double pos[3];
830
831	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
832	<
833	<	current_atom = comp_stamps[current_comp]->getAtom( k );
834	<	if( !current_atom->havePosition() ){
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup:initFromBass error.\n"
837	<	"\tComponent %s, atom %s does not have a position specified.\n"
838	<	"\tThe initialization routine is unable to give a start"
839	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
831	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
832	>	current_atom = comp_stamps[current_comp]->getAtom(k);
833	>	if (!current_atom->havePosition()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup:initFromBass error.\n"
836	>	"\tComponent %s, atom %s does not have a position specified.\n"
837	>	"\tThe initialization routine is unable to give a start"
838	>	" position.\n",
839	>	comp_stamps[current_comp]->getID(), current_atom->getType());
840		painCave.isFatal = 1;
841		simError();
842		}
843	<
843	>
844		pos[0] = x + current_atom->getPosX();
845		pos[1] = y + current_atom->getPosY();
846		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
847
848	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
848	>	info[0].atoms[current_atom_ndx]->setPos(pos);
849
850	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
850	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
851	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
852
853		rotMat[0][0] = 1.0;
854		rotMat[0][1] = 0.0;
#	Line 575 | Line 862 | void SimSetup::makeElement( double x, double y, double
862		rotMat[2][1] = 0.0;
863		rotMat[2][2] = 1.0;
864
865	<	dAtom->setA( rotMat );
865	>	dAtom->setA(rotMat);
866		}
867
868		current_atom_ndx++;
#	Line 584 | Line 871 | void SimSetup::makeElement( double x, double y, double
871		current_mol++;
872		current_comp_mol++;
873
874	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
874	>	if (current_comp_mol >= components_nmol[current_comp]){
875		current_comp_mol = 0;
876		current_comp++;
877		}
878		}
879
880
881	<	void SimSetup::gatherInfo( void ){
882	<	int i,j,k;
881	>	void SimSetup::gatherInfo(void){
882	>	int i;
883
884		ensembleCase = -1;
885		ffCase = -1;
886
887		// set the easy ones first
888
889	<	for( i=0; i<nInfo; i++){
889	>	for (i = 0; i < nInfo; i++){
890		info[i].target_temp = globals->getTargetTemp();
891		info[i].dt = globals->getDt();
892		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 896 | void SimSetup::gatherInfo( void ){
896
897		// get the forceField
898
899	<	strcpy( force_field, globals->getForceField() );
899	>	strcpy(force_field, globals->getForceField());
900
901	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
902	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
903	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
901	>	if (!strcasecmp(force_field, "DUFF")){
902	>	ffCase = FF_DUFF;
903	>	}
904	>	else if (!strcasecmp(force_field, "LJ")){
905	>	ffCase = FF_LJ;
906	>	}
907	>	else if (!strcasecmp(force_field, "EAM")){
908	>	ffCase = FF_EAM;
909	>	}
910	>	else if (!strcasecmp(force_field, "WATER")){
911	>	ffCase = FF_H2O;
912	>	}
913		else{
914	<	sprintf( painCave.errMsg,
915	<	"SimSetup Error. Unrecognized force field -> %s\n",
916	<	force_field );
917	<	painCave.isFatal = 1;
623	<	simError();
914	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915	>	force_field);
916	>	painCave.isFatal = 1;
917	>	simError();
918		}
919
920	<	// get the ensemble
920	>	// get the ensemble
921
922	<	strcpy( ensemble, globals->getEnsemble() );
922	>	strcpy(ensemble, globals->getEnsemble());
923
924	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	<	ensembleCase = NPTi_ENS;
634	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	<	else{
638	<	sprintf( painCave.errMsg,
639	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	<	"reverting to NVE for this simulation.\n",
641	<	ensemble );
642	<	painCave.isFatal = 0;
643	<	simError();
644	<	strcpy( ensemble, "NVE" );
924	>	if (!strcasecmp(ensemble, "NVE")){
925		ensembleCase = NVE_ENS;
646	–	}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
651	–
652	–	// get the mixing rule
653	–
654	–	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	–	info[i].usePBC = globals->getPBC();
926		}
927	<
927	>	else if (!strcasecmp(ensemble, "NVT")){
928	>	ensembleCase = NVT_ENS;
929	>	}
930	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
931	>	ensembleCase = NPTi_ENS;
932	>	}
933	>	else if (!strcasecmp(ensemble, "NPTf")){
934	>	ensembleCase = NPTf_ENS;
935	>	}
936	>	else if (!strcasecmp(ensemble, "NPTxyz")){
937	>	ensembleCase = NPTxyz_ENS;
938	>	}
939	>	else{
940	>	sprintf(painCave.errMsg,
941	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
942	>	"\treverting to NVE for this simulation.\n",
943	>	ensemble);
944	>	painCave.isFatal = 0;
945	>	simError();
946	>	strcpy(ensemble, "NVE");
947	>	ensembleCase = NVE_ENS;
948	>	}
949	>
950	>	for (i = 0; i < nInfo; i++){
951	>	strcpy(info[i].ensemble, ensemble);
952	>
953	>	// get the mixing rule
954	>
955	>	strcpy(info[i].mixingRule, globals->getMixingRule());
956	>	info[i].usePBC = globals->getPBC();
957	>	}
958	>
959		// get the components and calculate the tot_nMol and indvidual n_mol
960	<
960	>
961		the_components = globals->getComponents();
962		components_nmol = new int[n_components];
963
964
965	<	if( !globals->haveNMol() ){
965	>	if (!globals->haveNMol()){
966		// we don't have the total number of molecules, so we assume it is
967		// given in each component
968
969		tot_nmol = 0;
970	<	for( i=0; i<n_components; i++ ){
971	<
972	<	if( !the_components[i]->haveNMol() ){
973	<	// we have a problem
974	<	sprintf( painCave.errMsg,
975	<	"SimSetup Error. No global NMol or component NMol"
976	<	" given. Cannot calculate the number of atoms.\n" );
977	<	painCave.isFatal = 1;
677	<	simError();
970	>	for (i = 0; i < n_components; i++){
971	>	if (!the_components[i]->haveNMol()){
972	>	// we have a problem
973	>	sprintf(painCave.errMsg,
974	>	"SimSetup Error. No global NMol or component NMol given.\n"
975	>	"\tCannot calculate the number of atoms.\n");
976	>	painCave.isFatal = 1;
977	>	simError();
978		}
979
980		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 982 | void SimSetup::gatherInfo( void ){
982		}
983		}
984		else{
985	<	sprintf( painCave.errMsg,
986	<	"SimSetup error.\n"
987	<	"\tSorry, the ability to specify total"
988	<	" nMols and then give molfractions in the components\n"
989	<	"\tis not currently supported."
990	<	" Please give nMol in the components.\n" );
985	>	sprintf(painCave.errMsg,
986	>	"SimSetup error.\n"
987	>	"\tSorry, the ability to specify total"
988	>	" nMols and then give molfractions in the components\n"
989	>	"\tis not currently supported."
990	>	" Please give nMol in the components.\n");
991		painCave.isFatal = 1;
992		simError();
993		}
994
995	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
996	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
997	+	sprintf(painCave.errMsg,
998	+	"Sample time is not divisible by dt.\n"
999	+	"\tThis will result in samples that are not uniformly\n"
1000	+	"\tdistributed in time.  If this is a problem, change\n"
1001	+	"\tyour sampleTime variable.\n");
1002	+	painCave.isFatal = 0;
1003	+	simError();
1004	+	}
1005	+
1006	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1007	+	sprintf(painCave.errMsg,
1008	+	"Status time is not divisible by dt.\n"
1009	+	"\tThis will result in status reports that are not uniformly\n"
1010	+	"\tdistributed in time.  If this is a problem, change \n"
1011	+	"\tyour statusTime variable.\n");
1012	+	painCave.isFatal = 0;
1013	+	simError();
1014	+	}
1015	+
1016	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1017	+	sprintf(painCave.errMsg,
1018	+	"Thermal time is not divisible by dt.\n"
1019	+	"\tThis will result in thermalizations that are not uniformly\n"
1020	+	"\tdistributed in time.  If this is a problem, change \n"
1021	+	"\tyour thermalTime variable.\n");
1022	+	painCave.isFatal = 0;
1023	+	simError();
1024	+	}
1025	+
1026	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1027	+	sprintf(painCave.errMsg,
1028	+	"Reset time is not divisible by dt.\n"
1029	+	"\tThis will result in integrator resets that are not uniformly\n"
1030	+	"\tdistributed in time.  If this is a problem, change\n"
1031	+	"\tyour resetTime variable.\n");
1032	+	painCave.isFatal = 0;
1033	+	simError();
1034	+	}
1035	+
1036		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
1037
1038	<	if( globals->haveSampleTime() ){
1038	>	for (i = 0; i < nInfo; i++){
1039	>	if (globals->haveSampleTime()){
1040		info[i].sampleTime = globals->getSampleTime();
1041		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
1042		}
1043		else{
1044		info[i].sampleTime = globals->getRunTime();
1045		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
1046		}
1047	<
1048	<	if( globals->haveStatusTime() ){
1047	>
1048	>	if (globals->haveStatusTime()){
1049		info[i].statusTime = globals->getStatusTime();
1050		}
1051	<
1052	<	if( globals->haveThermalTime() ){
1051	>
1052	>	if (globals->haveThermalTime()){
1053		info[i].thermalTime = globals->getThermalTime();
1054	+	} else {
1055	+	info[i].thermalTime = globals->getRunTime();
1056		}
1057
1058	<	// check for the temperature set flag
1058	>	info[i].resetIntegrator = 0;
1059	>	if( globals->haveResetTime() ){
1060	>	info[i].resetTime = globals->getResetTime();
1061	>	info[i].resetIntegrator = 1;
1062	>	}
1063
1064	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
1064	>	// check for the temperature set flag
1065
1066	<	// get some of the tricky things that may still be in the globals
1067	<
1068	<	double boxVector[3];
1069	<	if( globals->haveBox() ){
1070	<	boxVector[0] = globals->getBox();
1071	<	boxVector[1] = globals->getBox();
1072	<	boxVector[2] = globals->getBox();
1073	<
1074	<	info[i].setBox( boxVector );
1075	<	}
1076	<	else if( globals->haveDensity() ){
1077	<
1078	<	double vol;
1079	<	vol = (double)tot_nmol / globals->getDensity();
1080	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
1081	<	boxVector[1] = boxVector[0];
1082	<	boxVector[2] = boxVector[0];
1083	<
1084	<	info[i].setBox( boxVector );
1085	<	}
1086	<	else{
1087	<	if( !globals->haveBoxX() ){
1088	<	sprintf( painCave.errMsg,
1089	<	"SimSetup error, no periodic BoxX size given.\n" );
1066	>	if (globals->haveTempSet())
1067	>	info[i].setTemp = globals->getTempSet();
1068	>
1069	>	// check for the extended State init
1070	>
1071	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1072	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1073	>
1074	>	// check for thermodynamic integration
1075	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1076	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1077	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1078	>	info[i].thermIntLambda = globals->getThermIntLambda();
1079	>	info[i].thermIntK = globals->getThermIntK();
1080	>
1081	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1082	>	info[i].restraint = myRestraint;
1083	>	}
1084	>	else {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimSetup Error:\n"
1087	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1088	>	"\tthermodynamicIntegrationLambda (and/or\n"
1089	>	"\tthermodynamicIntegrationK) was not specified.\n"
1090	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1091		painCave.isFatal = 1;
1092	<	simError();
1092	>	simError();
1093		}
1094	<	boxVector[0] = globals->getBoxX();
1095	<
1096	<	if( !globals->haveBoxY() ){
1094	>	}
1095	>	else if(globals->getUseLiquidThermInt()) {
1096	>	if (globals->getUseSolidThermInt()) {
1097		sprintf( painCave.errMsg,
1098	<	"SimSetup error, no periodic BoxY size given.\n" );
1099	<	painCave.isFatal = 1;
1098	>	"SimSetup Warning: It appears that you have both solid and\n"
1099	>	"\tliquid thermodynamic integration activated in your .bass\n"
1100	>	"\tfile. To avoid confusion, specify only one technique in\n"
1101	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1102	>	"\twill be assumed for the current simulation. If this is not\n"
1103	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1104	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1105	>	painCave.isFatal = 0;
1106		simError();
1107		}
1108	<	boxVector[1] = globals->getBoxY();
1109	<
1110	<	if( !globals->haveBoxZ() ){
1111	<	sprintf( painCave.errMsg,
1112	<	"SimSetup error, no periodic BoxZ size given.\n" );
1108	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1109	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1110	>	info[i].thermIntLambda = globals->getThermIntLambda();
1111	>	info[i].thermIntK = globals->getThermIntK();
1112	>	}
1113	>	else {
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error:\n"
1116	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1117	>	"\tthermodynamicIntegrationLambda (and/or\n"
1118	>	"\tthermodynamicIntegrationK) was not specified.\n"
1119	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1120		painCave.isFatal = 1;
1121	<	simError();
1121	>	simError();
1122		}
765	–	boxVector[2] = globals->getBoxZ();
766	–
767	–	info[i].setBox( boxVector );
1123		}
1124	<
1124	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1125	>	sprintf(painCave.errMsg,
1126	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1127	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1128	>	"\t'true' in your .bass file.  These keywords are set to\n"
1129	>	"\t'false' by default, so your lambda and/or k values are\n"
1130	>	"\tbeing ignored.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	}
1134		}
1135	+
1136	+	//setup seed for random number generator
1137	+	int seedValue;
1138	+
1139	+	if (globals->haveSeed()){
1140	+	seedValue = globals->getSeed();
1141	+
1142	+	if(seedValue / 1E9 == 0){
1143	+	sprintf(painCave.errMsg,
1144	+	"Seed for sprng library should contain at least 9 digits\n"
1145	+	"OOPSE will generate a seed for user\n");
1146	+	painCave.isFatal = 0;
1147	+	simError();
1148	+
1149	+	//using seed generated by system instead of invalid seed set by user
1150	+	#ifndef IS_MPI
1151	+	seedValue = make_sprng_seed();
1152	+	#else
1153	+	if (worldRank == 0){
1154	+	seedValue = make_sprng_seed();
1155	+	}
1156	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1157	+	#endif
1158	+	}
1159	+	}//end of if branch of globals->haveSeed()
1160	+	else{
1161
1162	+	#ifndef IS_MPI
1163	+	seedValue = make_sprng_seed();
1164	+	#else
1165	+	if (worldRank == 0){
1166	+	seedValue = make_sprng_seed();
1167	+	}
1168	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1169	+	#endif
1170	+	}//end of globals->haveSeed()
1171	+
1172	+	for (int i = 0; i < nInfo; i++){
1173	+	info[i].setSeed(seedValue);
1174	+	}
1175	+
1176		#ifdef IS_MPI
1177	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1177	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1178		MPIcheckPoint();
1179		#endif // is_mpi
776	–
1180		}
1181
1182
1183	<	void SimSetup::finalInfoCheck( void ){
1183	>	void SimSetup::finalInfoCheck(void){
1184		int index;
1185		int usesDipoles;
1186	+	int usesCharges;
1187		int i;
1188
1189	<	for(i=0; i<nInfo; i++){
1189	>	for (i = 0; i < nInfo; i++){
1190		// check electrostatic parameters
1191	<
1191	>
1192		index = 0;
1193		usesDipoles = 0;
1194	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1194	>	while ((index < info[i].n_atoms) && !usesDipoles){
1195		usesDipoles = (info[i].atoms[index])->hasDipole();
1196		index++;
1197		}
1198	<
1198	>	index = 0;
1199	>	usesCharges = 0;
1200	>	while ((index < info[i].n_atoms) && !usesCharges){
1201	>	usesCharges= (info[i].atoms[index])->hasCharge();
1202	>	index++;
1203	>	}
1204		#ifdef IS_MPI
1205		int myUse = usesDipoles;
1206	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1206	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1207		#endif //is_mpi
1208	<
1209	<	double theEcr, theEst;
1210	<
1211	<	if (globals->getUseRF() ) {
1212	<	info[i].useReactionField = 1;
1208	>
1209	>	double theRcut, theRsw;
1210	>
1211	>	if (globals->haveRcut()) {
1212	>	theRcut = globals->getRcut();
1213	>
1214	>	if (globals->haveRsw())
1215	>	theRsw = globals->getRsw();
1216	>	else
1217	>	theRsw = theRcut;
1218
1219	<	if( !globals->haveECR() ){
1220	<	sprintf( painCave.errMsg,
1221	<	"SimSetup Warning: using default value of 1/2 the smallest "
808	<	"box length for the electrostaticCutoffRadius.\n"
809	<	"I hope you have a very fast processor!\n");
810	<	painCave.isFatal = 0;
811	<	simError();
812	<	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();
819	<	}
1219	>	info[i].setDefaultRcut(theRcut, theRsw);
1220	>
1221	>	} else {
1222
1223	<	if( !globals->haveEST() ){
1224	<	sprintf( painCave.errMsg,
1225	<	"SimSetup Warning: using default value of 0.05 * the "
1226	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1227	<	);
1228	<	painCave.isFatal = 0;
1229	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
831	<	}
1223	>	the_ff->calcRcut();
1224	>	theRcut = info[i].getRcut();
1225	>
1226	>	if (globals->haveRsw())
1227	>	theRsw = globals->getRsw();
1228	>	else
1229	>	theRsw = theRcut;
1230
1231	<	info[i].setEcr( theEcr, theEst );
1231	>	info[i].setDefaultRcut(theRcut, theRsw);
1232	>	}
1233	>
1234	>	if (globals->getUseRF()){
1235	>	info[i].useReactionField = 1;
1236
1237	<	if(!globals->haveDielectric() ){
1238	<	sprintf( painCave.errMsg,
1239	<	"SimSetup Error: You are trying to use Reaction Field without"
1240	<	"setting a dielectric constant!\n"
1241	<	);
1242	<	painCave.isFatal = 1;
1243	<	simError();
1237	>	if (!globals->haveRcut()){
1238	>	sprintf(painCave.errMsg,
1239	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1240	>	"\tOOPSE will use a default value of 15.0 angstroms"
1241	>	"\tfor the cutoffRadius.\n");
1242	>	painCave.isFatal = 0;
1243	>	simError();
1244	>	theRcut = 15.0;
1245		}
1246	<	info[i].dielectric = globals->getDielectric();
1247	<	}
1248	<	else {
1249	<	if (usesDipoles) {
1246	>	else{
1247	>	theRcut = globals->getRcut();
1248	>	}
1249	>
1250	>	if (!globals->haveRsw()){
1251	>	sprintf(painCave.errMsg,
1252	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1253	>	"\tOOPSE will use a default value of\n"
1254	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1255	>	painCave.isFatal = 0;
1256	>	simError();
1257	>	theRsw = 0.95 * theRcut;
1258	>	}
1259	>	else{
1260	>	theRsw = globals->getRsw();
1261	>	}
1262	>
1263	>	info[i].setDefaultRcut(theRcut, theRsw);
1264	>
1265	>	if (!globals->haveDielectric()){
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error: No Dielectric constant was set.\n"
1268	>	"\tYou are trying to use Reaction Field without"
1269	>	"\tsetting a dielectric constant!\n");
1270	>	painCave.isFatal = 1;
1271	>	simError();
1272	>	}
1273	>	info[i].dielectric = globals->getDielectric();
1274	>	}
1275	>	else{
1276	>	if (usesDipoles || usesCharges){
1277	>
1278	>	if (!globals->haveRcut()){
1279	>	sprintf(painCave.errMsg,
1280	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1281	>	"\tOOPSE will use a default value of 15.0 angstroms"
1282	>	"\tfor the cutoffRadius.\n");
1283	>	painCave.isFatal = 0;
1284	>	simError();
1285	>	theRcut = 15.0;
1286	>	}
1287	>	else{
1288	>	theRcut = globals->getRcut();
1289	>	}
1290	>
1291	>	if (!globals->haveRsw()){
1292	>	sprintf(painCave.errMsg,
1293	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1294	>	"\tOOPSE will use a default value of\n"
1295	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1296	>	painCave.isFatal = 0;
1297	>	simError();
1298	>	theRsw = 0.95 * theRcut;
1299	>	}
1300	>	else{
1301	>	theRsw = globals->getRsw();
1302	>	}
1303	>
1304	>	info[i].setDefaultRcut(theRcut, theRsw);
1305
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 );
1306		}
1307	<	}
1307	>	}
1308		}
881	–
1309		#ifdef IS_MPI
1310	<	strcpy( checkPointMsg, "post processing checks out" );
1310	>	strcpy(checkPointMsg, "post processing checks out");
1311		MPIcheckPoint();
1312		#endif // is_mpi
1313
1314	+	// clean up the forcefield
1315	+	the_ff->cleanMe();
1316		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
1317
1318	+	void SimSetup::initSystemCoords(void){
1319	+	int i;
1320	+
1321		char* inName;
1322
1323	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1324
1325	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1326	<
1327	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1328	<
899	<	if( globals->haveInitialConfig() ){
900	<
1325	>	for (i = 0; i < info[0].n_atoms; i++)
1326	>	info[0].atoms[i]->setCoords();
1327	>
1328	>	if (globals->haveInitialConfig()){
1329		InitializeFromFile* fileInit;
1330		#ifdef IS_MPI // is_mpi
1331	<	if( worldRank == 0 ){
1331	>	if (worldRank == 0){
1332		#endif //is_mpi
1333		inName = globals->getInitialConfig();
1334	<	fileInit = new InitializeFromFile( inName );
1334	>	fileInit = new InitializeFromFile(inName);
1335		#ifdef IS_MPI
1336	<	}else fileInit = new InitializeFromFile( NULL );
1336	>	}
1337	>	else
1338	>	fileInit = new InitializeFromFile(NULL);
1339		#endif
1340	<	fileInit->readInit( info ); // default velocities on
1341	<
1340	>	fileInit->readInit(info); // default velocities on
1341	>
1342		delete fileInit;
1343		}
1344		else{
1345
916	–	#ifdef IS_MPI
917	–
1346		// no init from bass
1347
1348	<	sprintf( painCave.errMsg,
1349	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1350	<	painCave.isFatal;
1348	>	sprintf(painCave.errMsg,
1349	>	"Cannot intialize a simulation without an initial configuration file.\n");
1350	>	painCave.isFatal = 1;;
1351		simError();
1352
925	–	#else
926	–
927	–	initFromBass();
928	–
929	–
930	–	#endif
1353		}
1354	<
1354	>
1355		#ifdef IS_MPI
1356	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1356	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1357		MPIcheckPoint();
1358		#endif // is_mpi
937	–
1359		}
1360
1361
1362	<	void SimSetup::makeOutNames( void ){
942	<
1362	>	void SimSetup::makeOutNames(void){
1363		int k;
1364
945	–
946	–	for(k=0; k<nInfo; k++){
1365
1366	+	for (k = 0; k < nInfo; k++){
1367		#ifdef IS_MPI
1368	<	if( worldRank == 0 ){
1368	>	if (worldRank == 0){
1369		#endif // is_mpi
1370	<
1371	<	if( globals->haveFinalConfig() ){
1372	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1370	>
1371	>	if (globals->haveFinalConfig()){
1372	>	strcpy(info[k].finalName, globals->getFinalConfig());
1373		}
1374		else{
1375	<	strcpy( info[k].finalName, inFileName );
1376	<	char* endTest;
1377	<	int nameLength = strlen( info[k].finalName );
1378	<	endTest = &(info[k].finalName[nameLength - 5]);
1379	<	if( !strcmp( endTest, ".bass" ) ){
1380	<	strcpy( endTest, ".eor" );
1381	<	}
1382	<	else if( !strcmp( endTest, ".BASS" ) ){
1383	<	strcpy( endTest, ".eor" );
1384	<	}
1385	<	else{
1386	<	endTest = &(info[k].finalName[nameLength - 4]);
1387	<	if( !strcmp( endTest, ".bss" ) ){
1388	<	strcpy( endTest, ".eor" );
1389	<	}
1390	<	else if( !strcmp( endTest, ".mdl" ) ){
1391	<	strcpy( endTest, ".eor" );
1392	<	}
1393	<	else{
1394	<	strcat( info[k].finalName, ".eor" );
1395	<	}
1396	<	}
1375	>	strcpy(info[k].finalName, inFileName);
1376	>	char* endTest;
1377	>	int nameLength = strlen(info[k].finalName);
1378	>	endTest = &(info[k].finalName[nameLength - 5]);
1379	>	if (!strcmp(endTest, ".bass")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else if (!strcmp(endTest, ".BASS")){
1383	>	strcpy(endTest, ".eor");
1384	>	}
1385	>	else{
1386	>	endTest = &(info[k].finalName[nameLength - 4]);
1387	>	if (!strcmp(endTest, ".bss")){
1388	>	strcpy(endTest, ".eor");
1389	>	}
1390	>	else if (!strcmp(endTest, ".mdl")){
1391	>	strcpy(endTest, ".eor");
1392	>	}
1393	>	else{
1394	>	strcat(info[k].finalName, ".eor");
1395	>	}
1396	>	}
1397		}
1398	<
1398	>
1399		// make the sample and status out names
1400	<
1401	<	strcpy( info[k].sampleName, inFileName );
1400	>
1401	>	strcpy(info[k].sampleName, inFileName);
1402		char* endTest;
1403	<	int nameLength = strlen( info[k].sampleName );
1403	>	int nameLength = strlen(info[k].sampleName);
1404		endTest = &(info[k].sampleName[nameLength - 5]);
1405	<	if( !strcmp( endTest, ".bass" ) ){
1406	<	strcpy( endTest, ".dump" );
1405	>	if (!strcmp(endTest, ".bass")){
1406	>	strcpy(endTest, ".dump");
1407		}
1408	<	else if( !strcmp( endTest, ".BASS" ) ){
1409	<	strcpy( endTest, ".dump" );
1408	>	else if (!strcmp(endTest, ".BASS")){
1409	>	strcpy(endTest, ".dump");
1410		}
1411		else{
1412	<	endTest = &(info[k].sampleName[nameLength - 4]);
1413	<	if( !strcmp( endTest, ".bss" ) ){
1414	<	strcpy( endTest, ".dump" );
1415	<	}
1416	<	else if( !strcmp( endTest, ".mdl" ) ){
1417	<	strcpy( endTest, ".dump" );
1418	<	}
1419	<	else{
1420	<	strcat( info[k].sampleName, ".dump" );
1421	<	}
1412	>	endTest = &(info[k].sampleName[nameLength - 4]);
1413	>	if (!strcmp(endTest, ".bss")){
1414	>	strcpy(endTest, ".dump");
1415	>	}
1416	>	else if (!strcmp(endTest, ".mdl")){
1417	>	strcpy(endTest, ".dump");
1418	>	}
1419	>	else{
1420	>	strcat(info[k].sampleName, ".dump");
1421	>	}
1422		}
1423	<
1424	<	strcpy( info[k].statusName, inFileName );
1425	<	nameLength = strlen( info[k].statusName );
1423	>
1424	>	strcpy(info[k].statusName, inFileName);
1425	>	nameLength = strlen(info[k].statusName);
1426		endTest = &(info[k].statusName[nameLength - 5]);
1427	<	if( !strcmp( endTest, ".bass" ) ){
1428	<	strcpy( endTest, ".stat" );
1427	>	if (!strcmp(endTest, ".bass")){
1428	>	strcpy(endTest, ".stat");
1429		}
1430	<	else if( !strcmp( endTest, ".BASS" ) ){
1431	<	strcpy( endTest, ".stat" );
1430	>	else if (!strcmp(endTest, ".BASS")){
1431	>	strcpy(endTest, ".stat");
1432		}
1433		else{
1434	<	endTest = &(info[k].statusName[nameLength - 4]);
1435	<	if( !strcmp( endTest, ".bss" ) ){
1436	<	strcpy( endTest, ".stat" );
1437	<	}
1438	<	else if( !strcmp( endTest, ".mdl" ) ){
1439	<	strcpy( endTest, ".stat" );
1440	<	}
1441	<	else{
1442	<	strcat( info[k].statusName, ".stat" );
1443	<	}
1434	>	endTest = &(info[k].statusName[nameLength - 4]);
1435	>	if (!strcmp(endTest, ".bss")){
1436	>	strcpy(endTest, ".stat");
1437	>	}
1438	>	else if (!strcmp(endTest, ".mdl")){
1439	>	strcpy(endTest, ".stat");
1440	>	}
1441	>	else{
1442	>	strcat(info[k].statusName, ".stat");
1443	>	}
1444		}
1445	<
1445	>
1446	>	strcpy(info[k].rawPotName, inFileName);
1447	>	nameLength = strlen(info[k].rawPotName);
1448	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1449	>	if (!strcmp(endTest, ".bass")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else if (!strcmp(endTest, ".BASS")){
1453	>	strcpy(endTest, ".raw");
1454	>	}
1455	>	else{
1456	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1457	>	if (!strcmp(endTest, ".bss")){
1458	>	strcpy(endTest, ".raw");
1459	>	}
1460	>	else if (!strcmp(endTest, ".mdl")){
1461	>	strcpy(endTest, ".raw");
1462	>	}
1463	>	else{
1464	>	strcat(info[k].rawPotName, ".raw");
1465	>	}
1466	>	}
1467	>
1468		#ifdef IS_MPI
1469	+
1470		}
1471		#endif // is_mpi
1472		}
1473		}
1474
1475
1476	<	void SimSetup::sysObjectsCreation( void ){
1477	<
1478	<	int i,k;
1037	<
1476	>	void SimSetup::sysObjectsCreation(void){
1477	>	int i, k;
1478	>
1479		// create the forceField
1480
1481		createFF();
#	Line 1049 | Line 1490 | void SimSetup::sysObjectsCreation( void ){
1490
1491		#ifdef IS_MPI
1492		// divide the molecules among the processors
1493	<
1493	>
1494		mpiMolDivide();
1495		#endif //is_mpi
1496	<
1496	>
1497		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1498	<
1498	>
1499		makeSysArrays();
1500
1501		// make and initialize the molecules (all but atomic coordinates)
1502	<
1502	>
1503		makeMolecules();
1504	<
1505	<	for(k=0; k<nInfo; k++){
1504	>
1505	>	for (k = 0; k < nInfo; k++){
1506		info[k].identArray = new int[info[k].n_atoms];
1507	<	for(i=0; i<info[k].n_atoms; i++){
1507	>	for (i = 0; i < info[k].n_atoms; i++){
1508		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1509		}
1510		}
1511		}
1512
1513
1514	<	void SimSetup::createFF( void ){
1514	>	void SimSetup::createFF(void){
1515	>	switch (ffCase){
1516	>	case FF_DUFF:
1517	>	the_ff = new DUFF();
1518	>	break;
1519
1520	<	switch( ffCase ){
1520	>	case FF_LJ:
1521	>	the_ff = new LJFF();
1522	>	break;
1523
1524	<	case FF_DUFF:
1525	<	the_ff = new DUFF();
1526	<	break;
1524	>	case FF_EAM:
1525	>	the_ff = new EAM_FF();
1526	>	break;
1527
1528	<	case FF_LJ:
1529	<	the_ff = new LJFF();
1530	<	break;
1528	>	case FF_H2O:
1529	>	the_ff = new WATER();
1530	>	break;
1531
1532	<	case FF_EAM:
1533	<	the_ff = new EAM_FF();
1534	<	break;
1535	<
1536	<	default:
1090	<	sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	<	painCave.isFatal = 1;
1093	<	simError();
1532	>	default:
1533	>	sprintf(painCave.errMsg,
1534	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537		}
1538
1539		#ifdef IS_MPI
1540	<	strcpy( checkPointMsg, "ForceField creation successful" );
1540	>	strcpy(checkPointMsg, "ForceField creation successful");
1541		MPIcheckPoint();
1542		#endif // is_mpi
1100	–
1543		}
1544
1545
1546	<	void SimSetup::compList( void ){
1105	<
1546	>	void SimSetup::compList(void){
1547		int i;
1548		char* id;
1549		LinkedMolStamp* headStamp = new LinkedMolStamp();
1550		LinkedMolStamp* currentStamp = NULL;
1551	<	comp_stamps = new MoleculeStamp*[n_components];
1551	>	comp_stamps = new MoleculeStamp * [n_components];
1552	>	bool haveCutoffGroups;
1553	>
1554	>	haveCutoffGroups = false;
1555
1556		// make an array of molecule stamps that match the components used.
1557		// also extract the used stamps out into a separate linked list
1558	<
1559	<	for(i=0; i<nInfo; i++){
1558	>
1559	>	for (i = 0; i < nInfo; i++){
1560		info[i].nComponents = n_components;
1561		info[i].componentsNmol = components_nmol;
1562		info[i].compStamps = comp_stamps;
1563		info[i].headStamp = headStamp;
1564		}
1121	–
1565
1123	–	for( i=0; i<n_components; i++ ){
1566
1567	+	for (i = 0; i < n_components; i++){
1568		id = the_components[i]->getType();
1569		comp_stamps[i] = NULL;
1570	<
1570	>
1571		// check to make sure the component isn't already in the list
1572
1573	<	comp_stamps[i] = headStamp->match( id );
1574	<	if( comp_stamps[i] == NULL ){
1132	<
1573	>	comp_stamps[i] = headStamp->match(id);
1574	>	if (comp_stamps[i] == NULL){
1575		// extract the component from the list;
1576	<
1577	<	currentStamp = stamps->extractMolStamp( id );
1578	<	if( currentStamp == NULL ){
1579	<	sprintf( painCave.errMsg,
1580	<	"SimSetup error: Component \"%s\" was not found in the "
1581	<	"list of declared molecules\n",
1582	<	id );
1583	<	painCave.isFatal = 1;
1584	<	simError();
1576	>
1577	>	currentStamp = stamps->extractMolStamp(id);
1578	>	if (currentStamp == NULL){
1579	>	sprintf(painCave.errMsg,
1580	>	"SimSetup error: Component \"%s\" was not found in the "
1581	>	"list of declared molecules\n",
1582	>	id);
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585		}
1586	<
1587	<	headStamp->add( currentStamp );
1588	<	comp_stamps[i] = headStamp->match( id );
1586	>
1587	>	headStamp->add(currentStamp);
1588	>	comp_stamps[i] = headStamp->match(id);
1589		}
1590	+
1591	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1592	+	haveCutoffGroups = true;
1593		}
1594	+
1595	+	for (i = 0; i < nInfo; i++)
1596	+	info[i].haveCutoffGroups = haveCutoffGroups;
1597
1598		#ifdef IS_MPI
1599	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1599	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1600		MPIcheckPoint();
1601		#endif // is_mpi
1602	+	}
1603
1604	+	void SimSetup::calcSysValues(void){
1605	+	int i, j;
1606	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1607
1608	<	}
1608	>	int* molMembershipArray;
1609	>	CutoffGroupStamp* cg;
1610
1158	–	void SimSetup::calcSysValues( void ){
1159	–	int i, j, k;
1160	–
1161	–	int *molMembershipArray;
1162	–
1611		tot_atoms = 0;
1612		tot_bonds = 0;
1613		tot_bends = 0;
1614		tot_torsions = 0;
1615	<	for( i=0; i<n_components; i++ ){
1616	<
1617	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1618	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1619	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1615	>	tot_rigid = 0;
1616	>	tot_groups = 0;
1617	>	for (i = 0; i < n_components; i++){
1618	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1619	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1620	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1621		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1622	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1623	+
1624	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1625	+	atomsingroups = 0;
1626	+	for (j=0; j < ncutgroups; j++) {
1627	+	cg = comp_stamps[i]->getCutoffGroup(j);
1628	+	atomsingroups += cg->getNMembers();
1629	+	}
1630	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1631	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1632		}
1633
1634		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1635		molMembershipArray = new int[tot_atoms];
1636	<
1637	<	for(i=0; i<nInfo; i++){
1636	>
1637	>	for (i = 0; i < nInfo; i++){
1638		info[i].n_atoms = tot_atoms;
1639		info[i].n_bonds = tot_bonds;
1640		info[i].n_bends = tot_bends;
1641		info[i].n_torsions = tot_torsions;
1642		info[i].n_SRI = tot_SRI;
1643		info[i].n_mol = tot_nmol;
1644	<
1644	>	info[i].ngroup = tot_groups;
1645		info[i].molMembershipArray = molMembershipArray;
1646	<	}
1646	>	}
1647		}
1648
1649		#ifdef IS_MPI
1650
1651	<	void SimSetup::mpiMolDivide( void ){
1193	<
1651	>	void SimSetup::mpiMolDivide(void){
1652		int i, j, k;
1653		int localMol, allMol;
1654		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1655	+	int local_rigid, local_groups;
1656	+	vector<int> globalMolIndex;
1657	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1658	+	CutoffGroupStamp* cg;
1659
1660	<	mpiSim = new mpiSimulation( info );
1199	<
1200	<	globalIndex = mpiSim->divideLabor();
1660	>	mpiSim = new mpiSimulation(info);
1661
1662	+	mpiSim->divideLabor();
1663	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1664	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1665	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1666	+
1667		// set up the local variables
1668	<
1668	>
1669		mol2proc = mpiSim->getMolToProcMap();
1670		molCompType = mpiSim->getMolComponentType();
1671	<
1671	>
1672		allMol = 0;
1673		localMol = 0;
1674		local_atoms = 0;
1675		local_bonds = 0;
1676		local_bends = 0;
1677		local_torsions = 0;
1678	<	globalAtomIndex = 0;
1678	>	local_rigid = 0;
1679	>	local_groups = 0;
1680	>	globalAtomCounter = 0;
1681
1682	<
1683	<	for( i=0; i<n_components; i++ ){
1682	>	for (i = 0; i < n_components; i++){
1683	>	for (j = 0; j < components_nmol[i]; j++){
1684	>	if (mol2proc[allMol] == worldRank){
1685	>	local_atoms += comp_stamps[i]->getNAtoms();
1686	>	local_bonds += comp_stamps[i]->getNBonds();
1687	>	local_bends += comp_stamps[i]->getNBends();
1688	>	local_torsions += comp_stamps[i]->getNTorsions();
1689	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1690
1691	<	for( j=0; j<components_nmol[i]; j++ ){
1692	<
1693	<	if( mol2proc[allMol] == worldRank ){
1694	<
1695	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1696	<	local_bonds +=    comp_stamps[i]->getNBonds();
1697	<	local_bends +=    comp_stamps[i]->getNBends();
1698	<	local_torsions += comp_stamps[i]->getNTorsions();
1699	<	localMol++;
1691	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1692	>	atomsingroups = 0;
1693	>	for (k=0; k < ncutgroups; k++) {
1694	>	cg = comp_stamps[i]->getCutoffGroup(k);
1695	>	atomsingroups += cg->getNMembers();
1696	>	}
1697	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1698	>	ncutgroups;
1699	>	local_groups += ngroupsinstamp;
1700	>
1701	>	localMol++;
1702		}
1703	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1704	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1705	<	globalAtomIndex++;
1703	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1704	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1705	>	globalAtomCounter++;
1706		}
1707
1708	<	allMol++;
1708	>	allMol++;
1709		}
1710		}
1711		local_SRI = local_bonds + local_bends + local_torsions;
1712	+
1713	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1714
1715	<	info[0].n_atoms = mpiSim->getMyNlocal();
1716	<
1717	<	if( local_atoms != info[0].n_atoms ){
1718	<	sprintf( painCave.errMsg,
1719	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	<	" localAtom (%d) are not equal.\n",
1244	<	info[0].n_atoms,
1245	<	local_atoms );
1715	>	if (local_atoms != info[0].n_atoms){
1716	>	sprintf(painCave.errMsg,
1717	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1718	>	"\tlocalAtom (%d) are not equal.\n",
1719	>	info[0].n_atoms, local_atoms);
1720		painCave.isFatal = 1;
1721		simError();
1722		}
1723
1724	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1725	+	if (local_groups != info[0].ngroup){
1726	+	sprintf(painCave.errMsg,
1727	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1728	+	"\tlocalGroups (%d) are not equal.\n",
1729	+	info[0].ngroup, local_groups);
1730	+	painCave.isFatal = 1;
1731	+	simError();
1732	+	}
1733	+
1734		info[0].n_bonds = local_bonds;
1735		info[0].n_bends = local_bends;
1736		info[0].n_torsions = local_torsions;
1737		info[0].n_SRI = local_SRI;
1738		info[0].n_mol = localMol;
1739
1740	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1740	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1741		MPIcheckPoint();
1742		}
1743	<
1743	>
1744		#endif // is_mpi
1745
1746
1747	<	void SimSetup::makeSysArrays( void ){
1748	<	int i, j, k, l;
1747	>	void SimSetup::makeSysArrays(void){
1748	>
1749	>	#ifndef IS_MPI
1750	>	int k, j;
1751	>	#endif // is_mpi
1752	>	int i, l;
1753
1754		Atom** the_atoms;
1755		Molecule* the_molecules;
1268	–	Exclude** the_excludes;
1756
1757	<
1271	<	for(l=0; l<nInfo; l++){
1272	<
1757	>	for (l = 0; l < nInfo; l++){
1758		// create the atom and short range interaction arrays
1759	<
1760	<	the_atoms = new Atom*[info[l].n_atoms];
1759	>
1760	>	the_atoms = new Atom * [info[l].n_atoms];
1761		the_molecules = new Molecule[info[l].n_mol];
1762		int molIndex;
1763
1764		// initialize the molecule's stampID's
1765	<
1765	>
1766		#ifdef IS_MPI
1767	<
1768	<
1767	>
1768	>
1769		molIndex = 0;
1770	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1771	<
1772	<	if(mol2proc[i] == worldRank ){
1773	<	the_molecules[molIndex].setStampID( molCompType[i] );
1774	<	the_molecules[molIndex].setMyIndex( molIndex );
1775	<	the_molecules[molIndex].setGlobalIndex( i );
1291	<	molIndex++;
1770	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1771	>	if (mol2proc[i] == worldRank){
1772	>	the_molecules[molIndex].setStampID(molCompType[i]);
1773	>	the_molecules[molIndex].setMyIndex(molIndex);
1774	>	the_molecules[molIndex].setGlobalIndex(i);
1775	>	molIndex++;
1776		}
1777		}
1778	<
1778	>
1779		#else // is_mpi
1780	<
1780	>
1781		molIndex = 0;
1782	<	globalAtomIndex = 0;
1783	<	for(i=0; i<n_components; i++){
1784	<	for(j=0; j<components_nmol[i]; j++ ){
1785	<	the_molecules[molIndex].setStampID( i );
1786	<	the_molecules[molIndex].setMyIndex( molIndex );
1787	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1788	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1789	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1790	<	globalAtomIndex++;
1791	<	}
1792	<	molIndex++;
1782	>	globalAtomCounter = 0;
1783	>	for (i = 0; i < n_components; i++){
1784	>	for (j = 0; j < components_nmol[i]; j++){
1785	>	the_molecules[molIndex].setStampID(i);
1786	>	the_molecules[molIndex].setMyIndex(molIndex);
1787	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1788	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1789	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1790	>	globalAtomCounter++;
1791	>	}
1792	>	molIndex++;
1793		}
1794		}
1311	–
1312	–
1313	–	#endif // is_mpi
1795
1796
1797	<	if( info[l].n_SRI ){
1317	<
1318	<	Exclude::createArray(info[l].n_SRI);
1319	<	the_excludes = new Exclude*[info[l].n_SRI];
1320	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	<	the_excludes[ex] = new Exclude(ex);
1322	<	}
1323	<	info[l].globalExcludes = new int;
1324	<	info[l].n_exclude = info[l].n_SRI;
1325	<	}
1326	<	else{
1327	<
1328	<	Exclude::createArray( 1 );
1329	<	the_excludes = new Exclude*;
1330	<	the_excludes[0] = new Exclude(0);
1331	<	the_excludes[0]->setPair( 0,0 );
1332	<	info[l].globalExcludes = new int;
1333	<	info[l].globalExcludes[0] = 0;
1334	<	info[l].n_exclude = 0;
1335	<	}
1797	>	#endif // is_mpi
1798
1799	+	info[l].globalExcludes = new int;
1800	+	info[l].globalExcludes[0] = 0;
1801	+
1802		// set the arrays into the SimInfo object
1803
1804		info[l].atoms = the_atoms;
1805		info[l].molecules = the_molecules;
1806		info[l].nGlobalExcludes = 0;
1342	–	info[l].excludes = the_excludes;
1343	–
1344	–	the_ff->setSimInfo( info );
1807
1808	+	the_ff->setSimInfo(info);
1809		}
1810		}
1811
1812	<	void SimSetup::makeIntegrator( void ){
1350	<
1812	>	void SimSetup::makeIntegrator(void){
1813		int k;
1814
1815	<	NVT<RealIntegrator>*  myNVT = NULL;
1816	<	NPTi<RealIntegrator>* myNPTi = NULL;
1817	<	NPTf<RealIntegrator>* myNPTf = NULL;
1818	<	NPTim<RealIntegrator>* myNPTim = NULL;
1819	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1820	<
1821	<	for(k=0; k<nInfo; k++){
1822	<
1823	<	switch( ensembleCase ){
1824	<
1825	<	case NVE_ENS:
1826	<	if (globals->haveZconstraints()){
1827	<	setupZConstraint(info[k]);
1828	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1815	>	NVE<RealIntegrator>* myNVE = NULL;
1816	>	NVT<RealIntegrator>* myNVT = NULL;
1817	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1818	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1819	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1820	>
1821	>	for (k = 0; k < nInfo; k++){
1822	>	switch (ensembleCase){
1823	>	case NVE_ENS:
1824	>	if (globals->haveZconstraints()){
1825	>	setupZConstraint(info[k]);
1826	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1827	>	}
1828	>	else{
1829	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1830		}
1831	+
1832	+	info->the_integrator = myNVE;
1833	+	break;
1834
1835	<	else
1836	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1837	<	break;
1838	<
1839	<	case NVT_ENS:
1840	<	if (globals->haveZconstraints()){
1841	<	setupZConstraint(info[k]);
1376	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	<	}
1378	<	else
1379	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1835	>	case NVT_ENS:
1836	>	if (globals->haveZconstraints()){
1837	>	setupZConstraint(info[k]);
1838	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1839	>	}
1840	>	else
1841	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1842
1843	<	myNVT->setTargetTemp(globals->getTargetTemp());
1382	<
1383	<	if (globals->haveTauThermostat())
1384	<	myNVT->setTauThermostat(globals->getTauThermostat());
1385	<
1386	<	else {
1387	<	sprintf( painCave.errMsg,
1388	<	"SimSetup error: If you use the NVT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1390	<	painCave.isFatal = 1;
1391	<	simError();
1392	<	}
1393	<	break;
1394	<
1395	<	case NPTi_ENS:
1396	<	if (globals->haveZconstraints()){
1397	<	setupZConstraint(info[k]);
1398	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	<	}
1400	<	else
1401	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1843	>	myNVT->setTargetTemp(globals->getTargetTemp());
1844
1845	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1846	<
1847	<	if (globals->haveTargetPressure())
1848	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1849	<	else {
1850	<	sprintf( painCave.errMsg,
1851	<	"SimSetup error: If you use a constant pressure\n"
1852	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1853	<	painCave.isFatal = 1;
1412	<	simError();
1413	<	}
1414	<
1415	<	if( globals->haveTauThermostat() )
1416	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	<	else{
1418	<	sprintf( painCave.errMsg,
1419	<	"SimSetup error: If you use an NPT\n"
1420	<	"    ensemble, you must set tauThermostat.\n");
1421	<	painCave.isFatal = 1;
1422	<	simError();
1423	<	}
1424	<
1425	<	if( globals->haveTauBarostat() )
1426	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	<	else{
1428	<	sprintf( painCave.errMsg,
1429	<	"SimSetup error: If you use an NPT\n"
1430	<	"    ensemble, you must set tauBarostat.\n");
1431	<	painCave.isFatal = 1;
1432	<	simError();
1433	<	}
1434	<	break;
1435	<
1436	<	case NPTf_ENS:
1437	<	if (globals->haveZconstraints()){
1438	<	setupZConstraint(info[k]);
1439	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	<	}
1441	<	else
1442	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1845	>	if (globals->haveTauThermostat())
1846	>	myNVT->setTauThermostat(globals->getTauThermostat());
1847	>	else{
1848	>	sprintf(painCave.errMsg,
1849	>	"SimSetup error: If you use the NVT\n"
1850	>	"\tensemble, you must set tauThermostat.\n");
1851	>	painCave.isFatal = 1;
1852	>	simError();
1853	>	}
1854
1855	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1856	<
1446	<	if (globals->haveTargetPressure())
1447	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	<	else {
1449	<	sprintf( painCave.errMsg,
1450	<	"SimSetup error: If you use a constant pressure\n"
1451	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	<	painCave.isFatal = 1;
1453	<	simError();
1454	<	}
1455	<
1456	<	if( globals->haveTauThermostat() )
1457	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	<	else{
1459	<	sprintf( painCave.errMsg,
1460	<	"SimSetup error: If you use an NPT\n"
1461	<	"    ensemble, you must set tauThermostat.\n");
1462	<	painCave.isFatal = 1;
1463	<	simError();
1464	<	}
1465	<
1466	<	if( globals->haveTauBarostat() )
1467	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	<	else{
1469	<	sprintf( painCave.errMsg,
1470	<	"SimSetup error: If you use an NPT\n"
1471	<	"    ensemble, you must set tauBarostat.\n");
1472	<	painCave.isFatal = 1;
1473	<	simError();
1474	<	}
1475	<	break;
1476	<
1477	<	case NPTim_ENS:
1478	<	if (globals->haveZconstraints()){
1479	<	setupZConstraint(info[k]);
1480	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	<	}
1482	<	else
1483	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1855	>	info->the_integrator = myNVT;
1856	>	break;
1857
1858	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1859	<
1860	<	if (globals->haveTargetPressure())
1861	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1862	<	else {
1863	<	sprintf( painCave.errMsg,
1864	<	"SimSetup error: If you use a constant pressure\n"
1492	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	<	painCave.isFatal = 1;
1494	<	simError();
1495	<	}
1496	<
1497	<	if( globals->haveTauThermostat() )
1498	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	<	else{
1500	<	sprintf( painCave.errMsg,
1501	<	"SimSetup error: If you use an NPT\n"
1502	<	"    ensemble, you must set tauThermostat.\n");
1503	<	painCave.isFatal = 1;
1504	<	simError();
1505	<	}
1506	<
1507	<	if( globals->haveTauBarostat() )
1508	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	<	else{
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup error: If you use an NPT\n"
1512	<	"    ensemble, you must set tauBarostat.\n");
1513	<	painCave.isFatal = 1;
1514	<	simError();
1515	<	}
1516	<	break;
1517	<
1518	<	case NPTfm_ENS:
1519	<	if (globals->haveZconstraints()){
1520	<	setupZConstraint(info[k]);
1521	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	<	}
1523	<	else
1524	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1858	>	case NPTi_ENS:
1859	>	if (globals->haveZconstraints()){
1860	>	setupZConstraint(info[k]);
1861	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1862	>	}
1863	>	else
1864	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1865
1866	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1867	<
1868	<	if (globals->haveTargetPressure())
1869	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1870	<	else {
1871	<	sprintf( painCave.errMsg,
1872	<	"SimSetup error: If you use a constant pressure\n"
1873	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1874	<	painCave.isFatal = 1;
1875	<	simError();
1876	<	}
1877	<
1878	<	if( globals->haveTauThermostat() )
1879	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1880	<	else{
1881	<	sprintf( painCave.errMsg,
1882	<	"SimSetup error: If you use an NPT\n"
1883	<	"    ensemble, you must set tauThermostat.\n");
1884	<	painCave.isFatal = 1;
1885	<	simError();
1886	<	}
1887	<
1888	<	if( globals->haveTauBarostat() )
1889	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1890	<	else{
1891	<	sprintf( painCave.errMsg,
1892	<	"SimSetup error: If you use an NPT\n"
1893	<	"    ensemble, you must set tauBarostat.\n");
1894	<	painCave.isFatal = 1;
1895	<	simError();
1896	<	}
1897	<	break;
1898	<
1899	<	default:
1900	<	sprintf( painCave.errMsg,
1901	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1902	<	painCave.isFatal = 1;
1903	<	simError();
1866	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1867	>
1868	>	if (globals->haveTargetPressure())
1869	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1870	>	else{
1871	>	sprintf(painCave.errMsg,
1872	>	"SimSetup error: If you use a constant pressure\n"
1873	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1874	>	painCave.isFatal = 1;
1875	>	simError();
1876	>	}
1877	>
1878	>	if (globals->haveTauThermostat())
1879	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1880	>	else{
1881	>	sprintf(painCave.errMsg,
1882	>	"SimSetup error: If you use an NPT\n"
1883	>	"\tensemble, you must set tauThermostat.\n");
1884	>	painCave.isFatal = 1;
1885	>	simError();
1886	>	}
1887	>
1888	>	if (globals->haveTauBarostat())
1889	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1890	>	else{
1891	>	sprintf(painCave.errMsg,
1892	>	"SimSetup error: If you use an NPT\n"
1893	>	"\tensemble, you must set tauBarostat.\n");
1894	>	painCave.isFatal = 1;
1895	>	simError();
1896	>	}
1897	>
1898	>	info->the_integrator = myNPTi;
1899	>	break;
1900	>
1901	>	case NPTf_ENS:
1902	>	if (globals->haveZconstraints()){
1903	>	setupZConstraint(info[k]);
1904	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1905	>	}
1906	>	else
1907	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1908	>
1909	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1910	>
1911	>	if (globals->haveTargetPressure())
1912	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1913	>	else{
1914	>	sprintf(painCave.errMsg,
1915	>	"SimSetup error: If you use a constant pressure\n"
1916	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1917	>	painCave.isFatal = 1;
1918	>	simError();
1919	>	}
1920	>
1921	>	if (globals->haveTauThermostat())
1922	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1923	>
1924	>	else{
1925	>	sprintf(painCave.errMsg,
1926	>	"SimSetup error: If you use an NPT\n"
1927	>	"\tensemble, you must set tauThermostat.\n");
1928	>	painCave.isFatal = 1;
1929	>	simError();
1930	>	}
1931	>
1932	>	if (globals->haveTauBarostat())
1933	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1934	>
1935	>	else{
1936	>	sprintf(painCave.errMsg,
1937	>	"SimSetup error: If you use an NPT\n"
1938	>	"\tensemble, you must set tauBarostat.\n");
1939	>	painCave.isFatal = 1;
1940	>	simError();
1941	>	}
1942	>
1943	>	info->the_integrator = myNPTf;
1944	>	break;
1945	>
1946	>	case NPTxyz_ENS:
1947	>	if (globals->haveZconstraints()){
1948	>	setupZConstraint(info[k]);
1949	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1950	>	}
1951	>	else
1952	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1953	>
1954	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1955	>
1956	>	if (globals->haveTargetPressure())
1957	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1958	>	else{
1959	>	sprintf(painCave.errMsg,
1960	>	"SimSetup error: If you use a constant pressure\n"
1961	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1962	>	painCave.isFatal = 1;
1963	>	simError();
1964	>	}
1965	>
1966	>	if (globals->haveTauThermostat())
1967	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1968	>	else{
1969	>	sprintf(painCave.errMsg,
1970	>	"SimSetup error: If you use an NPT\n"
1971	>	"\tensemble, you must set tauThermostat.\n");
1972	>	painCave.isFatal = 1;
1973	>	simError();
1974	>	}
1975	>
1976	>	if (globals->haveTauBarostat())
1977	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1978	>	else{
1979	>	sprintf(painCave.errMsg,
1980	>	"SimSetup error: If you use an NPT\n"
1981	>	"\tensemble, you must set tauBarostat.\n");
1982	>	painCave.isFatal = 1;
1983	>	simError();
1984	>	}
1985	>
1986	>	info->the_integrator = myNPTxyz;
1987	>	break;
1988	>
1989	>	default:
1990	>	sprintf(painCave.errMsg,
1991	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1992	>	painCave.isFatal = 1;
1993	>	simError();
1994		}
1995		}
1996		}
1997
1998	<	void SimSetup::initFortran( void ){
1569	<
1998	>	void SimSetup::initFortran(void){
1999		info[0].refreshSim();
2000	<
2001	<	if( !strcmp( info[0].mixingRule, "standard") ){
2002	<	the_ff->initForceField( LB_MIXING_RULE );
2000	>
2001	>	if (!strcmp(info[0].mixingRule, "standard")){
2002	>	the_ff->initForceField(LB_MIXING_RULE);
2003		}
2004	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
2005	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
2004	>	else if (!strcmp(info[0].mixingRule, "explicit")){
2005	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
2006		}
2007		else{
2008	<	sprintf( painCave.errMsg,
2009	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info[0].mixingRule );
2008	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2009	>	info[0].mixingRule);
2010		painCave.isFatal = 1;
2011		simError();
2012		}
2013
2014
2015		#ifdef IS_MPI
2016	<	strcpy( checkPointMsg,
1589	<	"Successfully intialized the mixingRule for Fortran." );
2016	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2017		MPIcheckPoint();
2018		#endif // is_mpi
1592	–
2019		}
2020
2021	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
2022	<	{
2023	<	int nZConstraints;
1598	<	ZconStamp** zconStamp;
1599	<
1600	<	if(globals->haveZconstraintTime()){
1601	<
1602	<	//add sample time of z-constraint  into SimInfo's property list
1603	<	DoubleData* zconsTimeProp = new DoubleData();
1604	<	zconsTimeProp->setID(ZCONSTIME_ID);
1605	<	zconsTimeProp->setData(globals->getZconsTime());
1606	<	theInfo.addProperty(zconsTimeProp);
1607	<	}
1608	<	else{
1609	<	sprintf( painCave.errMsg,
1610	<	"ZConstraint error: If you use an ZConstraint\n"
1611	<	" , you must set sample time.\n");
1612	<	painCave.isFatal = 1;
1613	<	simError();
1614	<	}
2021	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
2022	>	int nZConstraints;
2023	>	ZconStamp** zconStamp;
2024
2025	<	//
2026	<	nZConstraints = globals->getNzConstraints();
2027	<	zconStamp = globals->getZconStamp();
2028	<	ZConsParaItem tempParaItem;
2025	>	if (globals->haveZconstraintTime()){
2026	>	//add sample time of z-constraint  into SimInfo's property list
2027	>	DoubleData* zconsTimeProp = new DoubleData();
2028	>	zconsTimeProp->setID(ZCONSTIME_ID);
2029	>	zconsTimeProp->setData(globals->getZconsTime());
2030	>	theInfo.addProperty(zconsTimeProp);
2031	>	}
2032	>	else{
2033	>	sprintf(painCave.errMsg,
2034	>	"ZConstraint error: If you use a ZConstraint,\n"
2035	>	"\tyou must set zconsTime.\n");
2036	>	painCave.isFatal = 1;
2037	>	simError();
2038	>	}
2039
2040	<	ZConsParaData* zconsParaData = new ZConsParaData();
2041	<	zconsParaData->setID(ZCONSPARADATA_ID);
2042	<
2043	<	for(int i = 0; i < nZConstraints; i++){
2040	>	//push zconsTol into siminfo, if user does not specify
2041	>	//value for zconsTol, a default value will be used
2042	>	DoubleData* zconsTol = new DoubleData();
2043	>	zconsTol->setID(ZCONSTOL_ID);
2044	>	if (globals->haveZconsTol()){
2045	>	zconsTol->setData(globals->getZconsTol());
2046	>	}
2047	>	else{
2048	>	double defaultZConsTol = 0.01;
2049	>	sprintf(painCave.errMsg,
2050	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2051	>	"\tOOPSE will use a default value of %f.\n"
2052	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2053	>	defaultZConsTol);
2054	>	painCave.isFatal = 0;
2055	>	simError();
2056	>
2057	>	zconsTol->setData(defaultZConsTol);
2058	>	}
2059	>	theInfo.addProperty(zconsTol);
2060	>
2061	>	//set Force Subtraction Policy
2062	>	StringData* zconsForcePolicy = new StringData();
2063	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2064	>
2065	>	if (globals->haveZconsForcePolicy()){
2066	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2067	>	}
2068	>	else{
2069	>	sprintf(painCave.errMsg,
2070	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2071	>	"\tOOPSE will use PolicyByMass.\n"
2072	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2073	>	painCave.isFatal = 0;
2074	>	simError();
2075	>	zconsForcePolicy->setData("BYMASS");
2076	>	}
2077	>
2078	>	theInfo.addProperty(zconsForcePolicy);
2079	>
2080	>	//set zcons gap
2081	>	DoubleData* zconsGap = new DoubleData();
2082	>	zconsGap->setID(ZCONSGAP_ID);
2083	>
2084	>	if (globals->haveZConsGap()){
2085	>	zconsGap->setData(globals->getZconsGap());
2086	>	theInfo.addProperty(zconsGap);
2087	>	}
2088	>
2089	>	//set zcons fixtime
2090	>	DoubleData* zconsFixtime = new DoubleData();
2091	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
2092	>
2093	>	if (globals->haveZConsFixTime()){
2094	>	zconsFixtime->setData(globals->getZconsFixtime());
2095	>	theInfo.addProperty(zconsFixtime);
2096	>	}
2097	>
2098	>	//set zconsUsingSMD
2099	>	IntData* zconsUsingSMD = new IntData();
2100	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2101	>
2102	>	if (globals->haveZConsUsingSMD()){
2103	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2104	>	theInfo.addProperty(zconsUsingSMD);
2105	>	}
2106	>
2107	>	//Determine the name of ouput file and add it into SimInfo's property list
2108	>	//Be careful, do not use inFileName, since it is a pointer which
2109	>	//point to a string at master node, and slave nodes do not contain that string
2110	>
2111	>	string zconsOutput(theInfo.finalName);
2112	>
2113	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2114	>
2115	>	StringData* zconsFilename = new StringData();
2116	>	zconsFilename->setID(ZCONSFILENAME_ID);
2117	>	zconsFilename->setData(zconsOutput);
2118	>
2119	>	theInfo.addProperty(zconsFilename);
2120	>
2121	>	//setup index, pos and other parameters of z-constraint molecules
2122	>	nZConstraints = globals->getNzConstraints();
2123	>	theInfo.nZconstraints = nZConstraints;
2124	>
2125	>	zconStamp = globals->getZconStamp();
2126	>	ZConsParaItem tempParaItem;
2127	>
2128	>	ZConsParaData* zconsParaData = new ZConsParaData();
2129	>	zconsParaData->setID(ZCONSPARADATA_ID);
2130	>
2131	>	for (int i = 0; i < nZConstraints; i++){
2132		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2133		tempParaItem.zPos = zconStamp[i]->getZpos();
2134		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2135		tempParaItem.kRatio = zconStamp[i]->getKratio();
2136	<
2136	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2137	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2138		zconsParaData->addItem(tempParaItem);
2139	+	}
2140	+
2141	+	//check the uniqueness of index
2142	+	if(!zconsParaData->isIndexUnique()){
2143	+	sprintf(painCave.errMsg,
2144	+	"ZConstraint Error: molIndex is not unique!\n");
2145	+	painCave.isFatal = 1;
2146	+	simError();
2147	+	}
2148	+
2149	+	//sort the parameters by index of molecules
2150	+	zconsParaData->sortByIndex();
2151	+
2152	+	//push data into siminfo, therefore, we can retrieve later
2153	+	theInfo.addProperty(zconsParaData);
2154	+	}
2155	+
2156	+	void SimSetup::makeMinimizer(){
2157	+
2158	+	OOPSEMinimizer* myOOPSEMinimizer;
2159	+	MinimizerParameterSet* param;
2160	+	char minimizerName[100];
2161	+
2162	+	for (int i = 0; i < nInfo; i++){
2163	+
2164	+	//prepare parameter set for minimizer
2165	+	param = new MinimizerParameterSet();
2166	+	param->setDefaultParameter();
2167	+
2168	+	if (globals->haveMinimizer()){
2169	+	param->setFTol(globals->getMinFTol());
2170		}
2171
2172	<	//sort the parameters by index of molecules
2173	<	zconsParaData->sortByIndex();
2174	<
1636	<	//push data into siminfo, therefore, we can retrieve later
1637	<	theInfo.addProperty(zconsParaData);
2172	>	if (globals->haveMinGTol()){
2173	>	param->setGTol(globals->getMinGTol());
2174	>	}
2175
2176	<	//push zconsTol into siminfo, if user does not specify
2177	<	//value for zconsTol, a default value will be used
1641	<	DoubleData* zconsTol = new DoubleData();
1642	<	zconsTol->setID(ZCONSTOL_ID);
1643	<	if(globals->haveZconsTol()){
1644	<	zconsTol->setData(globals->getZconsTol());
2176	>	if (globals->haveMinMaxIter()){
2177	>	param->setMaxIteration(globals->getMinMaxIter());
2178		}
1646	–	else{
1647	–	double defaultZConsTol = 1E-6;
1648	–	sprintf( painCave.errMsg,
1649	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650	–	" , default value %f is used.\n", defaultZConsTol);
1651	–	painCave.isFatal = 0;
1652	–	simError();
2179
2180	<	zconsTol->setData(defaultZConsTol);
2181	<	}
2182	<	theInfo.addProperty(zconsTol);
2183	<
2184	<	//Determine the name of ouput file and add it into SimInfo's property list
2185	<	//Be careful, do not use inFileName, since it is a pointer which
2186	<	//point to a string at master node, and slave nodes do not contain that string
2180	>	if (globals->haveMinWriteFrq()){
2181	>	param->setMaxIteration(globals->getMinMaxIter());
2182	>	}
2183	>
2184	>	if (globals->haveMinWriteFrq()){
2185	>	param->setWriteFrq(globals->getMinWriteFrq());
2186	>	}
2187
2188	<	string zconsOutput(theInfo.finalName);
2189	<
2190	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2191	<
2192	<	StringData* zconsFilename = new StringData();
2193	<	zconsFilename->setID(ZCONSFILENAME_ID);
2194	<	zconsFilename->setData(zconsOutput);
2195	<
2196	<	theInfo.addProperty(zconsFilename);
2188	>	if (globals->haveMinStepSize()){
2189	>	param->setStepSize(globals->getMinStepSize());
2190	>	}
2191	>
2192	>	if (globals->haveMinLSMaxIter()){
2193	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2194	>	}
2195	>
2196	>	if (globals->haveMinLSTol()){
2197	>	param->setLineSearchTol(globals->getMinLSTol());
2198	>	}
2199	>
2200	>	strcpy(minimizerName, globals->getMinimizer());
2201	>
2202	>	if (!strcasecmp(minimizerName, "CG")){
2203	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2204	>	}
2205	>	else if (!strcasecmp(minimizerName, "SD")){
2206	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2207	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2208	>	}
2209	>	else{
2210	>	sprintf(painCave.errMsg,
2211	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2212	>	painCave.isFatal = 0;
2213	>	simError();
2214	>
2215	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2216	>	}
2217	>	info[i].the_integrator = myOOPSEMinimizer;
2218	>
2219	>	//store the minimizer into simInfo
2220	>	info[i].the_minimizer = myOOPSEMinimizer;
2221	>	info[i].has_minimizer = true;
2222	>	}
2223	>
2224		}

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