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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 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 20 | Line 26
26		#define NVT_ENS        1
27		#define NPTi_ENS       2
28		#define NPTf_ENS       3
29	<	#define NPTim_ENS      4
24	<	#define NPTfm_ENS      5
29	>	#define NPTxyz_ENS     4
30
26	–	#define FF_DUFF 0
27	–	#define FF_LJ   1
28	–	#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 49 | 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 ){
60	<
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();
88	<	mpiEventLoop();
89	<
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
96	–	int i, j, k, globalAtomIndex;
97	–
128		// gather all of the information from the Bass file
129	<
129	>
130		gatherInfo();
131
132		// creation of complex system objects
#	Line 104 | Line 134 | void SimSetup::createSim(void){
134		sysObjectsCreation();
135
136		// check on the post processing info
137	<
137	>
138		finalInfoCheck();
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();
117	–
118	–	// make the integrator
152
120	–	makeIntegrator();
121	–
153		#ifdef IS_MPI
154		mpiSim->mpiRefresh();
155		#endif
#	Line 127 | 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
157	–
218		// init the atoms
219
220	<	double ux, uy, uz, u, uSqr;
161	<
162	<	for(k=0; k<nInfo; k++){
163	<
164	<	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]);
179	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	–	molInfo.myBends = new Bend*[molInfo.nBends];
182	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
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),
217	<	info[k].getConfiguration() );
218	<	}
219	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	<
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	<
223	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	<
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;
237	<
238	<	// exclude_I must always be the smaller of the pair
239	<	if( exI > exJ ){
240	<	tempEx = exI;
241	<	exI = exJ;
242	<	exJ = tempEx;
243	<	}
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	<
253	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	<	#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;
257	<
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();
311	<	}
312	<	}
313	<
314	<	if( !theBends[j].isGhost ){
315	<
316	<	exI = theBends[j].a;
317	<	exJ = theBends[j].c;
318	<	}
319	<	else{
320	<
321	<	exI = theBends[j].a;
322	<	exJ = theBends[j].b;
323	<	}
324	<
325	<	// exclude_I must always be the smaller of the pair
326	<	if( exI > exJ ){
327	<	tempEx = exI;
328	<	exI = exJ;
329	<	exJ = tempEx;
330	<	}
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
388	<	}
389	<	excludeOffset += molInfo.nBends;
390	<
391	<	for(j=0; j<molInfo.nTorsions; j++){
392	<
346	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
354	<
355	<	// exclude_I must always be the smaller of the pair
356	<	if( exI > exJ ){
357	<	tempEx = exI;
358	<	exI = exJ;
359	<	exJ = tempEx;
360	<	}
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	<	tempEx = exI;
395	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
396	<	tempEx = exJ;
397	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
398	<
399	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
400	<	#else  // isn't MPI
401	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
402	<	#endif  //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.nTorsions;
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	>	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	>
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	<
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	>
705		#ifdef IS_MPI
706	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
706	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
707		MPIcheckPoint();
708		#endif // is_mpi
397	–
398	–	// clean up the forcefield
709
400	–	the_ff->calcRcut();
401	–	the_ff->cleanMe();
402	–
710		}
711
712	<	void SimSetup::initFromBass( void ){
406	<
712	>	void SimSetup::initFromBass(void){
713		int i, j, k;
714		int n_cells;
715		double cellx, celly, cellz;
#	Line 417 | 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 453 | 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,
461	<	j * celly,
462	<	k * cellz );
768	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
769
770	<	makeElement( i * cellx + 0.5 * cellx,
465	<	j * celly + 0.5 * celly,
466	<	k * cellz );
770	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
771
772	<	makeElement( i * cellx,
469	<	j * celly + 0.5 * celly,
470	<	k * cellz + 0.5 * cellz );
471	<
472	<	makeElement( i * cellx + 0.5 * cellx,
473	<	j * celly,
474	<	k * cellz + 0.5 * cellz );
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	<	}
493	<	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 ){
503	<	makeElement( i * cellx + 0.5 * cellx,
504	<	j * celly + 0.5 * celly,
505	<	k * cellz );
506	<	done = ( current_mol >= tot_nmol );
507	<	}
508	<
509	<	if( !done && n_per_extra > 2){
510	<	makeElement( i * cellx,
511	<	j * celly + 0.5 * celly,
512	<	k * cellz + 0.5 * cellz );
513	<	done = ( current_mol >= tot_nmol );
514	<	}
515	<
516	<	if( !done && n_per_extra > 3){
517	<	makeElement( i * cellx + 0.5 * cellx,
518	<	j * celly,
519	<	k * cellz + 0.5 * cellz );
520	<	done = ( current_mol >= tot_nmol );
521	<	}
522	<	}
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 ){
533	<
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",
549	<	comp_stamps[current_comp]->getID(),
550	<	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();
558	–
559	–	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 574 | 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 583 | 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] ){
587	<
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 609 | 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;
622	<	simError();
914	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915	>	force_field);
916	>	painCave.isFatal = 1;
917	>	simError();
918		}
919	<
919	>	if (globals->haveForceFieldVariant()) {
920	>	strcpy(forcefield_variant, globals->getForceFieldVariant());
921	>	has_forcefield_variant = 1;
922	>	}
923	>
924		// get the ensemble
925
926	<	strcpy( ensemble, globals->getEnsemble() );
926	>	strcpy(ensemble, globals->getEnsemble());
927
928	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
632	<	ensembleCase = NPTi_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
636	<	else{
637	<	sprintf( painCave.errMsg,
638	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	<	"reverting to NVE for this simulation.\n",
640	<	ensemble );
641	<	painCave.isFatal = 0;
642	<	simError();
643	<	strcpy( ensemble, "NVE" );
928	>	if (!strcasecmp(ensemble, "NVE")){
929		ensembleCase = NVE_ENS;
930	<	}
931	<
932	<	for(i=0; i<nInfo; i++){
933	<
934	<	strcpy( info[i].ensemble, ensemble );
930	>	}
931	>	else if (!strcasecmp(ensemble, "NVT")){
932	>	ensembleCase = NVT_ENS;
933	>	}
934	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
935	>	ensembleCase = NPTi_ENS;
936	>	}
937	>	else if (!strcasecmp(ensemble, "NPTf")){
938	>	ensembleCase = NPTf_ENS;
939	>	}
940	>	else if (!strcasecmp(ensemble, "NPTxyz")){
941	>	ensembleCase = NPTxyz_ENS;
942	>	}
943	>	else{
944	>	sprintf(painCave.errMsg,
945	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
946	>	"\treverting to NVE for this simulation.\n",
947	>	ensemble);
948	>	painCave.isFatal = 0;
949	>	simError();
950	>	strcpy(ensemble, "NVE");
951	>	ensembleCase = NVE_ENS;
952	>	}
953
954	+	for (i = 0; i < nInfo; i++){
955	+	strcpy(info[i].ensemble, ensemble);
956	+
957		// get the mixing rule
958
959	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
959	>	strcpy(info[i].mixingRule, globals->getMixingRule());
960		info[i].usePBC = globals->getPBC();
961		}
962	<
962	>
963		// get the components and calculate the tot_nMol and indvidual n_mol
964	<
964	>
965		the_components = globals->getComponents();
966		components_nmol = new int[n_components];
967
968
969	<	if( !globals->haveNMol() ){
969	>	if (!globals->haveNMol()){
970		// we don't have the total number of molecules, so we assume it is
971		// given in each component
972
973		tot_nmol = 0;
974	<	for( i=0; i<n_components; i++ ){
975	<
976	<	if( !the_components[i]->haveNMol() ){
977	<	// we have a problem
978	<	sprintf( painCave.errMsg,
979	<	"SimSetup Error. No global NMol or component NMol"
980	<	" given. Cannot calculate the number of atoms.\n" );
981	<	painCave.isFatal = 1;
676	<	simError();
974	>	for (i = 0; i < n_components; i++){
975	>	if (!the_components[i]->haveNMol()){
976	>	// we have a problem
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup Error. No global NMol or component NMol given.\n"
979	>	"\tCannot calculate the number of atoms.\n");
980	>	painCave.isFatal = 1;
981	>	simError();
982		}
983
984		tot_nmol += the_components[i]->getNMol();
#	Line 681 | Line 986 | void SimSetup::gatherInfo( void ){
986		}
987		}
988		else{
989	<	sprintf( painCave.errMsg,
990	<	"SimSetup error.\n"
991	<	"\tSorry, the ability to specify total"
992	<	" nMols and then give molfractions in the components\n"
993	<	"\tis not currently supported."
994	<	" Please give nMol in the components.\n" );
989	>	sprintf(painCave.errMsg,
990	>	"SimSetup error.\n"
991	>	"\tSorry, the ability to specify total"
992	>	" nMols and then give molfractions in the components\n"
993	>	"\tis not currently supported."
994	>	" Please give nMol in the components.\n");
995		painCave.isFatal = 1;
996		simError();
997		}
998
999	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
1000	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001	+	sprintf(painCave.errMsg,
1002	+	"Sample time is not divisible by dt.\n"
1003	+	"\tThis will result in samples that are not uniformly\n"
1004	+	"\tdistributed in time.  If this is a problem, change\n"
1005	+	"\tyour sampleTime variable.\n");
1006	+	painCave.isFatal = 0;
1007	+	simError();
1008	+	}
1009	+
1010	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011	+	sprintf(painCave.errMsg,
1012	+	"Status time is not divisible by dt.\n"
1013	+	"\tThis will result in status reports that are not uniformly\n"
1014	+	"\tdistributed in time.  If this is a problem, change \n"
1015	+	"\tyour statusTime variable.\n");
1016	+	painCave.isFatal = 0;
1017	+	simError();
1018	+	}
1019	+
1020	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1021	+	sprintf(painCave.errMsg,
1022	+	"Thermal time is not divisible by dt.\n"
1023	+	"\tThis will result in thermalizations that are not uniformly\n"
1024	+	"\tdistributed in time.  If this is a problem, change \n"
1025	+	"\tyour thermalTime variable.\n");
1026	+	painCave.isFatal = 0;
1027	+	simError();
1028	+	}
1029	+
1030	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1031	+	sprintf(painCave.errMsg,
1032	+	"Reset time is not divisible by dt.\n"
1033	+	"\tThis will result in integrator resets that are not uniformly\n"
1034	+	"\tdistributed in time.  If this is a problem, change\n"
1035	+	"\tyour resetTime variable.\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	}
1039	+
1040		// set the status, sample, and thermal kick times
695	–
696	–	for(i=0; i<nInfo; i++){
1041
1042	<	if( globals->haveSampleTime() ){
1042	>	for (i = 0; i < nInfo; i++){
1043	>	if (globals->haveSampleTime()){
1044		info[i].sampleTime = globals->getSampleTime();
1045		info[i].statusTime = info[i].sampleTime;
701	–	info[i].thermalTime = info[i].sampleTime;
1046		}
1047		else{
1048		info[i].sampleTime = globals->getRunTime();
1049		info[i].statusTime = info[i].sampleTime;
706	–	info[i].thermalTime = info[i].sampleTime;
1050		}
1051	<
1052	<	if( globals->haveStatusTime() ){
1051	>
1052	>	if (globals->haveStatusTime()){
1053		info[i].statusTime = globals->getStatusTime();
1054		}
1055	<
1056	<	if( globals->haveThermalTime() ){
1055	>
1056	>	if (globals->haveThermalTime()){
1057		info[i].thermalTime = globals->getThermalTime();
1058	+	} else {
1059	+	info[i].thermalTime = globals->getRunTime();
1060		}
1061
1062	<	// check for the temperature set flag
1062	>	info[i].resetIntegrator = 0;
1063	>	if( globals->haveResetTime() ){
1064	>	info[i].resetTime = globals->getResetTime();
1065	>	info[i].resetIntegrator = 1;
1066	>	}
1067
1068	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
1068	>	// check for the temperature set flag
1069
1070	<	// get some of the tricky things that may still be in the globals
1071	<
1072	<	double boxVector[3];
1073	<	if( globals->haveBox() ){
1074	<	boxVector[0] = globals->getBox();
1075	<	boxVector[1] = globals->getBox();
1076	<	boxVector[2] = globals->getBox();
1077	<
1078	<	info[i].setBox( boxVector );
1079	<	}
1080	<	else if( globals->haveDensity() ){
1081	<
1082	<	double vol;
1083	<	vol = (double)tot_nmol / globals->getDensity();
1084	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
1085	<	boxVector[1] = boxVector[0];
1086	<	boxVector[2] = boxVector[0];
1087	<
1088	<	info[i].setBox( boxVector );
1089	<	}
1090	<	else{
1091	<	if( !globals->haveBoxX() ){
1092	<	sprintf( painCave.errMsg,
1093	<	"SimSetup error, no periodic BoxX size given.\n" );
1070	>	if (globals->haveTempSet())
1071	>	info[i].setTemp = globals->getTempSet();
1072	>
1073	>	// check for the extended State init
1074	>
1075	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1076	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077	>
1078	>	// check for thermodynamic integration
1079	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082	>	info[i].thermIntLambda = globals->getThermIntLambda();
1083	>	info[i].thermIntK = globals->getThermIntK();
1084	>
1085	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086	>	info[i].restraint = myRestraint;
1087	>	}
1088	>	else {
1089	>	sprintf(painCave.errMsg,
1090	>	"SimSetup Error:\n"
1091	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1092	>	"\tthermodynamicIntegrationLambda (and/or\n"
1093	>	"\tthermodynamicIntegrationK) was not specified.\n"
1094	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1095		painCave.isFatal = 1;
1096	<	simError();
1096	>	simError();
1097		}
1098	<	boxVector[0] = globals->getBoxX();
1099	<
1100	<	if( !globals->haveBoxY() ){
1098	>	}
1099	>	else if(globals->getUseLiquidThermInt()) {
1100	>	if (globals->getUseSolidThermInt()) {
1101		sprintf( painCave.errMsg,
1102	<	"SimSetup error, no periodic BoxY size given.\n" );
1103	<	painCave.isFatal = 1;
1102	>	"SimSetup Warning: It appears that you have both solid and\n"
1103	>	"\tliquid thermodynamic integration activated in your .bass\n"
1104	>	"\tfile. To avoid confusion, specify only one technique in\n"
1105	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1106	>	"\twill be assumed for the current simulation. If this is not\n"
1107	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1108	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109	>	painCave.isFatal = 0;
1110		simError();
1111		}
1112	<	boxVector[1] = globals->getBoxY();
1113	<
1114	<	if( !globals->haveBoxZ() ){
1115	<	sprintf( painCave.errMsg,
1116	<	"SimSetup error, no periodic BoxZ size given.\n" );
1112	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114	>	info[i].thermIntLambda = globals->getThermIntLambda();
1115	>	info[i].thermIntK = globals->getThermIntK();
1116	>	}
1117	>	else {
1118	>	sprintf(painCave.errMsg,
1119	>	"SimSetup Error:\n"
1120	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1121	>	"\tthermodynamicIntegrationLambda (and/or\n"
1122	>	"\tthermodynamicIntegrationK) was not specified.\n"
1123	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1124		painCave.isFatal = 1;
1125	<	simError();
1125	>	simError();
1126		}
764	–	boxVector[2] = globals->getBoxZ();
765	–
766	–	info[i].setBox( boxVector );
1127		}
1128	<
1128	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1129	>	sprintf(painCave.errMsg,
1130	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1131	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132	>	"\t'true' in your .bass file.  These keywords are set to\n"
1133	>	"\t'false' by default, so your lambda and/or k values are\n"
1134	>	"\tbeing ignored.\n");
1135	>	painCave.isFatal = 0;
1136	>	simError();
1137	>	}
1138		}
1139	+
1140	+	//setup seed for random number generator
1141	+	int seedValue;
1142	+
1143	+	if (globals->haveSeed()){
1144	+	seedValue = globals->getSeed();
1145	+
1146	+	if(seedValue / 1E9 == 0){
1147	+	sprintf(painCave.errMsg,
1148	+	"Seed for sprng library should contain at least 9 digits\n"
1149	+	"OOPSE will generate a seed for user\n");
1150	+	painCave.isFatal = 0;
1151	+	simError();
1152	+
1153	+	//using seed generated by system instead of invalid seed set by user
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}
1163	+	}//end of if branch of globals->haveSeed()
1164	+	else{
1165
1166	+	#ifndef IS_MPI
1167	+	seedValue = make_sprng_seed();
1168	+	#else
1169	+	if (worldRank == 0){
1170	+	seedValue = make_sprng_seed();
1171	+	}
1172	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1173	+	#endif
1174	+	}//end of globals->haveSeed()
1175	+
1176	+	for (int i = 0; i < nInfo; i++){
1177	+	info[i].setSeed(seedValue);
1178	+	}
1179	+
1180		#ifdef IS_MPI
1181	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1181	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1182		MPIcheckPoint();
1183		#endif // is_mpi
775	–
1184		}
1185
1186
1187	<	void SimSetup::finalInfoCheck( void ){
1187	>	void SimSetup::finalInfoCheck(void){
1188		int index;
1189		int usesDipoles;
1190	+	int usesCharges;
1191		int i;
1192
1193	<	for(i=0; i<nInfo; i++){
1193	>	for (i = 0; i < nInfo; i++){
1194		// check electrostatic parameters
1195	<
1195	>
1196		index = 0;
1197		usesDipoles = 0;
1198	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1198	>	while ((index < info[i].n_atoms) && !usesDipoles){
1199		usesDipoles = (info[i].atoms[index])->hasDipole();
1200		index++;
1201		}
1202	<
1202	>	index = 0;
1203	>	usesCharges = 0;
1204	>	while ((index < info[i].n_atoms) && !usesCharges){
1205	>	usesCharges= (info[i].atoms[index])->hasCharge();
1206	>	index++;
1207	>	}
1208		#ifdef IS_MPI
1209		int myUse = usesDipoles;
1210	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1210	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211		#endif //is_mpi
1212	<
1213	<	double theEcr, theEst;
1214	<
1215	<	if (globals->getUseRF() ) {
1216	<	info[i].useReactionField = 1;
1212	>
1213	>	double theRcut, theRsw;
1214	>
1215	>	if (globals->haveRcut()) {
1216	>	theRcut = globals->getRcut();
1217	>
1218	>	if (globals->haveRsw())
1219	>	theRsw = globals->getRsw();
1220	>	else
1221	>	theRsw = theRcut;
1222
1223	<	if( !globals->haveECR() ){
1224	<	sprintf( painCave.errMsg,
1225	<	"SimSetup Warning: using default value of 1/2 the smallest "
807	<	"box length for the electrostaticCutoffRadius.\n"
808	<	"I hope you have a very fast processor!\n");
809	<	painCave.isFatal = 0;
810	<	simError();
811	<	double smallest;
812	<	smallest = info[i].boxL[0];
813	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	<	theEcr = 0.5 * smallest;
816	<	} else {
817	<	theEcr = globals->getECR();
818	<	}
1223	>	info[i].setDefaultRcut(theRcut, theRsw);
1224	>
1225	>	} else {
1226
1227	<	if( !globals->haveEST() ){
1228	<	sprintf( painCave.errMsg,
1229	<	"SimSetup Warning: using default value of 0.05 * the "
1230	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1231	<	);
1232	<	painCave.isFatal = 0;
1233	<	simError();
827	<	theEst = 0.05 * theEcr;
828	<	} else {
829	<	theEst= globals->getEST();
830	<	}
1227	>	the_ff->calcRcut();
1228	>	theRcut = info[i].getRcut();
1229	>
1230	>	if (globals->haveRsw())
1231	>	theRsw = globals->getRsw();
1232	>	else
1233	>	theRsw = theRcut;
1234
1235	<	info[i].setEcr( theEcr, theEst );
1235	>	info[i].setDefaultRcut(theRcut, theRsw);
1236	>	}
1237	>
1238	>	if (globals->getUseRF()){
1239	>	info[i].useReactionField = 1;
1240
1241	<	if(!globals->haveDielectric() ){
1242	<	sprintf( painCave.errMsg,
1243	<	"SimSetup Error: You are trying to use Reaction Field without"
1244	<	"setting a dielectric constant!\n"
1245	<	);
1246	<	painCave.isFatal = 1;
1247	<	simError();
1241	>	if (!globals->haveRcut()){
1242	>	sprintf(painCave.errMsg,
1243	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1244	>	"\tOOPSE will use a default value of 15.0 angstroms"
1245	>	"\tfor the cutoffRadius.\n");
1246	>	painCave.isFatal = 0;
1247	>	simError();
1248	>	theRcut = 15.0;
1249		}
1250	<	info[i].dielectric = globals->getDielectric();
1251	<	}
1252	<	else {
1253	<	if (usesDipoles) {
1250	>	else{
1251	>	theRcut = globals->getRcut();
1252	>	}
1253	>
1254	>	if (!globals->haveRsw()){
1255	>	sprintf(painCave.errMsg,
1256	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1257	>	"\tOOPSE will use a default value of\n"
1258	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1259	>	painCave.isFatal = 0;
1260	>	simError();
1261	>	theRsw = 0.95 * theRcut;
1262	>	}
1263	>	else{
1264	>	theRsw = globals->getRsw();
1265	>	}
1266	>
1267	>	info[i].setDefaultRcut(theRcut, theRsw);
1268	>
1269	>	if (!globals->haveDielectric()){
1270	>	sprintf(painCave.errMsg,
1271	>	"SimSetup Error: No Dielectric constant was set.\n"
1272	>	"\tYou are trying to use Reaction Field without"
1273	>	"\tsetting a dielectric constant!\n");
1274	>	painCave.isFatal = 1;
1275	>	simError();
1276	>	}
1277	>	info[i].dielectric = globals->getDielectric();
1278	>	}
1279	>	else{
1280	>	if (usesDipoles || usesCharges){
1281	>
1282	>	if (!globals->haveRcut()){
1283	>	sprintf(painCave.errMsg,
1284	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1285	>	"\tOOPSE will use a default value of 15.0 angstroms"
1286	>	"\tfor the cutoffRadius.\n");
1287	>	painCave.isFatal = 0;
1288	>	simError();
1289	>	theRcut = 15.0;
1290	>	}
1291	>	else{
1292	>	theRcut = globals->getRcut();
1293	>	}
1294	>
1295	>	if (!globals->haveRsw()){
1296	>	sprintf(painCave.errMsg,
1297	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1298	>	"\tOOPSE will use a default value of\n"
1299	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1300	>	painCave.isFatal = 0;
1301	>	simError();
1302	>	theRsw = 0.95 * theRcut;
1303	>	}
1304	>	else{
1305	>	theRsw = globals->getRsw();
1306	>	}
1307	>
1308	>	info[i].setDefaultRcut(theRcut, theRsw);
1309
847	–	if( !globals->haveECR() ){
848	–	sprintf( painCave.errMsg,
849	–	"SimSetup Warning: using default value of 1/2 the smallest "
850	–	"box length for the electrostaticCutoffRadius.\n"
851	–	"I hope you have a very fast processor!\n");
852	–	painCave.isFatal = 0;
853	–	simError();
854	–	double smallest;
855	–	smallest = info[i].boxL[0];
856	–	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	–	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	–	theEcr = 0.5 * smallest;
859	–	} else {
860	–	theEcr = globals->getECR();
861	–	}
862	–
863	–	if( !globals->haveEST() ){
864	–	sprintf( painCave.errMsg,
865	–	"SimSetup Warning: using default value of 0.05 * the "
866	–	"electrostaticCutoffRadius for the "
867	–	"electrostaticSkinThickness\n"
868	–	);
869	–	painCave.isFatal = 0;
870	–	simError();
871	–	theEst = 0.05 * theEcr;
872	–	} else {
873	–	theEst= globals->getEST();
874	–	}
875	–
876	–	info[i].setEcr( theEcr, theEst );
1310		}
1311	<	}
1311	>	}
1312		}
880	–
1313		#ifdef IS_MPI
1314	<	strcpy( checkPointMsg, "post processing checks out" );
1314	>	strcpy(checkPointMsg, "post processing checks out");
1315		MPIcheckPoint();
1316		#endif // is_mpi
1317
1318	<	}
1319	<
1320	<	void SimSetup::initSystemCoords( void ){
889	<	int i;
890	<
891	<	std::cerr << "Setting atom Coords\n";
892	<
893	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1318	>	// clean up the forcefield
1319	>	the_ff->cleanMe();
1320	>	}
1321
1322	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1323	<
1324	<	if( globals->haveInitialConfig() ){
1325	<
1322	>	void SimSetup::initSystemCoords(void){
1323	>	int i;
1324	>
1325	>	char* inName;
1326	>
1327	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1328	>
1329	>	for (i = 0; i < info[0].n_atoms; i++)
1330	>	info[0].atoms[i]->setCoords();
1331	>
1332	>	if (globals->haveInitialConfig()){
1333		InitializeFromFile* fileInit;
1334		#ifdef IS_MPI // is_mpi
1335	<	if( worldRank == 0 ){
1335	>	if (worldRank == 0){
1336		#endif //is_mpi
1337	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1337	>	inName = globals->getInitialConfig();
1338	>	fileInit = new InitializeFromFile(inName);
1339		#ifdef IS_MPI
1340	<	}else fileInit = new InitializeFromFile( NULL );
1340	>	}
1341	>	else
1342	>	fileInit = new InitializeFromFile(NULL);
1343		#endif
1344	<	fileInit->readInit( info ); // default velocities on
1345	<
1344	>	fileInit->readInit(info); // default velocities on
1345	>
1346		delete fileInit;
1347		}
1348		else{
1349
913	–	#ifdef IS_MPI
914	–
1350		// no init from bass
1351
1352	<	sprintf( painCave.errMsg,
1353	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1354	<	painCave.isFatal;
1352	>	sprintf(painCave.errMsg,
1353	>	"Cannot intialize a simulation without an initial configuration file.\n");
1354	>	painCave.isFatal = 1;;
1355		simError();
1356
922	–	#else
923	–
924	–	initFromBass();
925	–
926	–
927	–	#endif
1357		}
1358	<
1358	>
1359		#ifdef IS_MPI
1360	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1360	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1361		MPIcheckPoint();
1362		#endif // is_mpi
934	–
1363		}
1364
1365
1366	<	void SimSetup::makeOutNames( void ){
939	<
1366	>	void SimSetup::makeOutNames(void){
1367		int k;
1368
942	–
943	–	for(k=0; k<nInfo; k++){
1369
1370	+	for (k = 0; k < nInfo; k++){
1371		#ifdef IS_MPI
1372	<	if( worldRank == 0 ){
1372	>	if (worldRank == 0){
1373		#endif // is_mpi
1374	<
1375	<	if( globals->haveFinalConfig() ){
1376	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1374	>
1375	>	if (globals->haveFinalConfig()){
1376	>	strcpy(info[k].finalName, globals->getFinalConfig());
1377		}
1378		else{
1379	<	strcpy( info[k].finalName, inFileName );
1380	<	char* endTest;
1381	<	int nameLength = strlen( info[k].finalName );
1382	<	endTest = &(info[k].finalName[nameLength - 5]);
1383	<	if( !strcmp( endTest, ".bass" ) ){
1384	<	strcpy( endTest, ".eor" );
1385	<	}
1386	<	else if( !strcmp( endTest, ".BASS" ) ){
1387	<	strcpy( endTest, ".eor" );
1388	<	}
1389	<	else{
1390	<	endTest = &(info[k].finalName[nameLength - 4]);
1391	<	if( !strcmp( endTest, ".bss" ) ){
1392	<	strcpy( endTest, ".eor" );
1393	<	}
1394	<	else if( !strcmp( endTest, ".mdl" ) ){
1395	<	strcpy( endTest, ".eor" );
1396	<	}
1397	<	else{
1398	<	strcat( info[k].finalName, ".eor" );
1399	<	}
1400	<	}
1379	>	strcpy(info[k].finalName, inFileName);
1380	>	char* endTest;
1381	>	int nameLength = strlen(info[k].finalName);
1382	>	endTest = &(info[k].finalName[nameLength - 5]);
1383	>	if (!strcmp(endTest, ".bass")){
1384	>	strcpy(endTest, ".eor");
1385	>	}
1386	>	else if (!strcmp(endTest, ".BASS")){
1387	>	strcpy(endTest, ".eor");
1388	>	}
1389	>	else{
1390	>	endTest = &(info[k].finalName[nameLength - 4]);
1391	>	if (!strcmp(endTest, ".bss")){
1392	>	strcpy(endTest, ".eor");
1393	>	}
1394	>	else if (!strcmp(endTest, ".mdl")){
1395	>	strcpy(endTest, ".eor");
1396	>	}
1397	>	else{
1398	>	strcat(info[k].finalName, ".eor");
1399	>	}
1400	>	}
1401		}
1402	<
1402	>
1403		// make the sample and status out names
1404	<
1405	<	strcpy( info[k].sampleName, inFileName );
1404	>
1405	>	strcpy(info[k].sampleName, inFileName);
1406		char* endTest;
1407	<	int nameLength = strlen( info[k].sampleName );
1407	>	int nameLength = strlen(info[k].sampleName);
1408		endTest = &(info[k].sampleName[nameLength - 5]);
1409	<	if( !strcmp( endTest, ".bass" ) ){
1410	<	strcpy( endTest, ".dump" );
1409	>	if (!strcmp(endTest, ".bass")){
1410	>	strcpy(endTest, ".dump");
1411		}
1412	<	else if( !strcmp( endTest, ".BASS" ) ){
1413	<	strcpy( endTest, ".dump" );
1412	>	else if (!strcmp(endTest, ".BASS")){
1413	>	strcpy(endTest, ".dump");
1414		}
1415		else{
1416	<	endTest = &(info[k].sampleName[nameLength - 4]);
1417	<	if( !strcmp( endTest, ".bss" ) ){
1418	<	strcpy( endTest, ".dump" );
1419	<	}
1420	<	else if( !strcmp( endTest, ".mdl" ) ){
1421	<	strcpy( endTest, ".dump" );
1422	<	}
1423	<	else{
1424	<	strcat( info[k].sampleName, ".dump" );
1425	<	}
1416	>	endTest = &(info[k].sampleName[nameLength - 4]);
1417	>	if (!strcmp(endTest, ".bss")){
1418	>	strcpy(endTest, ".dump");
1419	>	}
1420	>	else if (!strcmp(endTest, ".mdl")){
1421	>	strcpy(endTest, ".dump");
1422	>	}
1423	>	else{
1424	>	strcat(info[k].sampleName, ".dump");
1425	>	}
1426		}
1427	<
1428	<	strcpy( info[k].statusName, inFileName );
1429	<	nameLength = strlen( info[k].statusName );
1427	>
1428	>	strcpy(info[k].statusName, inFileName);
1429	>	nameLength = strlen(info[k].statusName);
1430		endTest = &(info[k].statusName[nameLength - 5]);
1431	<	if( !strcmp( endTest, ".bass" ) ){
1432	<	strcpy( endTest, ".stat" );
1431	>	if (!strcmp(endTest, ".bass")){
1432	>	strcpy(endTest, ".stat");
1433		}
1434	<	else if( !strcmp( endTest, ".BASS" ) ){
1435	<	strcpy( endTest, ".stat" );
1434	>	else if (!strcmp(endTest, ".BASS")){
1435	>	strcpy(endTest, ".stat");
1436		}
1437		else{
1438	<	endTest = &(info[k].statusName[nameLength - 4]);
1439	<	if( !strcmp( endTest, ".bss" ) ){
1440	<	strcpy( endTest, ".stat" );
1441	<	}
1442	<	else if( !strcmp( endTest, ".mdl" ) ){
1443	<	strcpy( endTest, ".stat" );
1444	<	}
1445	<	else{
1446	<	strcat( info[k].statusName, ".stat" );
1447	<	}
1438	>	endTest = &(info[k].statusName[nameLength - 4]);
1439	>	if (!strcmp(endTest, ".bss")){
1440	>	strcpy(endTest, ".stat");
1441	>	}
1442	>	else if (!strcmp(endTest, ".mdl")){
1443	>	strcpy(endTest, ".stat");
1444	>	}
1445	>	else{
1446	>	strcat(info[k].statusName, ".stat");
1447	>	}
1448		}
1449	<
1449	>
1450	>	strcpy(info[k].rawPotName, inFileName);
1451	>	nameLength = strlen(info[k].rawPotName);
1452	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1453	>	if (!strcmp(endTest, ".bass")){
1454	>	strcpy(endTest, ".raw");
1455	>	}
1456	>	else if (!strcmp(endTest, ".BASS")){
1457	>	strcpy(endTest, ".raw");
1458	>	}
1459	>	else{
1460	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1461	>	if (!strcmp(endTest, ".bss")){
1462	>	strcpy(endTest, ".raw");
1463	>	}
1464	>	else if (!strcmp(endTest, ".mdl")){
1465	>	strcpy(endTest, ".raw");
1466	>	}
1467	>	else{
1468	>	strcat(info[k].rawPotName, ".raw");
1469	>	}
1470	>	}
1471	>
1472		#ifdef IS_MPI
1473	+
1474		}
1475		#endif // is_mpi
1476		}
1477		}
1478
1479
1480	<	void SimSetup::sysObjectsCreation( void ){
1481	<
1482	<	int i,k;
1034	<
1480	>	void SimSetup::sysObjectsCreation(void){
1481	>	int i, k;
1482	>
1483		// create the forceField
1484	<
1484	>
1485		createFF();
1486
1487		// extract componentList
#	Line 1046 | Line 1494 | void SimSetup::sysObjectsCreation( void ){
1494
1495		#ifdef IS_MPI
1496		// divide the molecules among the processors
1497	<
1497	>
1498		mpiMolDivide();
1499		#endif //is_mpi
1500	<
1500	>
1501		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1502	<
1502	>
1503		makeSysArrays();
1504
1505		// make and initialize the molecules (all but atomic coordinates)
1506	<
1506	>
1507		makeMolecules();
1508	<
1509	<	for(k=0; k<nInfo; k++){
1508	>
1509	>	for (k = 0; k < nInfo; k++){
1510		info[k].identArray = new int[info[k].n_atoms];
1511	<	for(i=0; i<info[k].n_atoms; i++){
1511	>	for (i = 0; i < info[k].n_atoms; i++){
1512		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1513		}
1514		}
1515		}
1516
1517
1518	<	void SimSetup::createFF( void ){
1518	>	void SimSetup::createFF(void){
1519	>	switch (ffCase){
1520	>	case FF_DUFF:
1521	>	the_ff = new DUFF();
1522	>	break;
1523
1524	<	switch( ffCase ){
1524	>	case FF_LJ:
1525	>	the_ff = new LJFF();
1526	>	break;
1527
1528	<	case FF_DUFF:
1529	<	the_ff = new DUFF();
1530	<	break;
1528	>	case FF_EAM:
1529	>	if (has_forcefield_variant)
1530	>	the_ff = new EAM_FF(forcefield_variant);
1531	>	else
1532	>	the_ff = new EAM_FF();
1533	>	break;
1534
1535	<	case FF_LJ:
1536	<	the_ff = new LJFF();
1537	<	break;
1535	>	case FF_H2O:
1536	>	the_ff = new WATER();
1537	>	break;
1538
1539	<	case FF_EAM:
1540	<	the_ff = new EAM_FF();
1541	<	break;
1542	<
1543	<	default:
1087	<	sprintf( painCave.errMsg,
1088	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	<	painCave.isFatal = 1;
1090	<	simError();
1539	>	default:
1540	>	sprintf(painCave.errMsg,
1541	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1542	>	painCave.isFatal = 1;
1543	>	simError();
1544		}
1545
1546	+
1547		#ifdef IS_MPI
1548	<	strcpy( checkPointMsg, "ForceField creation successful" );
1548	>	strcpy(checkPointMsg, "ForceField creation successful");
1549		MPIcheckPoint();
1550		#endif // is_mpi
1097	–
1551		}
1552
1553
1554	<	void SimSetup::compList( void ){
1102	<
1554	>	void SimSetup::compList(void){
1555		int i;
1556		char* id;
1557		LinkedMolStamp* headStamp = new LinkedMolStamp();
1558		LinkedMolStamp* currentStamp = NULL;
1559	<	comp_stamps = new MoleculeStamp*[n_components];
1559	>	comp_stamps = new MoleculeStamp * [n_components];
1560	>	bool haveCutoffGroups;
1561	>
1562	>	haveCutoffGroups = false;
1563
1564		// make an array of molecule stamps that match the components used.
1565		// also extract the used stamps out into a separate linked list
1566	<
1567	<	for(i=0; i<nInfo; i++){
1566	>
1567	>	for (i = 0; i < nInfo; i++){
1568		info[i].nComponents = n_components;
1569		info[i].componentsNmol = components_nmol;
1570		info[i].compStamps = comp_stamps;
1571		info[i].headStamp = headStamp;
1572		}
1118	–
1573
1120	–	for( i=0; i<n_components; i++ ){
1574
1575	+	for (i = 0; i < n_components; i++){
1576		id = the_components[i]->getType();
1577		comp_stamps[i] = NULL;
1578	<
1578	>
1579		// check to make sure the component isn't already in the list
1580
1581	<	comp_stamps[i] = headStamp->match( id );
1582	<	if( comp_stamps[i] == NULL ){
1129	<
1581	>	comp_stamps[i] = headStamp->match(id);
1582	>	if (comp_stamps[i] == NULL){
1583		// extract the component from the list;
1584	<
1585	<	currentStamp = stamps->extractMolStamp( id );
1586	<	if( currentStamp == NULL ){
1587	<	sprintf( painCave.errMsg,
1588	<	"SimSetup error: Component \"%s\" was not found in the "
1589	<	"list of declared molecules\n",
1590	<	id );
1591	<	painCave.isFatal = 1;
1592	<	simError();
1584	>
1585	>	currentStamp = stamps->extractMolStamp(id);
1586	>	if (currentStamp == NULL){
1587	>	sprintf(painCave.errMsg,
1588	>	"SimSetup error: Component \"%s\" was not found in the "
1589	>	"list of declared molecules\n",
1590	>	id);
1591	>	painCave.isFatal = 1;
1592	>	simError();
1593		}
1594	<
1595	<	headStamp->add( currentStamp );
1596	<	comp_stamps[i] = headStamp->match( id );
1594	>
1595	>	headStamp->add(currentStamp);
1596	>	comp_stamps[i] = headStamp->match(id);
1597		}
1598	+
1599	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1600	+	haveCutoffGroups = true;
1601		}
1602	+
1603	+	for (i = 0; i < nInfo; i++)
1604	+	info[i].haveCutoffGroups = haveCutoffGroups;
1605
1606		#ifdef IS_MPI
1607	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1607	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1608		MPIcheckPoint();
1609		#endif // is_mpi
1610	+	}
1611
1612	+	void SimSetup::calcSysValues(void){
1613	+	int i, j;
1614	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1615
1616	<	}
1616	>	int* molMembershipArray;
1617	>	CutoffGroupStamp* cg;
1618
1155	–	void SimSetup::calcSysValues( void ){
1156	–	int i, j, k;
1157	–
1158	–	int *molMembershipArray;
1159	–
1619		tot_atoms = 0;
1620		tot_bonds = 0;
1621		tot_bends = 0;
1622		tot_torsions = 0;
1623	<	for( i=0; i<n_components; i++ ){
1624	<
1625	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1626	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1627	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1623	>	tot_rigid = 0;
1624	>	tot_groups = 0;
1625	>	for (i = 0; i < n_components; i++){
1626	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631	+
1632	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633	+	atomsingroups = 0;
1634	+	for (j=0; j < ncutgroups; j++) {
1635	+	cg = comp_stamps[i]->getCutoffGroup(j);
1636	+	atomsingroups += cg->getNMembers();
1637	+	}
1638	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1640		}
1641
1642		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1643		molMembershipArray = new int[tot_atoms];
1644	<
1645	<	for(i=0; i<nInfo; i++){
1644	>
1645	>	for (i = 0; i < nInfo; i++){
1646		info[i].n_atoms = tot_atoms;
1647		info[i].n_bonds = tot_bonds;
1648		info[i].n_bends = tot_bends;
1649		info[i].n_torsions = tot_torsions;
1650		info[i].n_SRI = tot_SRI;
1651		info[i].n_mol = tot_nmol;
1652	<
1652	>	info[i].ngroup = tot_groups;
1653		info[i].molMembershipArray = molMembershipArray;
1654	<	}
1654	>	}
1655		}
1656
1657		#ifdef IS_MPI
1658
1659	<	void SimSetup::mpiMolDivide( void ){
1190	<
1659	>	void SimSetup::mpiMolDivide(void){
1660		int i, j, k;
1661		int localMol, allMol;
1662		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663	+	int local_rigid, local_groups;
1664	+	vector<int> globalMolIndex;
1665	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1666	+	CutoffGroupStamp* cg;
1667
1668	<	mpiSim = new mpiSimulation( info );
1196	<
1197	<	globalIndex = mpiSim->divideLabor();
1668	>	mpiSim = new mpiSimulation(info);
1669
1670	+	mpiSim->divideLabor();
1671	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1674	+
1675		// set up the local variables
1676	<
1676	>
1677		mol2proc = mpiSim->getMolToProcMap();
1678		molCompType = mpiSim->getMolComponentType();
1679	<
1679	>
1680		allMol = 0;
1681		localMol = 0;
1682		local_atoms = 0;
1683		local_bonds = 0;
1684		local_bends = 0;
1685		local_torsions = 0;
1686	<	globalAtomIndex = 0;
1686	>	local_rigid = 0;
1687	>	local_groups = 0;
1688	>	globalAtomCounter = 0;
1689
1690	+	for (i = 0; i < n_components; i++){
1691	+	for (j = 0; j < components_nmol[i]; j++){
1692	+	if (mol2proc[allMol] == worldRank){
1693	+	local_atoms += comp_stamps[i]->getNAtoms();
1694	+	local_bonds += comp_stamps[i]->getNBonds();
1695	+	local_bends += comp_stamps[i]->getNBends();
1696	+	local_torsions += comp_stamps[i]->getNTorsions();
1697	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1698
1699	<	for( i=0; i<n_components; i++ ){
1699	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700	>	atomsingroups = 0;
1701	>	for (k=0; k < ncutgroups; k++) {
1702	>	cg = comp_stamps[i]->getCutoffGroup(k);
1703	>	atomsingroups += cg->getNMembers();
1704	>	}
1705	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706	>	ncutgroups;
1707	>	local_groups += ngroupsinstamp;
1708
1709	<	for( j=0; j<components_nmol[i]; j++ ){
1216	<
1217	<	if( mol2proc[allMol] == worldRank ){
1218	<
1219	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	<	local_bonds +=    comp_stamps[i]->getNBonds();
1221	<	local_bends +=    comp_stamps[i]->getNBends();
1222	<	local_torsions += comp_stamps[i]->getNTorsions();
1223	<	localMol++;
1709	>	localMol++;
1710		}
1711	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1712	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1713	<	globalAtomIndex++;
1711	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1712	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1713	>	globalAtomCounter++;
1714		}
1715
1716	<	allMol++;
1716	>	allMol++;
1717		}
1718		}
1719		local_SRI = local_bonds + local_bends + local_torsions;
1720	+
1721	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1722
1723	<	info[0].n_atoms = mpiSim->getMyNlocal();
1724	<
1725	<	if( local_atoms != info[0].n_atoms ){
1726	<	sprintf( painCave.errMsg,
1727	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	<	" localAtom (%d) are not equal.\n",
1241	<	info[0].n_atoms,
1242	<	local_atoms );
1723	>	if (local_atoms != info[0].n_atoms){
1724	>	sprintf(painCave.errMsg,
1725	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1726	>	"\tlocalAtom (%d) are not equal.\n",
1727	>	info[0].n_atoms, local_atoms);
1728		painCave.isFatal = 1;
1729		simError();
1730		}
1731
1732	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1733	+	if (local_groups != info[0].ngroup){
1734	+	sprintf(painCave.errMsg,
1735	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736	+	"\tlocalGroups (%d) are not equal.\n",
1737	+	info[0].ngroup, local_groups);
1738	+	painCave.isFatal = 1;
1739	+	simError();
1740	+	}
1741	+
1742		info[0].n_bonds = local_bonds;
1743		info[0].n_bends = local_bends;
1744		info[0].n_torsions = local_torsions;
1745		info[0].n_SRI = local_SRI;
1746		info[0].n_mol = localMol;
1747
1748	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1748	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1749		MPIcheckPoint();
1750		}
1751	<
1751	>
1752		#endif // is_mpi
1753
1754
1755	<	void SimSetup::makeSysArrays( void ){
1756	<	int i, j, k, l;
1755	>	void SimSetup::makeSysArrays(void){
1756	>
1757	>	#ifndef IS_MPI
1758	>	int k, j;
1759	>	#endif // is_mpi
1760	>	int i, l;
1761
1762		Atom** the_atoms;
1763		Molecule* the_molecules;
1265	–	Exclude** the_excludes;
1764
1765	<
1268	<	for(l=0; l<nInfo; l++){
1269	<
1765	>	for (l = 0; l < nInfo; l++){
1766		// create the atom and short range interaction arrays
1767	<
1768	<	the_atoms = new Atom*[info[l].n_atoms];
1767	>
1768	>	the_atoms = new Atom * [info[l].n_atoms];
1769		the_molecules = new Molecule[info[l].n_mol];
1770		int molIndex;
1771
1772		// initialize the molecule's stampID's
1773	<
1773	>
1774		#ifdef IS_MPI
1775	<
1776	<
1775	>
1776	>
1777		molIndex = 0;
1778	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1779	<
1780	<	if(mol2proc[i] == worldRank ){
1781	<	the_molecules[molIndex].setStampID( molCompType[i] );
1782	<	the_molecules[molIndex].setMyIndex( molIndex );
1783	<	the_molecules[molIndex].setGlobalIndex( i );
1288	<	molIndex++;
1778	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779	>	if (mol2proc[i] == worldRank){
1780	>	the_molecules[molIndex].setStampID(molCompType[i]);
1781	>	the_molecules[molIndex].setMyIndex(molIndex);
1782	>	the_molecules[molIndex].setGlobalIndex(i);
1783	>	molIndex++;
1784		}
1785		}
1786	<
1786	>
1787		#else // is_mpi
1788	<
1788	>
1789		molIndex = 0;
1790	<	globalAtomIndex = 0;
1791	<	for(i=0; i<n_components; i++){
1792	<	for(j=0; j<components_nmol[i]; j++ ){
1793	<	the_molecules[molIndex].setStampID( i );
1794	<	the_molecules[molIndex].setMyIndex( molIndex );
1795	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1796	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1797	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1798	<	globalAtomIndex++;
1799	<	}
1800	<	molIndex++;
1790	>	globalAtomCounter = 0;
1791	>	for (i = 0; i < n_components; i++){
1792	>	for (j = 0; j < components_nmol[i]; j++){
1793	>	the_molecules[molIndex].setStampID(i);
1794	>	the_molecules[molIndex].setMyIndex(molIndex);
1795	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1796	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1797	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1798	>	globalAtomCounter++;
1799	>	}
1800	>	molIndex++;
1801		}
1802		}
1308	–
1309	–
1310	–	#endif // is_mpi
1803
1804
1805	<	if( info[l].n_SRI ){
1314	<
1315	<	Exclude::createArray(info[l].n_SRI);
1316	<	the_excludes = new Exclude*[info[l].n_SRI];
1317	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	<	the_excludes[ex] = new Exclude(ex);
1319	<	}
1320	<	info[l].globalExcludes = new int;
1321	<	info[l].n_exclude = info[l].n_SRI;
1322	<	}
1323	<	else{
1324	<
1325	<	Exclude::createArray( 1 );
1326	<	the_excludes = new Exclude*;
1327	<	the_excludes[0] = new Exclude(0);
1328	<	the_excludes[0]->setPair( 0,0 );
1329	<	info[l].globalExcludes = new int;
1330	<	info[l].globalExcludes[0] = 0;
1331	<	info[l].n_exclude = 0;
1332	<	}
1805	>	#endif // is_mpi
1806
1807	+	info[l].globalExcludes = new int;
1808	+	info[l].globalExcludes[0] = 0;
1809	+
1810		// set the arrays into the SimInfo object
1811
1812		info[l].atoms = the_atoms;
1813		info[l].molecules = the_molecules;
1814		info[l].nGlobalExcludes = 0;
1339	–	info[l].excludes = the_excludes;
1340	–
1341	–	the_ff->setSimInfo( info );
1815
1816	+	the_ff->setSimInfo(info);
1817		}
1818		}
1819
1820	<	void SimSetup::makeIntegrator( void ){
1347	<
1820	>	void SimSetup::makeIntegrator(void){
1821		int k;
1822
1823	<	NVT<RealIntegrator>*  myNVT = NULL;
1824	<	NPTi<RealIntegrator>* myNPTi = NULL;
1825	<	NPTf<RealIntegrator>* myNPTf = NULL;
1826	<	NPTim<RealIntegrator>* myNPTim = NULL;
1827	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1828	<
1829	<	for(k=0; k<nInfo; k++){
1830	<
1831	<	switch( ensembleCase ){
1832	<
1833	<	case NVE_ENS:
1834	<	if (haveZConstraint){
1835	<	setupZConstraint();
1836	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1823	>	NVE<Integrator<BaseIntegrator> >* myNVE = NULL;
1824	>	NVT<Integrator<BaseIntegrator> >* myNVT = NULL;
1825	>	NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL;
1826	>	NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL;
1827	>	NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL;
1828	>
1829	>	for (k = 0; k < nInfo; k++){
1830	>	switch (ensembleCase){
1831	>	case NVE_ENS:
1832	>	if (globals->haveZconstraints()){
1833	>	setupZConstraint(info[k]);
1834	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1835	>	}
1836	>	else{
1837	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1838		}
1839	+
1840	+	info->the_integrator = myNVE;
1841	+	break;
1842
1843	<	else
1844	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1845	<	break;
1846	<
1847	<	case NVT_ENS:
1848	<	if (haveZConstraint){
1849	<	setupZConstraint();
1373	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	<	}
1375	<	else
1376	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1843	>	case NVT_ENS:
1844	>	if (globals->haveZconstraints()){
1845	>	setupZConstraint(info[k]);
1846	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1847	>	}
1848	>	else
1849	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1850
1851	<	myNVT->setTargetTemp(globals->getTargetTemp());
1379	<
1380	<	if (globals->haveTauThermostat())
1381	<	myNVT->setTauThermostat(globals->getTauThermostat());
1382	<
1383	<	else {
1384	<	sprintf( painCave.errMsg,
1385	<	"SimSetup error: If you use the NVT\n"
1386	<	"    ensemble, you must set tauThermostat.\n");
1387	<	painCave.isFatal = 1;
1388	<	simError();
1389	<	}
1390	<	break;
1391	<
1392	<	case NPTi_ENS:
1393	<	if (haveZConstraint){
1394	<	setupZConstraint();
1395	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	<	}
1397	<	else
1398	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1851	>	myNVT->setTargetTemp(globals->getTargetTemp());
1852
1853	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1854	<
1855	<	if (globals->haveTargetPressure())
1856	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1857	<	else {
1858	<	sprintf( painCave.errMsg,
1859	<	"SimSetup error: If you use a constant pressure\n"
1860	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1861	<	painCave.isFatal = 1;
1409	<	simError();
1410	<	}
1411	<
1412	<	if( globals->haveTauThermostat() )
1413	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	<	else{
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use an NPT\n"
1417	<	"    ensemble, you must set tauThermostat.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<
1422	<	if( globals->haveTauBarostat() )
1423	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	<	else{
1425	<	sprintf( painCave.errMsg,
1426	<	"SimSetup error: If you use an NPT\n"
1427	<	"    ensemble, you must set tauBarostat.\n");
1428	<	painCave.isFatal = 1;
1429	<	simError();
1430	<	}
1431	<	break;
1432	<
1433	<	case NPTf_ENS:
1434	<	if (haveZConstraint){
1435	<	setupZConstraint();
1436	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	<	}
1438	<	else
1439	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1853	>	if (globals->haveTauThermostat())
1854	>	myNVT->setTauThermostat(globals->getTauThermostat());
1855	>	else{
1856	>	sprintf(painCave.errMsg,
1857	>	"SimSetup error: If you use the NVT\n"
1858	>	"\tensemble, you must set tauThermostat.\n");
1859	>	painCave.isFatal = 1;
1860	>	simError();
1861	>	}
1862
1863	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1864	<
1443	<	if (globals->haveTargetPressure())
1444	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	<	else {
1446	<	sprintf( painCave.errMsg,
1447	<	"SimSetup error: If you use a constant pressure\n"
1448	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	<	painCave.isFatal = 1;
1450	<	simError();
1451	<	}
1452	<
1453	<	if( globals->haveTauThermostat() )
1454	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	<	else{
1456	<	sprintf( painCave.errMsg,
1457	<	"SimSetup error: If you use an NPT\n"
1458	<	"    ensemble, you must set tauThermostat.\n");
1459	<	painCave.isFatal = 1;
1460	<	simError();
1461	<	}
1462	<
1463	<	if( globals->haveTauBarostat() )
1464	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	<	else{
1466	<	sprintf( painCave.errMsg,
1467	<	"SimSetup error: If you use an NPT\n"
1468	<	"    ensemble, you must set tauBarostat.\n");
1469	<	painCave.isFatal = 1;
1470	<	simError();
1471	<	}
1472	<	break;
1473	<
1474	<	case NPTim_ENS:
1475	<	if (haveZConstraint){
1476	<	setupZConstraint();
1477	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	<	}
1479	<	else
1480	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1863	>	info->the_integrator = myNVT;
1864	>	break;
1865
1866	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1867	<
1868	<	if (globals->haveTargetPressure())
1869	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1870	<	else {
1871	<	sprintf( painCave.errMsg,
1872	<	"SimSetup error: If you use a constant pressure\n"
1489	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<
1494	<	if( globals->haveTauThermostat() )
1495	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	<	else{
1497	<	sprintf( painCave.errMsg,
1498	<	"SimSetup error: If you use an NPT\n"
1499	<	"    ensemble, you must set tauThermostat.\n");
1500	<	painCave.isFatal = 1;
1501	<	simError();
1502	<	}
1503	<
1504	<	if( globals->haveTauBarostat() )
1505	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	<	else{
1507	<	sprintf( painCave.errMsg,
1508	<	"SimSetup error: If you use an NPT\n"
1509	<	"    ensemble, you must set tauBarostat.\n");
1510	<	painCave.isFatal = 1;
1511	<	simError();
1512	<	}
1513	<	break;
1514	<
1515	<	case NPTfm_ENS:
1516	<	if (haveZConstraint){
1517	<	setupZConstraint();
1518	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	<	}
1520	<	else
1521	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1866	>	case NPTi_ENS:
1867	>	if (globals->haveZconstraints()){
1868	>	setupZConstraint(info[k]);
1869	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1870	>	}
1871	>	else
1872	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1873
1874	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1875	<
1876	<	if (globals->haveTargetPressure())
1877	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1878	<	else {
1879	<	sprintf( painCave.errMsg,
1880	<	"SimSetup error: If you use a constant pressure\n"
1881	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1882	<	painCave.isFatal = 1;
1883	<	simError();
1884	<	}
1885	<
1886	<	if( globals->haveTauThermostat() )
1887	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1888	<	else{
1889	<	sprintf( painCave.errMsg,
1890	<	"SimSetup error: If you use an NPT\n"
1891	<	"    ensemble, you must set tauThermostat.\n");
1892	<	painCave.isFatal = 1;
1893	<	simError();
1894	<	}
1895	<
1896	<	if( globals->haveTauBarostat() )
1897	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1898	<	else{
1899	<	sprintf( painCave.errMsg,
1900	<	"SimSetup error: If you use an NPT\n"
1901	<	"    ensemble, you must set tauBarostat.\n");
1902	<	painCave.isFatal = 1;
1903	<	simError();
1904	<	}
1905	<	break;
1906	<
1907	<	default:
1908	<	sprintf( painCave.errMsg,
1909	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1910	<	painCave.isFatal = 1;
1911	<	simError();
1874	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1875	>
1876	>	if (globals->haveTargetPressure())
1877	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1878	>	else{
1879	>	sprintf(painCave.errMsg,
1880	>	"SimSetup error: If you use a constant pressure\n"
1881	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1882	>	painCave.isFatal = 1;
1883	>	simError();
1884	>	}
1885	>
1886	>	if (globals->haveTauThermostat())
1887	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1888	>	else{
1889	>	sprintf(painCave.errMsg,
1890	>	"SimSetup error: If you use an NPT\n"
1891	>	"\tensemble, you must set tauThermostat.\n");
1892	>	painCave.isFatal = 1;
1893	>	simError();
1894	>	}
1895	>
1896	>	if (globals->haveTauBarostat())
1897	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1898	>	else{
1899	>	sprintf(painCave.errMsg,
1900	>	"SimSetup error: If you use an NPT\n"
1901	>	"\tensemble, you must set tauBarostat.\n");
1902	>	painCave.isFatal = 1;
1903	>	simError();
1904	>	}
1905	>
1906	>	info->the_integrator = myNPTi;
1907	>	break;
1908	>
1909	>	case NPTf_ENS:
1910	>	if (globals->haveZconstraints()){
1911	>	setupZConstraint(info[k]);
1912	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1913	>	}
1914	>	else
1915	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1916	>
1917	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1918	>
1919	>	if (globals->haveTargetPressure())
1920	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1921	>	else{
1922	>	sprintf(painCave.errMsg,
1923	>	"SimSetup error: If you use a constant pressure\n"
1924	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1925	>	painCave.isFatal = 1;
1926	>	simError();
1927	>	}
1928	>
1929	>	if (globals->haveTauThermostat())
1930	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1931	>
1932	>	else{
1933	>	sprintf(painCave.errMsg,
1934	>	"SimSetup error: If you use an NPT\n"
1935	>	"\tensemble, you must set tauThermostat.\n");
1936	>	painCave.isFatal = 1;
1937	>	simError();
1938	>	}
1939	>
1940	>	if (globals->haveTauBarostat())
1941	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1942	>
1943	>	else{
1944	>	sprintf(painCave.errMsg,
1945	>	"SimSetup error: If you use an NPT\n"
1946	>	"\tensemble, you must set tauBarostat.\n");
1947	>	painCave.isFatal = 1;
1948	>	simError();
1949	>	}
1950	>
1951	>	info->the_integrator = myNPTf;
1952	>	break;
1953	>
1954	>	case NPTxyz_ENS:
1955	>	if (globals->haveZconstraints()){
1956	>	setupZConstraint(info[k]);
1957	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1958	>	}
1959	>	else
1960	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1961	>
1962	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1963	>
1964	>	if (globals->haveTargetPressure())
1965	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1966	>	else{
1967	>	sprintf(painCave.errMsg,
1968	>	"SimSetup error: If you use a constant pressure\n"
1969	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1970	>	painCave.isFatal = 1;
1971	>	simError();
1972	>	}
1973	>
1974	>	if (globals->haveTauThermostat())
1975	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1976	>	else{
1977	>	sprintf(painCave.errMsg,
1978	>	"SimSetup error: If you use an NPT\n"
1979	>	"\tensemble, you must set tauThermostat.\n");
1980	>	painCave.isFatal = 1;
1981	>	simError();
1982	>	}
1983	>
1984	>	if (globals->haveTauBarostat())
1985	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1986	>	else{
1987	>	sprintf(painCave.errMsg,
1988	>	"SimSetup error: If you use an NPT\n"
1989	>	"\tensemble, you must set tauBarostat.\n");
1990	>	painCave.isFatal = 1;
1991	>	simError();
1992	>	}
1993	>
1994	>	info->the_integrator = myNPTxyz;
1995	>	break;
1996	>
1997	>	default:
1998	>	sprintf(painCave.errMsg,
1999	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
2000	>	painCave.isFatal = 1;
2001	>	simError();
2002		}
2003		}
2004		}
2005
2006	<	void SimSetup::initFortran( void ){
1566	<
2006	>	void SimSetup::initFortran(void){
2007		info[0].refreshSim();
2008	<
2009	<	if( !strcmp( info[0].mixingRule, "standard") ){
2010	<	the_ff->initForceField( LB_MIXING_RULE );
2008	>
2009	>	if (!strcmp(info[0].mixingRule, "standard")){
2010	>	the_ff->initForceField(LB_MIXING_RULE);
2011		}
2012	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
2013	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
2012	>	else if (!strcmp(info[0].mixingRule, "explicit")){
2013	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
2014		}
2015		else{
2016	<	sprintf( painCave.errMsg,
2017	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	<	info[0].mixingRule );
2016	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2017	>	info[0].mixingRule);
2018		painCave.isFatal = 1;
2019		simError();
2020		}
2021
2022
2023		#ifdef IS_MPI
2024	<	strcpy( checkPointMsg,
1586	<	"Successfully intialized the mixingRule for Fortran." );
2024	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2025		MPIcheckPoint();
2026		#endif // is_mpi
2027	+	}
2028
2029	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2030	+	int nZConstraints;
2031	+	ZconStamp** zconStamp;
2032	+
2033	+	if (globals->haveZconstraintTime()){
2034	+	//add sample time of z-constraint  into SimInfo's property list
2035	+	DoubleData* zconsTimeProp = new DoubleData();
2036	+	zconsTimeProp->setID(ZCONSTIME_ID);
2037	+	zconsTimeProp->setData(globals->getZconsTime());
2038	+	theInfo.addProperty(zconsTimeProp);
2039	+	}
2040	+	else{
2041	+	sprintf(painCave.errMsg,
2042	+	"ZConstraint error: If you use a ZConstraint,\n"
2043	+	"\tyou must set zconsTime.\n");
2044	+	painCave.isFatal = 1;
2045	+	simError();
2046	+	}
2047	+
2048	+	//push zconsTol into siminfo, if user does not specify
2049	+	//value for zconsTol, a default value will be used
2050	+	DoubleData* zconsTol = new DoubleData();
2051	+	zconsTol->setID(ZCONSTOL_ID);
2052	+	if (globals->haveZconsTol()){
2053	+	zconsTol->setData(globals->getZconsTol());
2054	+	}
2055	+	else{
2056	+	double defaultZConsTol = 0.01;
2057	+	sprintf(painCave.errMsg,
2058	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2059	+	"\tOOPSE will use a default value of %f.\n"
2060	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2061	+	defaultZConsTol);
2062	+	painCave.isFatal = 0;
2063	+	simError();
2064	+
2065	+	zconsTol->setData(defaultZConsTol);
2066	+	}
2067	+	theInfo.addProperty(zconsTol);
2068	+
2069	+	//set Force Subtraction Policy
2070	+	StringData* zconsForcePolicy = new StringData();
2071	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2072	+
2073	+	if (globals->haveZconsForcePolicy()){
2074	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2075	+	}
2076	+	else{
2077	+	sprintf(painCave.errMsg,
2078	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2079	+	"\tOOPSE will use PolicyByMass.\n"
2080	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2081	+	painCave.isFatal = 0;
2082	+	simError();
2083	+	zconsForcePolicy->setData("BYMASS");
2084	+	}
2085	+
2086	+	theInfo.addProperty(zconsForcePolicy);
2087	+
2088	+	//set zcons gap
2089	+	DoubleData* zconsGap = new DoubleData();
2090	+	zconsGap->setID(ZCONSGAP_ID);
2091	+
2092	+	if (globals->haveZConsGap()){
2093	+	zconsGap->setData(globals->getZconsGap());
2094	+	theInfo.addProperty(zconsGap);
2095	+	}
2096	+
2097	+	//set zcons fixtime
2098	+	DoubleData* zconsFixtime = new DoubleData();
2099	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2100	+
2101	+	if (globals->haveZConsFixTime()){
2102	+	zconsFixtime->setData(globals->getZconsFixtime());
2103	+	theInfo.addProperty(zconsFixtime);
2104	+	}
2105	+
2106	+	//set zconsUsingSMD
2107	+	IntData* zconsUsingSMD = new IntData();
2108	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2109	+
2110	+	if (globals->haveZConsUsingSMD()){
2111	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2112	+	theInfo.addProperty(zconsUsingSMD);
2113	+	}
2114	+
2115	+	//Determine the name of ouput file and add it into SimInfo's property list
2116	+	//Be careful, do not use inFileName, since it is a pointer which
2117	+	//point to a string at master node, and slave nodes do not contain that string
2118	+
2119	+	string zconsOutput(theInfo.finalName);
2120	+
2121	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2122	+
2123	+	StringData* zconsFilename = new StringData();
2124	+	zconsFilename->setID(ZCONSFILENAME_ID);
2125	+	zconsFilename->setData(zconsOutput);
2126	+
2127	+	theInfo.addProperty(zconsFilename);
2128	+
2129	+	//setup index, pos and other parameters of z-constraint molecules
2130	+	nZConstraints = globals->getNzConstraints();
2131	+	theInfo.nZconstraints = nZConstraints;
2132	+
2133	+	zconStamp = globals->getZconStamp();
2134	+	ZConsParaItem tempParaItem;
2135	+
2136	+	ZConsParaData* zconsParaData = new ZConsParaData();
2137	+	zconsParaData->setID(ZCONSPARADATA_ID);
2138	+
2139	+	for (int i = 0; i < nZConstraints; i++){
2140	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2141	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2142	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2143	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2144	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2145	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2146	+	zconsParaData->addItem(tempParaItem);
2147	+	}
2148	+
2149	+	//check the uniqueness of index
2150	+	if(!zconsParaData->isIndexUnique()){
2151	+	sprintf(painCave.errMsg,
2152	+	"ZConstraint Error: molIndex is not unique!\n");
2153	+	painCave.isFatal = 1;
2154	+	simError();
2155	+	}
2156	+
2157	+	//sort the parameters by index of molecules
2158	+	zconsParaData->sortByIndex();
2159	+
2160	+	//push data into siminfo, therefore, we can retrieve later
2161	+	theInfo.addProperty(zconsParaData);
2162		}
2163
2164	<	void SimSetup::setupZConstraint()
1593	<	{
1594	<	int k;
2164	>	void SimSetup::makeMinimizer(){
2165
2166	<	for(k=0; k<nInfo; k++){
2166	>	OOPSEMinimizer* myOOPSEMinimizer;
2167	>	MinimizerParameterSet* param;
2168	>	char minimizerName[100];
2169	>
2170	>	for (int i = 0; i < nInfo; i++){
2171
2172	<	if(globals->haveZConsTime()){
2173	<
2174	<	//add sample time of z-constraint  into SimInfo's property list
2175	<	DoubleData* zconsTimeProp = new DoubleData();
2176	<	zconsTimeProp->setID("zconstime");
2177	<	zconsTimeProp->setData(globals->getZConsTime());
1604	<	info[k].addProperty(zconsTimeProp);
2172	>	//prepare parameter set for minimizer
2173	>	param = new MinimizerParameterSet();
2174	>	param->setDefaultParameter();
2175	>
2176	>	if (globals->haveMinimizer()){
2177	>	param->setFTol(globals->getMinFTol());
2178		}
2179	<	else{
2180	<	sprintf( painCave.errMsg,
2181	<	"ZConstraint error: If you use an ZConstraint\n"
1609	<	" , you must set sample time.\n");
1610	<	painCave.isFatal = 1;
1611	<	simError();
2179	>
2180	>	if (globals->haveMinGTol()){
2181	>	param->setGTol(globals->getMinGTol());
2182		}
2183	+
2184	+	if (globals->haveMinMaxIter()){
2185	+	param->setMaxIteration(globals->getMinMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinWriteFrq()){
2189	+	param->setMaxIteration(globals->getMinMaxIter());
2190	+	}
2191	+
2192	+	if (globals->haveMinWriteFrq()){
2193	+	param->setWriteFrq(globals->getMinWriteFrq());
2194	+	}
2195
2196	<	if(globals->haveIndexOfAllZConsMols()){
2197	<
1616	<	//add index of z-constraint molecules into SimInfo's property list
1617	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618	<
1619	<	//sort the index
1620	<	sort(tempIndex.begin(), tempIndex.end());
1621	<
1622	<	IndexData* zconsIndex = new IndexData();
1623	<	zconsIndex->setID("zconsindex");
1624	<	zconsIndex->setIndexData(tempIndex);
1625	<	info[k].addProperty(zconsIndex);
2196	>	if (globals->haveMinStepSize()){
2197	>	param->setStepSize(globals->getMinStepSize());
2198		}
2199	+
2200	+	if (globals->haveMinLSMaxIter()){
2201	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2202	+	}
2203	+
2204	+	if (globals->haveMinLSTol()){
2205	+	param->setLineSearchTol(globals->getMinLSTol());
2206	+	}
2207	+
2208	+	strcpy(minimizerName, globals->getMinimizer());
2209	+
2210	+	if (!strcasecmp(minimizerName, "CG")){
2211	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2212	+	}
2213	+	else if (!strcasecmp(minimizerName, "SD")){
2214	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2215	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2216	+	}
2217		else{
2218	<	sprintf( painCave.errMsg,
2219	<	"SimSetup error: If you use an ZConstraint\n"
2220	<	" , you must set index of z-constraint molecules.\n");
2221	<	painCave.isFatal = 1;
2222	<	simError();
2223	<
2218	>	sprintf(painCave.errMsg,
2219	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2220	>	painCave.isFatal = 0;
2221	>	simError();
2222	>
2223	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2224		}
2225	<
2226	<	//Determine the name of ouput file and add it into SimInfo's property list
2227	<	//Be careful, do not use inFileName, since it is a pointer which
2228	<	//point to a string at master node, and slave nodes do not contain that string
2229	<
1640	<	string zconsOutput(info[k].finalName);
1641	<
1642	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	<
1644	<	StringData* zconsFilename = new StringData();
1645	<	zconsFilename->setID("zconsfilename");
1646	<	zconsFilename->setData(zconsOutput);
1647	<
1648	<	info[k].addProperty(zconsFilename);
2225	>	info[i].the_integrator = myOOPSEMinimizer;
2226	>
2227	>	//store the minimizer into simInfo
2228	>	info[i].the_minimizer = myOOPSEMinimizer;
2229	>	info[i].has_minimizer = true;
2230		}
2231	+
2232		}

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