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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 16 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
24	<	#define NPTfm_ENS 5
25	<	#define NVEZCONS_ENS 6
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
32	<	#define FF_EAM  2
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 51 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
86	<	}
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89
90	<	void SimSetup::parseFile( char* fileName ){
62	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
90	<	mpiEventLoop();
91	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
98	–	int i, j, k, globalAtomIndex;
99	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 106 | Line 132 | void SimSetup::createSim( void ){
132		sysObjectsCreation();
133
134		// check on the post processing info
135	<
135	>
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	initSystemCoords();
141	<
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
150	<
151	<	// make the integrator
150	>
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157
123	–	makeIntegrator();
124	–
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
#	Line 129 | Line 162 | void SimSetup::createSim( void ){
162		// initialize the Fortran
163
164		initFortran();
132	–
133	–
134	–
165		}
166
167
168	<	void SimSetup::makeMolecules( void ){
169	<
170	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174		molInit molInfo;
175		DirectionalAtom* dAtom;
176	+	RigidBody* myRB;
177	+	StuntDouble* mySD;
178		LinkedAssign* extras;
179		LinkedAssign* current_extra;
180		AtomStamp* currentAtom;
181		BondStamp* currentBond;
182		BendStamp* currentBend;
183		TorsionStamp* currentTorsion;
184	+	RigidBodyStamp* currentRigidBody;
185
186		bond_pair* theBonds;
187		bend_set* theBends;
188		torsion_set* theTorsions;
189
190	<
190	>	set<int> skipList;
191	>
192	>	double phi, theta, psi;
193	>	char* molName;
194	>	char rbName[100];
195	>
196		//init the forceField paramters
197
198		the_ff->readParams();
199
159	–
200		// init the atoms
201
202	<	double ux, uy, uz, u, uSqr;
163	<
164	<	atomOffset = 0;
165	<	excludeOffset = 0;
166	<	for(i=0; i<info->n_mol; i++){
167	<
168	<	stampID = the_molecules[i].getStampID();
202	>	int nMembers, nNew, rb1, rb2;
203
204	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
205	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
172	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
173	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
174	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
204	>	for (k = 0; k < nInfo; k++){
205	>	the_ff->setSimInfo(&(info[k]));
206
207	<	molInfo.myAtoms = &the_atoms[atomOffset];
177	<	molInfo.myExcludes = &the_excludes[excludeOffset];
178	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
179	<	molInfo.myBends = new Bend*[molInfo.nBends];
180	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
207	>	atomOffset = 0;
208
209	<	theBonds = new bond_pair[molInfo.nBonds];
210	<	theBends = new bend_set[molInfo.nBends];
211	<	theTorsions = new torsion_set[molInfo.nTorsions];
212	<
213	<	// make the Atoms
214	<
215	<	for(j=0; j<molInfo.nAtoms; j++){
209	>	for (i = 0; i < info[k].n_mol; i++){
210	>	stampID = info[k].molecules[i].getStampID();
211	>	molName = comp_stamps[stampID]->getID();
212	>
213	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
214	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
215	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
216	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
217	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
218
219	<	currentAtom = comp_stamps[stampID]->getAtom( j );
191	<	if( currentAtom->haveOrientation() ){
192	<
193	<	dAtom = new DirectionalAtom(j + atomOffset);
194	<	info->n_oriented++;
195	<	molInfo.myAtoms[j] = dAtom;
196	<
197	<	ux = currentAtom->getOrntX();
198	<	uy = currentAtom->getOrntY();
199	<	uz = currentAtom->getOrntZ();
200	<
201	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	<
203	<	u = sqrt( uSqr );
204	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx( ux );
209	<	dAtom->setSUy( uy );
210	<	dAtom->setSUz( uz );
211	<	}
212	<	else{
213	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
214	<	}
215	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
216	<
217	<	#ifdef IS_MPI
218	<
219	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
220	<
221	<	#endif // is_mpi
222	<	}
223	<
224	<	// make the bonds
225	<	for(j=0; j<molInfo.nBonds; j++){
226	<
227	<	currentBond = comp_stamps[stampID]->getBond( j );
228	<	theBonds[j].a = currentBond->getA() + atomOffset;
229	<	theBonds[j].b = currentBond->getB() + atomOffset;
219	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
220
221	<	exI = theBonds[j].a;
222	<	exJ = theBonds[j].b;
221	>	if (molInfo.nBonds > 0)
222	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
223	>	else
224	>	molInfo.myBonds = NULL;
225
226	<	// exclude_I must always be the smaller of the pair
227	<	if( exI > exJ ){
228	<	tempEx = exI;
229	<	exI = exJ;
238	<	exJ = tempEx;
239	<	}
240	<	#ifdef IS_MPI
241	<	tempEx = exI;
242	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
243	<	tempEx = exJ;
244	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
245	<
246	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
247	<	#else  // isn't MPI
226	>	if (molInfo.nBends > 0)
227	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
228	>	else
229	>	molInfo.myBends = NULL;
230
231	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
232	<	#endif  //is_mpi
233	<	}
234	<	excludeOffset += molInfo.nBonds;
231	>	if (molInfo.nTorsions > 0)
232	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
233	>	else
234	>	molInfo.myTorsions = NULL;
235
236	<	//make the bends
237	<	for(j=0; j<molInfo.nBends; j++){
236	>	theBonds = new bond_pair[molInfo.nBonds];
237	>	theBends = new bend_set[molInfo.nBends];
238	>	theTorsions = new torsion_set[molInfo.nTorsions];
239
240	<	currentBend = comp_stamps[stampID]->getBend( j );
241	<	theBends[j].a = currentBend->getA() + atomOffset;
242	<	theBends[j].b = currentBend->getB() + atomOffset;
243	<	theBends[j].c = currentBend->getC() + atomOffset;
244	<
245	<	if( currentBend->haveExtras() ){
246	<
247	<	extras = currentBend->getExtras();
248	<	current_extra = extras;
249	<
250	<	while( current_extra != NULL ){
251	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
252	<
253	<	switch( current_extra->getType() ){
254	<
255	<	case 0:
256	<	theBends[j].ghost =
257	<	current_extra->getInt() + atomOffset;
258	<	theBends[j].isGhost = 1;
259	<	break;
260	<
261	<	case 1:
262	<	theBends[j].ghost =
263	<	(int)current_extra->getDouble() + atomOffset;
264	<	theBends[j].isGhost = 1;
265	<	break;
266	<
267	<	default:
268	<	sprintf( painCave.errMsg,
286	<	"SimSetup Error: ghostVectorSource was neither a "
287	<	"double nor an int.\n"
288	<	"-->Bend[%d] in %s\n",
289	<	j, comp_stamps[stampID]->getID() );
290	<	painCave.isFatal = 1;
291	<	simError();
292	<	}
293	<	}
294	<
295	<	else{
296	<
297	<	sprintf( painCave.errMsg,
298	<	"SimSetup Error: unhandled bend assignment:\n"
299	<	"    -->%s in Bend[%d] in %s\n",
300	<	current_extra->getlhs(),
301	<	j, comp_stamps[stampID]->getID() );
302	<	painCave.isFatal = 1;
303	<	simError();
304	<	}
305	<
306	<	current_extra = current_extra->getNext();
307	<	}
308	<	}
309	<
310	<	if( !theBends[j].isGhost ){
311	<
312	<	exI = theBends[j].a;
313	<	exJ = theBends[j].c;
314	<	}
315	<	else{
316	<
317	<	exI = theBends[j].a;
318	<	exJ = theBends[j].b;
319	<	}
320	<
321	<	// exclude_I must always be the smaller of the pair
322	<	if( exI > exJ ){
323	<	tempEx = exI;
324	<	exI = exJ;
325	<	exJ = tempEx;
326	<	}
240	>	// make the Atoms
241	>
242	>	for (j = 0; j < molInfo.nAtoms; j++){
243	>	currentAtom = comp_stamps[stampID]->getAtom(j);
244	>
245	>	if (currentAtom->haveOrientation()){
246	>	dAtom = new DirectionalAtom((j + atomOffset),
247	>	info[k].getConfiguration());
248	>	info[k].n_oriented++;
249	>	molInfo.myAtoms[j] = dAtom;
250	>
251	>	// Directional Atoms have standard unit vectors which are oriented
252	>	// in space using the three Euler angles.  We assume the standard
253	>	// unit vector was originally along the z axis below.
254	>
255	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
256	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
257	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
258	>
259	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
260	>
261	>	}
262	>	else{
263	>
264	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
265	>	}
266	>
267	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
268	>
269		#ifdef IS_MPI
328	–	tempEx = exI;
329	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
330	–	tempEx = exJ;
331	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
332	–
333	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
334	–	#else  // isn't MPI
335	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
336	–	#endif  //is_mpi
337	–	}
338	–	excludeOffset += molInfo.nBends;
270
271	<	for(j=0; j<molInfo.nTorsions; j++){
341	<
342	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
343	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
344	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
345	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
346	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
347	<
348	<	exI = theTorsions[j].a;
349	<	exJ = theTorsions[j].d;
271	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
272
273	<	// exclude_I must always be the smaller of the pair
274	<	if( exI > exJ ){
275	<	tempEx = exI;
276	<	exI = exJ;
277	<	exJ = tempEx;
273	>	#endif // is_mpi
274	>	}
275	>
276	>	// make the bonds
277	>	for (j = 0; j < molInfo.nBonds; j++){
278	>	currentBond = comp_stamps[stampID]->getBond(j);
279	>	theBonds[j].a = currentBond->getA() + atomOffset;
280	>	theBonds[j].b = currentBond->getB() + atomOffset;
281	>
282	>	tempI = theBonds[j].a;
283	>	tempJ = theBonds[j].b;
284	>
285	>	#ifdef IS_MPI
286	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
287	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
288	>	#else
289	>	exI = tempI + 1;
290	>	exJ = tempJ + 1;
291	>	#endif
292	>
293	>	info[k].excludes->addPair(exI, exJ);
294		}
295	+
296	+	//make the bends
297	+	for (j = 0; j < molInfo.nBends; j++){
298	+	currentBend = comp_stamps[stampID]->getBend(j);
299	+	theBends[j].a = currentBend->getA() + atomOffset;
300	+	theBends[j].b = currentBend->getB() + atomOffset;
301	+	theBends[j].c = currentBend->getC() + atomOffset;
302	+
303	+	if (currentBend->haveExtras()){
304	+	extras = currentBend->getExtras();
305	+	current_extra = extras;
306	+
307	+	while (current_extra != NULL){
308	+	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
309	+	switch (current_extra->getType()){
310	+	case 0:
311	+	theBends[j].ghost = current_extra->getInt() + atomOffset;
312	+	theBends[j].isGhost = 1;
313	+	break;
314	+
315	+	case 1:
316	+	theBends[j].ghost = (int) current_extra->getDouble() +
317	+	atomOffset;
318	+	theBends[j].isGhost = 1;
319	+	break;
320	+
321	+	default:
322	+	sprintf(painCave.errMsg,
323	+	"SimSetup Error: ghostVectorSource was neither a "
324	+	"double nor an int.\n"
325	+	"-->Bend[%d] in %s\n",
326	+	j, comp_stamps[stampID]->getID());
327	+	painCave.isFatal = 1;
328	+	simError();
329	+	}
330	+	}
331	+	else{
332	+	sprintf(painCave.errMsg,
333	+	"SimSetup Error: unhandled bend assignment:\n"
334	+	"    -->%s in Bend[%d] in %s\n",
335	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
336	+	painCave.isFatal = 1;
337	+	simError();
338	+	}
339	+
340	+	current_extra = current_extra->getNext();
341	+	}
342	+	}
343	+
344	+	if (theBends[j].isGhost) {
345	+
346	+	tempI = theBends[j].a;
347	+	tempJ = theBends[j].b;
348	+
349		#ifdef IS_MPI
350	<	tempEx = exI;
351	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
352	<	tempEx = exJ;
353	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
354	<
355	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
356	<	#else  // isn't MPI
365	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
366	<	#endif  //is_mpi
367	<	}
368	<	excludeOffset += molInfo.nTorsions;
350	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
351	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
352	>	#else
353	>	exI = tempI + 1;
354	>	exJ = tempJ + 1;
355	>	#endif
356	>	info[k].excludes->addPair(exI, exJ);
357
358	<
371	<	// send the arrays off to the forceField for init.
358	>	} else {
359
360	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
361	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
362	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
363	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
360	>	tempI = theBends[j].a;
361	>	tempJ = theBends[j].b;
362	>	tempK = theBends[j].c;
363	>
364	>	#ifdef IS_MPI
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
368	>	#else
369	>	exI = tempI + 1;
370	>	exJ = tempJ + 1;
371	>	exK = tempK + 1;
372	>	#endif
373	>
374	>	info[k].excludes->addPair(exI, exK);
375	>	info[k].excludes->addPair(exI, exJ);
376	>	info[k].excludes->addPair(exJ, exK);
377	>	}
378	>	}
379
380	+	for (j = 0; j < molInfo.nTorsions; j++){
381	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
382	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
383	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
384	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
385	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
386
387	<	the_molecules[i].initialize( molInfo );
387	>	tempI = theTorsions[j].a;
388	>	tempJ = theTorsions[j].b;
389	>	tempK = theTorsions[j].c;
390	>	tempL = theTorsions[j].d;
391	>
392	>	#ifdef IS_MPI
393	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
394	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
395	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
396	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	exL = tempL + 1;
402	>	#endif
403	>
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exI, exK);
406	>	info[k].excludes->addPair(exI, exL);
407	>	info[k].excludes->addPair(exJ, exK);
408	>	info[k].excludes->addPair(exJ, exL);
409	>	info[k].excludes->addPair(exK, exL);
410	>	}
411
412	+	for (j = 0; j < molInfo.nRigidBodies; j++){
413
414	<	atomOffset += molInfo.nAtoms;
415	<	delete[] theBonds;
416	<	delete[] theBends;
417	<	delete[] theTorsions;
414	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
415	>	nMembers = currentRigidBody->getNMembers();
416	>
417	>	// Create the Rigid Body:
418	>
419	>	myRB = new RigidBody();
420	>
421	>	sprintf(rbName,"%s_RB_%s", molName, j);
422	>	myRB->setType(rbName);
423	>
424	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
425	>
426	>	// molI is atom numbering inside this molecule
427	>	molI = currentRigidBody->getMember(rb1);
428	>
429	>	// tempI is atom numbering on local processor
430	>	tempI = molI + atomOffset;
431	>
432	>	// currentAtom is the AtomStamp (which we need for
433	>	// rigid body reference positions)
434	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
435	>
436	>	// When we add to the rigid body, add the atom itself and
437	>	// the stamp info:
438	>
439	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
440	>
441	>	// Add this atom to the Skip List for the integrators
442	>	#ifdef IS_MPI
443	>	slI = info[k].atoms[tempI]->getGlobalIndex();
444	>	#else
445	>	slI = tempI;
446	>	#endif
447	>	skipList.insert(slI);
448	>
449	>	}
450	>
451	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
452	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
453	>
454	>	tempI = currentRigidBody->getMember(rb1);
455	>	tempJ = currentRigidBody->getMember(rb2);
456	>
457	>	// Some explanation is required here.
458	>	// Fortran indexing starts at 1, while c indexing starts at 0
459	>	// Also, in parallel computations, the GlobalIndex is
460	>	// used for the exclude list:
461	>
462	>	#ifdef IS_MPI
463	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
464	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
465	>	#else
466	>	exI = tempI + 1;
467	>	exJ = tempJ + 1;
468	>	#endif
469	>
470	>	info[k].excludes->addPair(exI, exJ);
471	>
472	>	}
473	>	}
474	>
475	>	molInfo.myRigidBodies.push_back(myRB);
476	>	info[k].rigidBodies.push_back(myRB);
477	>	}
478	>
479	>
480	>	// After this is all set up, scan through the atoms to
481	>	// see if they can be added to the integrableObjects:
482	>
483	>	for (j = 0; j < molInfo.nAtoms; j++){
484	>
485	>	#ifdef IS_MPI
486	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
487	>	#else
488	>	slJ = j+atomOffset;
489	>	#endif
490	>
491	>	// if they aren't on the skip list, then they can be integrated
492	>
493	>	if (skipList.find(slJ) == skipList.end()) {
494	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
495	>	info[k].integrableObjects.push_back(mySD);
496	>	molInfo.myIntegrableObjects.push_back(mySD);
497	>	}
498	>	}
499	>
500	>	// all rigid bodies are integrated:
501	>
502	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
503	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
504	>	info[k].integrableObjects.push_back(mySD);
505	>	molInfo.myIntegrableObjects.push_back(mySD);
506	>	}
507	>
508	>
509	>	// send the arrays off to the forceField for init.
510	>
511	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
512	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
513	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
514	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
515	>	theTorsions);
516	>
517	>	info[k].molecules[i].initialize(molInfo);
518	>
519	>
520	>	atomOffset += molInfo.nAtoms;
521	>	delete[] theBonds;
522	>	delete[] theBends;
523	>	delete[] theTorsions;
524	>	}
525		}
526
527		#ifdef IS_MPI
528	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
528	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
529		MPIcheckPoint();
530		#endif // is_mpi
531
532		// clean up the forcefield
394	–	the_ff->calcRcut();
395	–	the_ff->cleanMe();
533
534	<	}
534	>	if (!globals->haveLJrcut()){
535
536	<	void SimSetup::initFromBass( void ){
536	>	the_ff->calcRcut();
537
538	+	} else {
539	+
540	+	the_ff->setRcut( globals->getLJrcut() );
541	+	}
542	+
543	+	the_ff->cleanMe();
544	+	}
545	+
546	+	void SimSetup::initFromBass(void){
547		int i, j, k;
548		int n_cells;
549		double cellx, celly, cellz;
#	Line 406 | Line 552 | void SimSetup::initFromBass( void ){
552		int n_extra;
553		int have_extra, done;
554
555	<	temp1 = (double)tot_nmol / 4.0;
556	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
557	<	temp3 = ceil( temp2 );
555	>	double vel[3];
556	>	vel[0] = 0.0;
557	>	vel[1] = 0.0;
558	>	vel[2] = 0.0;
559
560	<	have_extra =0;
561	<	if( temp2 < temp3 ){ // we have a non-complete lattice
562	<	have_extra =1;
560	>	temp1 = (double) tot_nmol / 4.0;
561	>	temp2 = pow(temp1, (1.0 / 3.0));
562	>	temp3 = ceil(temp2);
563
564	<	n_cells = (int)temp3 - 1;
565	<	cellx = info->boxL[0] / temp3;
566	<	celly = info->boxL[1] / temp3;
567	<	cellz = info->boxL[2] / temp3;
421	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
422	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
423	<	n_per_extra = (int)ceil( temp1 );
564	>	have_extra = 0;
565	>	if (temp2 < temp3){
566	>	// we have a non-complete lattice
567	>	have_extra = 1;
568
569	<	if( n_per_extra > 4){
570	<	sprintf( painCave.errMsg,
571	<	"SimSetup error. There has been an error in constructing"
572	<	" the non-complete lattice.\n" );
569	>	n_cells = (int) temp3 - 1;
570	>	cellx = info[0].boxL[0] / temp3;
571	>	celly = info[0].boxL[1] / temp3;
572	>	cellz = info[0].boxL[2] / temp3;
573	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
574	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
575	>	n_per_extra = (int) ceil(temp1);
576	>
577	>	if (n_per_extra > 4){
578	>	sprintf(painCave.errMsg,
579	>	"SimSetup error. There has been an error in constructing"
580	>	" the non-complete lattice.\n");
581		painCave.isFatal = 1;
582		simError();
583		}
584		}
585		else{
586	<	n_cells = (int)temp3;
587	<	cellx = info->boxL[0] / temp3;
588	<	celly = info->boxL[1] / temp3;
589	<	cellz = info->boxL[2] / temp3;
586	>	n_cells = (int) temp3;
587	>	cellx = info[0].boxL[0] / temp3;
588	>	celly = info[0].boxL[1] / temp3;
589	>	cellz = info[0].boxL[2] / temp3;
590		}
591
592		current_mol = 0;
#	Line 442 | Line 594 | void SimSetup::initFromBass( void ){
594		current_comp = 0;
595		current_atom_ndx = 0;
596
597	<	for( i=0; i < n_cells ; i++ ){
598	<	for( j=0; j < n_cells; j++ ){
599	<	for( k=0; k < n_cells; k++ ){
597	>	for (i = 0; i < n_cells ; i++){
598	>	for (j = 0; j < n_cells; j++){
599	>	for (k = 0; k < n_cells; k++){
600	>	makeElement(i * cellx, j * celly, k * cellz);
601
602	<	makeElement( i * cellx,
450	<	j * celly,
451	<	k * cellz );
602	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
603
604	<	makeElement( i * cellx + 0.5 * cellx,
454	<	j * celly + 0.5 * celly,
455	<	k * cellz );
604	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
605
606	<	makeElement( i * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz + 0.5 * cellz );
460	<
461	<	makeElement( i * cellx + 0.5 * cellx,
462	<	j * celly,
463	<	k * cellz + 0.5 * cellz );
606	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
607		}
608		}
609		}
610
611	<	if( have_extra ){
611	>	if (have_extra){
612		done = 0;
613
614		int start_ndx;
615	<	for( i=0; i < (n_cells+1) && !done; i++ ){
616	<	for( j=0; j < (n_cells+1) && !done; j++ ){
615	>	for (i = 0; i < (n_cells + 1) && !done; i++){
616	>	for (j = 0; j < (n_cells + 1) && !done; j++){
617	>	if (i < n_cells){
618	>	if (j < n_cells){
619	>	start_ndx = n_cells;
620	>	}
621	>	else
622	>	start_ndx = 0;
623	>	}
624	>	else
625	>	start_ndx = 0;
626
627	<	if( i < n_cells ){
627	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
628	>	makeElement(i * cellx, j * celly, k * cellz);
629	>	done = (current_mol >= tot_nmol);
630
631	<	if( j < n_cells ){
632	<	start_ndx = n_cells;
633	<	}
634	<	else start_ndx = 0;
635	<	}
482	<	else start_ndx = 0;
631	>	if (!done && n_per_extra > 1){
632	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
633	>	k * cellz);
634	>	done = (current_mol >= tot_nmol);
635	>	}
636
637	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
638	<
639	<	makeElement( i * cellx,
640	<	j * celly,
641	<	k * cellz );
489	<	done = ( current_mol >= tot_nmol );
490	<
491	<	if( !done && n_per_extra > 1 ){
492	<	makeElement( i * cellx + 0.5 * cellx,
493	<	j * celly + 0.5 * celly,
494	<	k * cellz );
495	<	done = ( current_mol >= tot_nmol );
496	<	}
497	<
498	<	if( !done && n_per_extra > 2){
499	<	makeElement( i * cellx,
500	<	j * celly + 0.5 * celly,
501	<	k * cellz + 0.5 * cellz );
502	<	done = ( current_mol >= tot_nmol );
503	<	}
637	>	if (!done && n_per_extra > 2){
638	>	makeElement(i * cellx, j * celly + 0.5 * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642
643	<	if( !done && n_per_extra > 3){
644	<	makeElement( i * cellx + 0.5 * cellx,
645	<	j * celly,
646	<	k * cellz + 0.5 * cellz );
647	<	done = ( current_mol >= tot_nmol );
648	<	}
511	<	}
643	>	if (!done && n_per_extra > 3){
644	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
645	>	k * cellz + 0.5 * cellz);
646	>	done = (current_mol >= tot_nmol);
647	>	}
648	>	}
649		}
650		}
651		}
652
653	<
654	<	for( i=0; i<info->n_atoms; i++ ){
518	<	info->atoms[i]->set_vx( 0.0 );
519	<	info->atoms[i]->set_vy( 0.0 );
520	<	info->atoms[i]->set_vz( 0.0 );
653	>	for (i = 0; i < info[0].n_atoms; i++){
654	>	info[0].atoms[i]->setVel(vel);
655		}
656		}
657
658	<	void SimSetup::makeElement( double x, double y, double z ){
525	<
658	>	void SimSetup::makeElement(double x, double y, double z){
659		int k;
660		AtomStamp* current_atom;
661		DirectionalAtom* dAtom;
662		double rotMat[3][3];
663	+	double pos[3];
664
665	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
666	<
667	<	current_atom = comp_stamps[current_comp]->getAtom( k );
668	<	if( !current_atom->havePosition() ){
669	<	sprintf( painCave.errMsg,
670	<	"SimSetup:initFromBass error.\n"
671	<	"\tComponent %s, atom %s does not have a position specified.\n"
672	<	"\tThe initialization routine is unable to give a start"
673	<	" position.\n",
540	<	comp_stamps[current_comp]->getID(),
541	<	current_atom->getType() );
665	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
666	>	current_atom = comp_stamps[current_comp]->getAtom(k);
667	>	if (!current_atom->havePosition()){
668	>	sprintf(painCave.errMsg,
669	>	"SimSetup:initFromBass error.\n"
670	>	"\tComponent %s, atom %s does not have a position specified.\n"
671	>	"\tThe initialization routine is unable to give a start"
672	>	" position.\n",
673	>	comp_stamps[current_comp]->getID(), current_atom->getType());
674		painCave.isFatal = 1;
675		simError();
676		}
677
678	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
679	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
680	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
678	>	pos[0] = x + current_atom->getPosX();
679	>	pos[1] = y + current_atom->getPosY();
680	>	pos[2] = z + current_atom->getPosZ();
681
682	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
682	>	info[0].atoms[current_atom_ndx]->setPos(pos);
683
684	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
684	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
685	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
686
687		rotMat[0][0] = 1.0;
688		rotMat[0][1] = 0.0;
#	Line 563 | Line 696 | void SimSetup::makeElement( double x, double y, double
696		rotMat[2][1] = 0.0;
697		rotMat[2][2] = 1.0;
698
699	<	dAtom->setA( rotMat );
699	>	dAtom->setA(rotMat);
700		}
701
702		current_atom_ndx++;
#	Line 572 | Line 705 | void SimSetup::makeElement( double x, double y, double
705		current_mol++;
706		current_comp_mol++;
707
708	<	if( current_comp_mol >= components_nmol[current_comp] ){
576	<
708	>	if (current_comp_mol >= components_nmol[current_comp]){
709		current_comp_mol = 0;
710		current_comp++;
711		}
712		}
713
714
715	<	void SimSetup::gatherInfo( void ){
716	<	int i,j,k;
715	>	void SimSetup::gatherInfo(void){
716	>	int i;
717
718		ensembleCase = -1;
719		ffCase = -1;
720
589	–	// get the stamps and globals;
590	–	stamps = stamps;
591	–	globals = globals;
592	–
721		// set the easy ones first
722	<	info->target_temp = globals->getTargetTemp();
723	<	info->dt = globals->getDt();
724	<	info->run_time = globals->getRunTime();
722	>
723	>	for (i = 0; i < nInfo; i++){
724	>	info[i].target_temp = globals->getTargetTemp();
725	>	info[i].dt = globals->getDt();
726	>	info[i].run_time = globals->getRunTime();
727	>	}
728		n_components = globals->getNComponents();
729
730
731		// get the forceField
732
733	<	strcpy( force_field, globals->getForceField() );
733	>	strcpy(force_field, globals->getForceField());
734
735	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
736	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
737	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
735	>	if (!strcasecmp(force_field, "DUFF")){
736	>	ffCase = FF_DUFF;
737	>	}
738	>	else if (!strcasecmp(force_field, "LJ")){
739	>	ffCase = FF_LJ;
740	>	}
741	>	else if (!strcasecmp(force_field, "EAM")){
742	>	ffCase = FF_EAM;
743	>	}
744	>	else if (!strcasecmp(force_field, "WATER")){
745	>	ffCase = FF_H2O;
746	>	}
747		else{
748	<	sprintf( painCave.errMsg,
749	<	"SimSetup Error. Unrecognized force field -> %s\n",
750	<	force_field );
751	<	painCave.isFatal = 1;
612	<	simError();
748	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
749	>	force_field);
750	>	painCave.isFatal = 1;
751	>	simError();
752		}
753
754	<	// get the ensemble
754	>	// get the ensemble
755
756	<	strcpy( ensemble, globals->getEnsemble() );
756	>	strcpy(ensemble, globals->getEnsemble());
757
758	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
759	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
760	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
758	>	if (!strcasecmp(ensemble, "NVE")){
759	>	ensembleCase = NVE_ENS;
760	>	}
761	>	else if (!strcasecmp(ensemble, "NVT")){
762	>	ensembleCase = NVT_ENS;
763	>	}
764	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
765		ensembleCase = NPTi_ENS;
766	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
767	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
768	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
769	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
766	>	}
767	>	else if (!strcasecmp(ensemble, "NPTf")){
768	>	ensembleCase = NPTf_ENS;
769	>	}
770	>	else if (!strcasecmp(ensemble, "NPTxyz")){
771	>	ensembleCase = NPTxyz_ENS;
772	>	}
773		else{
774	<	sprintf( painCave.errMsg,
775	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
776	<	"reverting to NVE for this simulation.\n",
777	<	ensemble );
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	strcpy( ensemble, "NVE" );
781	<	ensembleCase = NVE_ENS;
774	>	sprintf(painCave.errMsg,
775	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
776	>	"\treverting to NVE for this simulation.\n",
777	>	ensemble);
778	>	painCave.isFatal = 0;
779	>	simError();
780	>	strcpy(ensemble, "NVE");
781	>	ensembleCase = NVE_ENS;
782		}
637	–	strcpy( info->ensemble, ensemble );
783
784	<	// get the mixing rule
784	>	for (i = 0; i < nInfo; i++){
785	>	strcpy(info[i].ensemble, ensemble);
786
787	<	strcpy( info->mixingRule, globals->getMixingRule() );
788	<	info->usePBC = globals->getPBC();
789	<
790	<
787	>	// get the mixing rule
788	>
789	>	strcpy(info[i].mixingRule, globals->getMixingRule());
790	>	info[i].usePBC = globals->getPBC();
791	>	}
792	>
793		// get the components and calculate the tot_nMol and indvidual n_mol
794	<
794	>
795		the_components = globals->getComponents();
796		components_nmol = new int[n_components];
797
798
799	<	if( !globals->haveNMol() ){
799	>	if (!globals->haveNMol()){
800		// we don't have the total number of molecules, so we assume it is
801		// given in each component
802
803		tot_nmol = 0;
804	<	for( i=0; i<n_components; i++ ){
805	<
806	<	if( !the_components[i]->haveNMol() ){
807	<	// we have a problem
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup Error. No global NMol or component NMol"
810	<	" given. Cannot calculate the number of atoms.\n" );
811	<	painCave.isFatal = 1;
664	<	simError();
804	>	for (i = 0; i < n_components; i++){
805	>	if (!the_components[i]->haveNMol()){
806	>	// we have a problem
807	>	sprintf(painCave.errMsg,
808	>	"SimSetup Error. No global NMol or component NMol given.\n"
809	>	"\tCannot calculate the number of atoms.\n");
810	>	painCave.isFatal = 1;
811	>	simError();
812		}
813
814		tot_nmol += the_components[i]->getNMol();
#	Line 669 | Line 816 | void SimSetup::gatherInfo( void ){
816		}
817		}
818		else{
819	<	sprintf( painCave.errMsg,
820	<	"SimSetup error.\n"
821	<	"\tSorry, the ability to specify total"
822	<	" nMols and then give molfractions in the components\n"
823	<	"\tis not currently supported."
824	<	" Please give nMol in the components.\n" );
819	>	sprintf(painCave.errMsg,
820	>	"SimSetup error.\n"
821	>	"\tSorry, the ability to specify total"
822	>	" nMols and then give molfractions in the components\n"
823	>	"\tis not currently supported."
824	>	" Please give nMol in the components.\n");
825		painCave.isFatal = 1;
826		simError();
827		}
828
829	<	// set the status, sample, and thermal kick times
830	<
831	<	if( globals->haveSampleTime() ){
832	<	info->sampleTime = globals->getSampleTime();
833	<	info->statusTime = info->sampleTime;
834	<	info->thermalTime = info->sampleTime;
829	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
830	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
831	>	sprintf(painCave.errMsg,
832	>	"Sample time is not divisible by dt.\n"
833	>	"\tThis will result in samples that are not uniformly\n"
834	>	"\tdistributed in time.  If this is a problem, change\n"
835	>	"\tyour sampleTime variable.\n");
836	>	painCave.isFatal = 0;
837	>	simError();
838		}
689	–	else{
690	–	info->sampleTime = globals->getRunTime();
691	–	info->statusTime = info->sampleTime;
692	–	info->thermalTime = info->sampleTime;
693	–	}
839
840	<	if( globals->haveStatusTime() ){
841	<	info->statusTime = globals->getStatusTime();
840	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
841	>	sprintf(painCave.errMsg,
842	>	"Status time is not divisible by dt.\n"
843	>	"\tThis will result in status reports that are not uniformly\n"
844	>	"\tdistributed in time.  If this is a problem, change \n"
845	>	"\tyour statusTime variable.\n");
846	>	painCave.isFatal = 0;
847	>	simError();
848		}
849
850	<	if( globals->haveThermalTime() ){
851	<	info->thermalTime = globals->getThermalTime();
852	<	}
850	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
851	>	sprintf(painCave.errMsg,
852	>	"Thermal time is not divisible by dt.\n"
853	>	"\tThis will result in thermalizations that are not uniformly\n"
854	>	"\tdistributed in time.  If this is a problem, change \n"
855	>	"\tyour thermalTime variable.\n");
856	>	painCave.isFatal = 0;
857	>	simError();
858	>	}
859
860	<	// check for the temperature set flag
861	<
862	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
860	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
861	>	sprintf(painCave.errMsg,
862	>	"Reset time is not divisible by dt.\n"
863	>	"\tThis will result in integrator resets that are not uniformly\n"
864	>	"\tdistributed in time.  If this is a problem, change\n"
865	>	"\tyour resetTime variable.\n");
866	>	painCave.isFatal = 0;
867	>	simError();
868	>	}
869
870	<	// get some of the tricky things that may still be in the globals
870	>	// set the status, sample, and thermal kick times
871
872	<	double boxVector[3];
873	<	if( globals->haveBox() ){
874	<	boxVector[0] = globals->getBox();
875	<	boxVector[1] = globals->getBox();
876	<	boxVector[2] = globals->getBox();
877	<
878	<	info->setBox( boxVector );
879	<	}
880	<	else if( globals->haveDensity() ){
872	>	for (i = 0; i < nInfo; i++){
873	>	if (globals->haveSampleTime()){
874	>	info[i].sampleTime = globals->getSampleTime();
875	>	info[i].statusTime = info[i].sampleTime;
876	>	info[i].thermalTime = info[i].sampleTime;
877	>	}
878	>	else{
879	>	info[i].sampleTime = globals->getRunTime();
880	>	info[i].statusTime = info[i].sampleTime;
881	>	info[i].thermalTime = info[i].sampleTime;
882	>	}
883
884	<	double vol;
885	<	vol = (double)tot_nmol / globals->getDensity();
721	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
722	<	boxVector[1] = boxVector[0];
723	<	boxVector[2] = boxVector[0];
724	<
725	<	info->setBox( boxVector );
726	<	}
727	<	else{
728	<	if( !globals->haveBoxX() ){
729	<	sprintf( painCave.errMsg,
730	<	"SimSetup error, no periodic BoxX size given.\n" );
731	<	painCave.isFatal = 1;
732	<	simError();
884	>	if (globals->haveStatusTime()){
885	>	info[i].statusTime = globals->getStatusTime();
886		}
734	–	boxVector[0] = globals->getBoxX();
887
888	<	if( !globals->haveBoxY() ){
889	<	sprintf( painCave.errMsg,
738	<	"SimSetup error, no periodic BoxY size given.\n" );
739	<	painCave.isFatal = 1;
740	<	simError();
888	>	if (globals->haveThermalTime()){
889	>	info[i].thermalTime = globals->getThermalTime();
890		}
742	–	boxVector[1] = globals->getBoxY();
891
892	<	if( !globals->haveBoxZ() ){
893	<	sprintf( painCave.errMsg,
894	<	"SimSetup error, no periodic BoxZ size given.\n" );
895	<	painCave.isFatal = 1;
748	<	simError();
892	>	info[i].resetIntegrator = 0;
893	>	if( globals->haveResetTime() ){
894	>	info[i].resetTime = globals->getResetTime();
895	>	info[i].resetIntegrator = 1;
896		}
750	–	boxVector[2] = globals->getBoxZ();
897
898	<	info->setBox( boxVector );
898	>	// check for the temperature set flag
899	>
900	>	if (globals->haveTempSet())
901	>	info[i].setTemp = globals->getTempSet();
902	>
903	>	// check for the extended State init
904	>
905	>	info[i].useInitXSstate = globals->getUseInitXSstate();
906	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
907	>
908		}
909	+
910	+	//setup seed for random number generator
911	+	int seedValue;
912
913	+	if (globals->haveSeed()){
914	+	seedValue = globals->getSeed();
915
916	+	if(seedValue / 1E9 == 0){
917	+	sprintf(painCave.errMsg,
918	+	"Seed for sprng library should contain at least 9 digits\n"
919	+	"OOPSE will generate a seed for user\n");
920	+	painCave.isFatal = 0;
921	+	simError();
922	+
923	+	//using seed generated by system instead of invalid seed set by user
924	+	#ifndef IS_MPI
925	+	seedValue = make_sprng_seed();
926	+	#else
927	+	if (worldRank == 0){
928	+	seedValue = make_sprng_seed();
929	+	}
930	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
931	+	#endif
932	+	}
933	+	}//end of if branch of globals->haveSeed()
934	+	else{
935
936	+	#ifndef IS_MPI
937	+	seedValue = make_sprng_seed();
938	+	#else
939	+	if (worldRank == 0){
940	+	seedValue = make_sprng_seed();
941	+	}
942	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
943	+	#endif
944	+	}//end of globals->haveSeed()
945	+
946	+	for (int i = 0; i < nInfo; i++){
947	+	info[i].setSeed(seedValue);
948	+	}
949	+
950		#ifdef IS_MPI
951	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
951	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
952		MPIcheckPoint();
953		#endif // is_mpi
761	–
954		}
955
956
957	<	void SimSetup::finalInfoCheck( void ){
957	>	void SimSetup::finalInfoCheck(void){
958		int index;
959		int usesDipoles;
960	<
960	>	int i;
961
962	<	// check electrostatic parameters
963	<
964	<	index = 0;
965	<	usesDipoles = 0;
966	<	while( (index < info->n_atoms) && !usesDipoles ){
967	<	usesDipoles = ((info->atoms)[index])->hasDipole();
968	<	index++;
969	<	}
970	<
962	>	for (i = 0; i < nInfo; i++){
963	>	// check electrostatic parameters
964	>
965	>	index = 0;
966	>	usesDipoles = 0;
967	>	while ((index < info[i].n_atoms) && !usesDipoles){
968	>	usesDipoles = (info[i].atoms[index])->hasDipole();
969	>	index++;
970	>	}
971	>
972		#ifdef IS_MPI
973	<	int myUse = usesDipoles;
974	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
973	>	int myUse = usesDipoles;
974	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
975		#endif //is_mpi
976
977	<	double theEcr, theEst;
977	>	double theEcr, theEst;
978
979	<	if (globals->getUseRF() ) {
980	<	info->useReactionField = 1;
788	<
789	<	if( !globals->haveECR() ){
790	<	sprintf( painCave.errMsg,
791	<	"SimSetup Warning: using default value of 1/2 the smallest "
792	<	"box length for the electrostaticCutoffRadius.\n"
793	<	"I hope you have a very fast processor!\n");
794	<	painCave.isFatal = 0;
795	<	simError();
796	<	double smallest;
797	<	smallest = info->boxL[0];
798	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
799	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
800	<	theEcr = 0.5 * smallest;
801	<	} else {
802	<	theEcr = globals->getECR();
803	<	}
979	>	if (globals->getUseRF()){
980	>	info[i].useReactionField = 1;
981
982	<	if( !globals->haveEST() ){
983	<	sprintf( painCave.errMsg,
984	<	"SimSetup Warning: using default value of 0.05 * the "
985	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
986	<	);
987	<	painCave.isFatal = 0;
988	<	simError();
989	<	theEst = 0.05 * theEcr;
990	<	} else {
991	<	theEst= globals->getEST();
992	<	}
982	>	if (!globals->haveECR()){
983	>	sprintf(painCave.errMsg,
984	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
985	>	"\tOOPSE will use a default value of 15.0 angstroms"
986	>	"\tfor the electrostaticCutoffRadius.\n");
987	>	painCave.isFatal = 0;
988	>	simError();
989	>	theEcr = 15.0;
990	>	}
991	>	else{
992	>	theEcr = globals->getECR();
993	>	}
994
995	<	info->setEcr( theEcr, theEst );
996	<
997	<	if(!globals->haveDielectric() ){
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: You are trying to use Reaction Field without"
1000	<	"setting a dielectric constant!\n"
1001	<	);
1002	<	painCave.isFatal = 1;
1003	<	simError();
995	>	if (!globals->haveEST()){
996	>	sprintf(painCave.errMsg,
997	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
998	>	"\tOOPSE will use a default value of\n"
999	>	"\t0.05 * electrostaticCutoffRadius\n"
1000	>	"\tfor the electrostaticSkinThickness\n");
1001	>	painCave.isFatal = 0;
1002	>	simError();
1003	>	theEst = 0.05 * theEcr;
1004	>	}
1005	>	else{
1006	>	theEst = globals->getEST();
1007	>	}
1008	>
1009	>	info[i].setDefaultEcr(theEcr, theEst);
1010	>
1011	>	if (!globals->haveDielectric()){
1012	>	sprintf(painCave.errMsg,
1013	>	"SimSetup Error: No Dielectric constant was set.\n"
1014	>	"\tYou are trying to use Reaction Field without"
1015	>	"\tsetting a dielectric constant!\n");
1016	>	painCave.isFatal = 1;
1017	>	simError();
1018	>	}
1019	>	info[i].dielectric = globals->getDielectric();
1020		}
1021	<	info->dielectric = globals->getDielectric();
1022	<	}
1023	<	else {
1024	<	if (usesDipoles) {
1025	<
1026	<	if( !globals->haveECR() ){
1027	<	sprintf( painCave.errMsg,
1028	<	"SimSetup Warning: using default value of 1/2 the smallest "
1029	<	"box length for the electrostaticCutoffRadius.\n"
1030	<	"I hope you have a very fast processor!\n");
1031	<	painCave.isFatal = 0;
1032	<	simError();
1033	<	double smallest;
1034	<	smallest = info->boxL[0];
1035	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
1036	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
1037	<	theEcr = 0.5 * smallest;
1038	<	} else {
1039	<	theEcr = globals->getECR();
1021	>	else{
1022	>	if (usesDipoles){
1023	>	if (!globals->haveECR()){
1024	>	sprintf(painCave.errMsg,
1025	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the electrostaticCutoffRadius.\n");
1028	>	painCave.isFatal = 0;
1029	>	simError();
1030	>	theEcr = 15.0;
1031	>	}
1032	>	else{
1033	>	theEcr = globals->getECR();
1034	>	}
1035	>
1036	>	if (!globals->haveEST()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1039	>	"\tOOPSE will use a default value of\n"
1040	>	"\t0.05 * electrostaticCutoffRadius\n"
1041	>	"\tfor the electrostaticSkinThickness\n");
1042	>	painCave.isFatal = 0;
1043	>	simError();
1044	>	theEst = 0.05 * theEcr;
1045	>	}
1046	>	else{
1047	>	theEst = globals->getEST();
1048	>	}
1049	>
1050	>	info[i].setDefaultEcr(theEcr, theEst);
1051		}
847	–
848	–	if( !globals->haveEST() ){
849	–	sprintf( painCave.errMsg,
850	–	"SimSetup Warning: using default value of 0.05 * the "
851	–	"electrostaticCutoffRadius for the "
852	–	"electrostaticSkinThickness\n"
853	–	);
854	–	painCave.isFatal = 0;
855	–	simError();
856	–	theEst = 0.05 * theEcr;
857	–	} else {
858	–	theEst= globals->getEST();
859	–	}
860	–
861	–	info->setEcr( theEcr, theEst );
1052		}
1053	<	}
864	<
1053	>	}
1054		#ifdef IS_MPI
1055	<	strcpy( checkPointMsg, "post processing checks out" );
1055	>	strcpy(checkPointMsg, "post processing checks out");
1056		MPIcheckPoint();
1057		#endif // is_mpi
869	–
1058		}
1059	+
1060	+	void SimSetup::initSystemCoords(void){
1061	+	int i;
1062
1063	<	void SimSetup::initSystemCoords( void ){
1063	>	char* inName;
1064
1065	<	if( globals->haveInitialConfig() ){
1066	<
1067	<	InitializeFromFile* fileInit;
1065	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1066	>
1067	>	for (i = 0; i < info[0].n_atoms; i++)
1068	>	info[0].atoms[i]->setCoords();
1069	>
1070	>	if (globals->haveInitialConfig()){
1071	>	InitializeFromFile* fileInit;
1072		#ifdef IS_MPI // is_mpi
1073	<	if( worldRank == 0 ){
1073	>	if (worldRank == 0){
1074		#endif //is_mpi
1075	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1075	>	inName = globals->getInitialConfig();
1076	>	fileInit = new InitializeFromFile(inName);
1077		#ifdef IS_MPI
1078	<	}else fileInit = new InitializeFromFile( NULL );
1078	>	}
1079	>	else
1080	>	fileInit = new InitializeFromFile(NULL);
1081		#endif
1082	<	fileInit->readInit( info ); // default velocities on
1082	>	fileInit->readInit(info); // default velocities on
1083
1084	<	delete fileInit;
1085	<	}
1086	<	else{
1084	>	delete fileInit;
1085	>	}
1086	>	else{
1087	>
1088	>	// no init from bass
1089	>
1090	>	sprintf(painCave.errMsg,
1091	>	"Cannot intialize a simulation without an initial configuration file.\n");
1092	>	painCave.isFatal = 1;;
1093	>	simError();
1094	>
1095	>	}
1096
890	–	#ifdef IS_MPI
891	–
892	–	// no init from bass
893	–
894	–	sprintf( painCave.errMsg,
895	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
896	–	painCave.isFatal;
897	–	simError();
898	–
899	–	#else
900	–
901	–	initFromBass();
902	–
903	–
904	–	#endif
905	–	}
906	–
1097		#ifdef IS_MPI
1098	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1098	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1099		MPIcheckPoint();
1100		#endif // is_mpi
911	–
1101		}
1102
1103
1104	<	void SimSetup::makeOutNames( void ){
1104	>	void SimSetup::makeOutNames(void){
1105	>	int k;
1106
1107	+
1108	+	for (k = 0; k < nInfo; k++){
1109		#ifdef IS_MPI
1110	<	if( worldRank == 0 ){
1110	>	if (worldRank == 0){
1111		#endif // is_mpi
1112	<
1113	<	if( globals->haveFinalConfig() ){
1114	<	strcpy( info->finalName, globals->getFinalConfig() );
923	<	}
924	<	else{
925	<	strcpy( info->finalName, inFileName );
926	<	char* endTest;
927	<	int nameLength = strlen( info->finalName );
928	<	endTest = &(info->finalName[nameLength - 5]);
929	<	if( !strcmp( endTest, ".bass" ) ){
930	<	strcpy( endTest, ".eor" );
1112	>
1113	>	if (globals->haveFinalConfig()){
1114	>	strcpy(info[k].finalName, globals->getFinalConfig());
1115		}
932	–	else if( !strcmp( endTest, ".BASS" ) ){
933	–	strcpy( endTest, ".eor" );
934	–	}
1116		else{
1117	<	endTest = &(info->finalName[nameLength - 4]);
1118	<	if( !strcmp( endTest, ".bss" ) ){
1119	<	strcpy( endTest, ".eor" );
1120	<	}
1121	<	else if( !strcmp( endTest, ".mdl" ) ){
1122	<	strcpy( endTest, ".eor" );
1123	<	}
1124	<	else{
1125	<	strcat( info->finalName, ".eor" );
1126	<	}
1117	>	strcpy(info[k].finalName, inFileName);
1118	>	char* endTest;
1119	>	int nameLength = strlen(info[k].finalName);
1120	>	endTest = &(info[k].finalName[nameLength - 5]);
1121	>	if (!strcmp(endTest, ".bass")){
1122	>	strcpy(endTest, ".eor");
1123	>	}
1124	>	else if (!strcmp(endTest, ".BASS")){
1125	>	strcpy(endTest, ".eor");
1126	>	}
1127	>	else{
1128	>	endTest = &(info[k].finalName[nameLength - 4]);
1129	>	if (!strcmp(endTest, ".bss")){
1130	>	strcpy(endTest, ".eor");
1131	>	}
1132	>	else if (!strcmp(endTest, ".mdl")){
1133	>	strcpy(endTest, ".eor");
1134	>	}
1135	>	else{
1136	>	strcat(info[k].finalName, ".eor");
1137	>	}
1138	>	}
1139		}
1140	<	}
1141	<
1142	<	// make the sample and status out names
1143	<
1144	<	strcpy( info->sampleName, inFileName );
1145	<	char* endTest;
1146	<	int nameLength = strlen( info->sampleName );
1147	<	endTest = &(info->sampleName[nameLength - 5]);
1148	<	if( !strcmp( endTest, ".bass" ) ){
956	<	strcpy( endTest, ".dump" );
957	<	}
958	<	else if( !strcmp( endTest, ".BASS" ) ){
959	<	strcpy( endTest, ".dump" );
960	<	}
961	<	else{
962	<	endTest = &(info->sampleName[nameLength - 4]);
963	<	if( !strcmp( endTest, ".bss" ) ){
964	<	strcpy( endTest, ".dump" );
1140	>
1141	>	// make the sample and status out names
1142	>
1143	>	strcpy(info[k].sampleName, inFileName);
1144	>	char* endTest;
1145	>	int nameLength = strlen(info[k].sampleName);
1146	>	endTest = &(info[k].sampleName[nameLength - 5]);
1147	>	if (!strcmp(endTest, ".bass")){
1148	>	strcpy(endTest, ".dump");
1149		}
1150	<	else if( !strcmp( endTest, ".mdl" ) ){
1151	<	strcpy( endTest, ".dump" );
1150	>	else if (!strcmp(endTest, ".BASS")){
1151	>	strcpy(endTest, ".dump");
1152		}
1153		else{
1154	<	strcat( info->sampleName, ".dump" );
1154	>	endTest = &(info[k].sampleName[nameLength - 4]);
1155	>	if (!strcmp(endTest, ".bss")){
1156	>	strcpy(endTest, ".dump");
1157	>	}
1158	>	else if (!strcmp(endTest, ".mdl")){
1159	>	strcpy(endTest, ".dump");
1160	>	}
1161	>	else{
1162	>	strcat(info[k].sampleName, ".dump");
1163	>	}
1164		}
1165	<	}
1166	<
1167	<	strcpy( info->statusName, inFileName );
1168	<	nameLength = strlen( info->statusName );
1169	<	endTest = &(info->statusName[nameLength - 5]);
1170	<	if( !strcmp( endTest, ".bass" ) ){
978	<	strcpy( endTest, ".stat" );
979	<	}
980	<	else if( !strcmp( endTest, ".BASS" ) ){
981	<	strcpy( endTest, ".stat" );
982	<	}
983	<	else{
984	<	endTest = &(info->statusName[nameLength - 4]);
985	<	if( !strcmp( endTest, ".bss" ) ){
986	<	strcpy( endTest, ".stat" );
1165	>
1166	>	strcpy(info[k].statusName, inFileName);
1167	>	nameLength = strlen(info[k].statusName);
1168	>	endTest = &(info[k].statusName[nameLength - 5]);
1169	>	if (!strcmp(endTest, ".bass")){
1170	>	strcpy(endTest, ".stat");
1171		}
1172	<	else if( !strcmp( endTest, ".mdl" ) ){
1173	<	strcpy( endTest, ".stat" );
1172	>	else if (!strcmp(endTest, ".BASS")){
1173	>	strcpy(endTest, ".stat");
1174		}
1175		else{
1176	<	strcat( info->statusName, ".stat" );
1176	>	endTest = &(info[k].statusName[nameLength - 4]);
1177	>	if (!strcmp(endTest, ".bss")){
1178	>	strcpy(endTest, ".stat");
1179	>	}
1180	>	else if (!strcmp(endTest, ".mdl")){
1181	>	strcpy(endTest, ".stat");
1182	>	}
1183	>	else{
1184	>	strcat(info[k].statusName, ".stat");
1185	>	}
1186		}
1187	<	}
995	<
1187	>
1188		#ifdef IS_MPI
997	–	}
998	–	#endif // is_mpi
1189
1190	+	}
1191	+	#endif // is_mpi
1192	+	}
1193		}
1194
1195
1196	<	void SimSetup::sysObjectsCreation( void ){
1196	>	void SimSetup::sysObjectsCreation(void){
1197	>	int i, k;
1198
1005	–	int i;
1006	–
1199		// create the forceField
1200
1201		createFF();
#	Line 1018 | Line 1210 | void SimSetup::sysObjectsCreation( void ){
1210
1211		#ifdef IS_MPI
1212		// divide the molecules among the processors
1213	<
1213	>
1214		mpiMolDivide();
1215		#endif //is_mpi
1216	<
1216	>
1217		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1218	<
1218	>
1219		makeSysArrays();
1220
1221		// make and initialize the molecules (all but atomic coordinates)
1222	<
1222	>
1223		makeMolecules();
1032	–	info->identArray = new int[info->n_atoms];
1033	–	for(i=0; i<info->n_atoms; i++){
1034	–	info->identArray[i] = the_atoms[i]->getIdent();
1035	–	}
1036	–
1224
1225	<
1225	>	for (k = 0; k < nInfo; k++){
1226	>	info[k].identArray = new int[info[k].n_atoms];
1227	>	for (i = 0; i < info[k].n_atoms; i++){
1228	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1229	>	}
1230	>	}
1231		}
1232
1233
1234	<	void SimSetup::createFF( void ){
1234	>	void SimSetup::createFF(void){
1235	>	switch (ffCase){
1236	>	case FF_DUFF:
1237	>	the_ff = new DUFF();
1238	>	break;
1239
1240	<	switch( ffCase ){
1240	>	case FF_LJ:
1241	>	the_ff = new LJFF();
1242	>	break;
1243
1244	<	case FF_DUFF:
1245	<	the_ff = new DUFF();
1246	<	break;
1244	>	case FF_EAM:
1245	>	the_ff = new EAM_FF();
1246	>	break;
1247
1248	<	case FF_LJ:
1249	<	the_ff = new LJFF();
1250	<	break;
1248	>	case FF_H2O:
1249	>	the_ff = new WATER();
1250	>	break;
1251
1252	<	case FF_EAM:
1253	<	the_ff = new EAM_FF();
1254	<	break;
1255	<
1256	<	default:
1059	<	sprintf( painCave.errMsg,
1060	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1061	<	painCave.isFatal = 1;
1062	<	simError();
1252	>	default:
1253	>	sprintf(painCave.errMsg,
1254	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1255	>	painCave.isFatal = 1;
1256	>	simError();
1257		}
1258
1259		#ifdef IS_MPI
1260	<	strcpy( checkPointMsg, "ForceField creation successful" );
1260	>	strcpy(checkPointMsg, "ForceField creation successful");
1261		MPIcheckPoint();
1262		#endif // is_mpi
1069	–
1263		}
1264
1265
1266	<	void SimSetup::compList( void ){
1074	<
1266	>	void SimSetup::compList(void){
1267		int i;
1268	+	char* id;
1269	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1270	+	LinkedMolStamp* currentStamp = NULL;
1271	+	comp_stamps = new MoleculeStamp * [n_components];
1272
1077	–	comp_stamps = new MoleculeStamp*[n_components];
1078	–
1273		// make an array of molecule stamps that match the components used.
1274		// also extract the used stamps out into a separate linked list
1275
1276	<	info->nComponents = n_components;
1277	<	info->componentsNmol = components_nmol;
1278	<	info->compStamps = comp_stamps;
1279	<	info->headStamp = new LinkedMolStamp();
1280	<
1281	<	char* id;
1088	<	LinkedMolStamp* headStamp = info->headStamp;
1089	<	LinkedMolStamp* currentStamp = NULL;
1090	<	for( i=0; i<n_components; i++ ){
1276	>	for (i = 0; i < nInfo; i++){
1277	>	info[i].nComponents = n_components;
1278	>	info[i].componentsNmol = components_nmol;
1279	>	info[i].compStamps = comp_stamps;
1280	>	info[i].headStamp = headStamp;
1281	>	}
1282
1283	+
1284	+	for (i = 0; i < n_components; i++){
1285		id = the_components[i]->getType();
1286		comp_stamps[i] = NULL;
1094	–
1095	–	// check to make sure the component isn't already in the list
1287
1288	<	comp_stamps[i] = headStamp->match( id );
1289	<	if( comp_stamps[i] == NULL ){
1290	<
1288	>	// check to make sure the component isn't already in the list
1289	>
1290	>	comp_stamps[i] = headStamp->match(id);
1291	>	if (comp_stamps[i] == NULL){
1292		// extract the component from the list;
1293	<
1294	<	currentStamp = stamps->extractMolStamp( id );
1295	<	if( currentStamp == NULL ){
1296	<	sprintf( painCave.errMsg,
1297	<	"SimSetup error: Component \"%s\" was not found in the "
1298	<	"list of declared molecules\n",
1299	<	id );
1300	<	painCave.isFatal = 1;
1301	<	simError();
1293	>
1294	>	currentStamp = stamps->extractMolStamp(id);
1295	>	if (currentStamp == NULL){
1296	>	sprintf(painCave.errMsg,
1297	>	"SimSetup error: Component \"%s\" was not found in the "
1298	>	"list of declared molecules\n",
1299	>	id);
1300	>	painCave.isFatal = 1;
1301	>	simError();
1302		}
1303	<
1304	<	headStamp->add( currentStamp );
1305	<	comp_stamps[i] = headStamp->match( id );
1303	>
1304	>	headStamp->add(currentStamp);
1305	>	comp_stamps[i] = headStamp->match(id);
1306		}
1307		}
1308
1309		#ifdef IS_MPI
1310	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1310	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1311		MPIcheckPoint();
1312		#endif // is_mpi
1121	–
1122	–
1313		}
1314
1315	<	void SimSetup::calcSysValues( void ){
1316	<	int i, j, k;
1315	>	void SimSetup::calcSysValues(void){
1316	>	int i;
1317
1318	+	int* molMembershipArray;
1319
1320		tot_atoms = 0;
1321		tot_bonds = 0;
1322		tot_bends = 0;
1323		tot_torsions = 0;
1324	<	for( i=0; i<n_components; i++ ){
1325	<
1326	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1327	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1328	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1324	>	tot_rigid = 0;
1325	>	for (i = 0; i < n_components; i++){
1326	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1327	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1328	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1329		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1330	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1331		}
1332	<
1332	>
1333		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1334	+	molMembershipArray = new int[tot_atoms];
1335
1336	<	info->n_atoms = tot_atoms;
1337	<	info->n_bonds = tot_bonds;
1338	<	info->n_bends = tot_bends;
1339	<	info->n_torsions = tot_torsions;
1340	<	info->n_SRI = tot_SRI;
1341	<	info->n_mol = tot_nmol;
1342	<
1343	<	info->molMembershipArray = new int[tot_atoms];
1336	>	for (i = 0; i < nInfo; i++){
1337	>	info[i].n_atoms = tot_atoms;
1338	>	info[i].n_bonds = tot_bonds;
1339	>	info[i].n_bends = tot_bends;
1340	>	info[i].n_torsions = tot_torsions;
1341	>	info[i].n_SRI = tot_SRI;
1342	>	info[i].n_mol = tot_nmol;
1343	>
1344	>	info[i].molMembershipArray = molMembershipArray;
1345	>	}
1346		}
1347
1153	–
1348		#ifdef IS_MPI
1349
1350	<	void SimSetup::mpiMolDivide( void ){
1157	<
1350	>	void SimSetup::mpiMolDivide(void){
1351		int i, j, k;
1352		int localMol, allMol;
1353		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1354	+	int local_rigid;
1355	+	vector<int> globalAtomIndex;
1356	+	vector<int> globalMolIndex;
1357
1358	<	mpiSim = new mpiSimulation( info );
1163	<
1164	<	globalIndex = mpiSim->divideLabor();
1358	>	mpiSim = new mpiSimulation(info);
1359
1360	+	mpiSim->divideLabor();
1361	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1362	+	globalMolIndex = mpiSim->getGlobalMolIndex();
1363	+
1364		// set up the local variables
1365	<
1365	>
1366		mol2proc = mpiSim->getMolToProcMap();
1367		molCompType = mpiSim->getMolComponentType();
1368	<
1368	>
1369		allMol = 0;
1370		localMol = 0;
1371		local_atoms = 0;
1372		local_bonds = 0;
1373		local_bends = 0;
1374		local_torsions = 0;
1375	<	globalAtomIndex = 0;
1375	>	local_rigid = 0;
1376	>	globalAtomCounter = 0;
1377
1378	<
1379	<	for( i=0; i<n_components; i++ ){
1380	<
1381	<	for( j=0; j<components_nmol[i]; j++ ){
1382	<
1383	<	if( mol2proc[allMol] == worldRank ){
1384	<
1385	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1386	<	local_bonds +=    comp_stamps[i]->getNBonds();
1188	<	local_bends +=    comp_stamps[i]->getNBends();
1189	<	local_torsions += comp_stamps[i]->getNTorsions();
1190	<	localMol++;
1378	>	for (i = 0; i < n_components; i++){
1379	>	for (j = 0; j < components_nmol[i]; j++){
1380	>	if (mol2proc[allMol] == worldRank){
1381	>	local_atoms += comp_stamps[i]->getNAtoms();
1382	>	local_bonds += comp_stamps[i]->getNBonds();
1383	>	local_bends += comp_stamps[i]->getNBends();
1384	>	local_torsions += comp_stamps[i]->getNTorsions();
1385	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1386	>	localMol++;
1387		}
1388	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1389	<	info->molMembershipArray[globalAtomIndex] = allMol;
1390	<	globalAtomIndex++;
1388	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1389	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1390	>	globalAtomCounter++;
1391		}
1392
1393	<	allMol++;
1393	>	allMol++;
1394		}
1395		}
1396		local_SRI = local_bonds + local_bends + local_torsions;
1397	+
1398	+	info[0].n_atoms = mpiSim->getMyNlocal();
1399
1400	<	info->n_atoms = mpiSim->getMyNlocal();
1401	<
1402	<	if( local_atoms != info->n_atoms ){
1403	<	sprintf( painCave.errMsg,
1404	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1405	<	" localAtom (%d) are not equal.\n",
1208	<	info->n_atoms,
1209	<	local_atoms );
1400	>
1401	>	if (local_atoms != info[0].n_atoms){
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1404	>	"\tlocalAtom (%d) are not equal.\n",
1405	>	info[0].n_atoms, local_atoms);
1406		painCave.isFatal = 1;
1407		simError();
1408		}
1409
1410	<	info->n_bonds = local_bonds;
1411	<	info->n_bends = local_bends;
1412	<	info->n_torsions = local_torsions;
1413	<	info->n_SRI = local_SRI;
1414	<	info->n_mol = localMol;
1410	>	info[0].n_bonds = local_bonds;
1411	>	info[0].n_bends = local_bends;
1412	>	info[0].n_torsions = local_torsions;
1413	>	info[0].n_SRI = local_SRI;
1414	>	info[0].n_mol = localMol;
1415
1416	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1416	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1417		MPIcheckPoint();
1418		}
1419	<
1419	>
1420		#endif // is_mpi
1421
1422
1423	<	void SimSetup::makeSysArrays( void ){
1424	<	int i, j, k;
1423	>	void SimSetup::makeSysArrays(void){
1424	>
1425	>	#ifndef IS_MPI
1426	>	int k, j;
1427	>	#endif // is_mpi
1428	>	int i, l;
1429
1430	+	Atom** the_atoms;
1431	+	Molecule* the_molecules;
1432
1433	<	// create the atom and short range interaction arrays
1433	>	for (l = 0; l < nInfo; l++){
1434	>	// create the atom and short range interaction arrays
1435
1436	<	Atom::createArrays(info->n_atoms);
1437	<	the_atoms = new Atom*[info->n_atoms];
1438	<	the_molecules = new Molecule[info->n_mol];
1236	<	int molIndex;
1436	>	the_atoms = new Atom * [info[l].n_atoms];
1437	>	the_molecules = new Molecule[info[l].n_mol];
1438	>	int molIndex;
1439
1440	<	// initialize the molecule's stampID's
1440	>	// initialize the molecule's stampID's
1441
1442		#ifdef IS_MPI
1241	–
1443
1444	<	molIndex = 0;
1445	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1446	<
1447	<	if(mol2proc[i] == worldRank ){
1448	<	the_molecules[molIndex].setStampID( molCompType[i] );
1449	<	the_molecules[molIndex].setMyIndex( molIndex );
1450	<	the_molecules[molIndex].setGlobalIndex( i );
1451	<	molIndex++;
1444	>
1445	>	molIndex = 0;
1446	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1447	>	if (mol2proc[i] == worldRank){
1448	>	the_molecules[molIndex].setStampID(molCompType[i]);
1449	>	the_molecules[molIndex].setMyIndex(molIndex);
1450	>	the_molecules[molIndex].setGlobalIndex(i);
1451	>	molIndex++;
1452	>	}
1453		}
1252	–	}
1454
1455		#else // is_mpi
1456	<
1457	<	molIndex = 0;
1458	<	globalAtomIndex = 0;
1459	<	for(i=0; i<n_components; i++){
1460	<	for(j=0; j<components_nmol[i]; j++ ){
1461	<	the_molecules[molIndex].setStampID( i );
1462	<	the_molecules[molIndex].setMyIndex( molIndex );
1463	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1464	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1465	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1466	<	globalAtomIndex++;
1456	>
1457	>	molIndex = 0;
1458	>	globalAtomCounter = 0;
1459	>	for (i = 0; i < n_components; i++){
1460	>	for (j = 0; j < components_nmol[i]; j++){
1461	>	the_molecules[molIndex].setStampID(i);
1462	>	the_molecules[molIndex].setMyIndex(molIndex);
1463	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1464	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1465	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1466	>	globalAtomCounter++;
1467	>	}
1468	>	molIndex++;
1469		}
1267	–	molIndex++;
1470		}
1269	–	}
1270	–
1471
1472	+
1473		#endif // is_mpi
1474
1475	<
1476	<	if( info->n_SRI ){
1475	>	info[l].globalExcludes = new int;
1476	>	info[l].globalExcludes[0] = 0;
1477
1478	<	Exclude::createArray(info->n_SRI);
1278	<	the_excludes = new Exclude*[info->n_SRI];
1279	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1280	<	info->globalExcludes = new int;
1281	<	info->n_exclude = info->n_SRI;
1282	<	}
1283	<	else{
1284	<
1285	<	Exclude::createArray( 1 );
1286	<	the_excludes = new Exclude*;
1287	<	the_excludes[0] = new Exclude(0);
1288	<	the_excludes[0]->setPair( 0,0 );
1289	<	info->globalExcludes = new int;
1290	<	info->globalExcludes[0] = 0;
1291	<	info->n_exclude = 0;
1292	<	}
1478	>	// set the arrays into the SimInfo object
1479
1480	<	// set the arrays into the SimInfo object
1480	>	info[l].atoms = the_atoms;
1481	>	info[l].molecules = the_molecules;
1482	>	info[l].nGlobalExcludes = 0;
1483
1484	<	info->atoms = the_atoms;
1485	<	info->molecules = the_molecules;
1298	<	info->nGlobalExcludes = 0;
1299	<	info->excludes = the_excludes;
1300	<
1301	<	the_ff->setSimInfo( info );
1302	<
1484	>	the_ff->setSimInfo(info);
1485	>	}
1486		}
1487
1488	<	void SimSetup::makeIntegrator( void ){
1488	>	void SimSetup::makeIntegrator(void){
1489	>	int k;
1490
1491	<	NVT<RealIntegrator>*  myNVT = NULL;
1492	<	NPTi<RealIntegrator>* myNPTi = NULL;
1493	<	NPTf<RealIntegrator>* myNPTf = NULL;
1494	<	NPTim<RealIntegrator>* myNPTim = NULL;
1495	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1312	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1313	<
1314	<	cerr << "setting integrator" <<endl;
1491	>	NVE<RealIntegrator>* myNVE = NULL;
1492	>	NVT<RealIntegrator>* myNVT = NULL;
1493	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1494	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1495	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1496
1497	<	switch( ensembleCase ){
1497	>	for (k = 0; k < nInfo; k++){
1498	>	switch (ensembleCase){
1499	>	case NVE_ENS:
1500	>	if (globals->haveZconstraints()){
1501	>	setupZConstraint(info[k]);
1502	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1503	>	}
1504	>	else{
1505	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1506	>	}
1507	>
1508	>	info->the_integrator = myNVE;
1509	>	break;
1510
1511	<	case NVE_ENS:
1512	<	new NVE<RealIntegrator>( info, the_ff );
1513	<	break;
1511	>	case NVT_ENS:
1512	>	if (globals->haveZconstraints()){
1513	>	setupZConstraint(info[k]);
1514	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1515	>	}
1516	>	else
1517	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1518
1519	<	case NVT_ENS:
1323	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1324	<	myNVT->setTargetTemp(globals->getTargetTemp());
1519	>	myNVT->setTargetTemp(globals->getTargetTemp());
1520
1521	<	if (globals->haveTauThermostat())
1522	<	myNVT->setTauThermostat(globals->getTauThermostat());
1521	>	if (globals->haveTauThermostat())
1522	>	myNVT->setTauThermostat(globals->getTauThermostat());
1523	>	else{
1524	>	sprintf(painCave.errMsg,
1525	>	"SimSetup error: If you use the NVT\n"
1526	>	"\tensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530
1531	<	else {
1532	<	sprintf( painCave.errMsg,
1331	<	"SimSetup error: If you use the NVT\n"
1332	<	"    ensemble, you must set tauThermostat.\n");
1333	<	painCave.isFatal = 1;
1334	<	simError();
1335	<	}
1336	<	break;
1531	>	info->the_integrator = myNVT;
1532	>	break;
1533
1534	<	case NPTi_ENS:
1535	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1536	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1534	>	case NPTi_ENS:
1535	>	if (globals->haveZconstraints()){
1536	>	setupZConstraint(info[k]);
1537	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1538	>	}
1539	>	else
1540	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1541
1542	<	if (globals->haveTargetPressure())
1343	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1344	<	else {
1345	<	sprintf( painCave.errMsg,
1346	<	"SimSetup error: If you use a constant pressure\n"
1347	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1348	<	painCave.isFatal = 1;
1349	<	simError();
1350	<	}
1351	<
1352	<	if( globals->haveTauThermostat() )
1353	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1354	<	else{
1355	<	sprintf( painCave.errMsg,
1356	<	"SimSetup error: If you use an NPT\n"
1357	<	"    ensemble, you must set tauThermostat.\n");
1358	<	painCave.isFatal = 1;
1359	<	simError();
1360	<	}
1542	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1543
1544	<	if( globals->haveTauBarostat() )
1545	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1546	<	else{
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use an NPT\n"
1549	<	"    ensemble, you must set tauBarostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1371	<	break;
1544	>	if (globals->haveTargetPressure())
1545	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1546	>	else{
1547	>	sprintf(painCave.errMsg,
1548	>	"SimSetup error: If you use a constant pressure\n"
1549	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553
1554	<	case NPTf_ENS:
1555	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1556	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1554	>	if (globals->haveTauThermostat())
1555	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1556	>	else{
1557	>	sprintf(painCave.errMsg,
1558	>	"SimSetup error: If you use an NPT\n"
1559	>	"\tensemble, you must set tauThermostat.\n");
1560	>	painCave.isFatal = 1;
1561	>	simError();
1562	>	}
1563
1564	<	if (globals->haveTargetPressure())
1565	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1566	<	else {
1567	<	sprintf( painCave.errMsg,
1568	<	"SimSetup error: If you use a constant pressure\n"
1569	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1570	<	painCave.isFatal = 1;
1571	<	simError();
1572	<	}
1564	>	if (globals->haveTauBarostat())
1565	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1566	>	else{
1567	>	sprintf(painCave.errMsg,
1568	>	"SimSetup error: If you use an NPT\n"
1569	>	"\tensemble, you must set tauBarostat.\n");
1570	>	painCave.isFatal = 1;
1571	>	simError();
1572	>	}
1573
1574	<	if( globals->haveTauThermostat() )
1575	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1389	<	else{
1390	<	sprintf( painCave.errMsg,
1391	<	"SimSetup error: If you use an NPT\n"
1392	<	"    ensemble, you must set tauThermostat.\n");
1393	<	painCave.isFatal = 1;
1394	<	simError();
1395	<	}
1574	>	info->the_integrator = myNPTi;
1575	>	break;
1576
1577	<	if( globals->haveTauBarostat() )
1578	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1579	<	else{
1580	<	sprintf( painCave.errMsg,
1581	<	"SimSetup error: If you use an NPT\n"
1582	<	"    ensemble, you must set tauBarostat.\n");
1583	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1406	<	break;
1407	<
1408	<	case NPTim_ENS:
1409	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1410	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1577	>	case NPTf_ENS:
1578	>	if (globals->haveZconstraints()){
1579	>	setupZConstraint(info[k]);
1580	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1581	>	}
1582	>	else
1583	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1584
1585	<	if (globals->haveTargetPressure())
1413	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1414	<	else {
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use a constant pressure\n"
1417	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<
1422	<	if( globals->haveTauThermostat() )
1423	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1424	<	else{
1425	<	sprintf( painCave.errMsg,
1426	<	"SimSetup error: If you use an NPT\n"
1427	<	"    ensemble, you must set tauThermostat.\n");
1428	<	painCave.isFatal = 1;
1429	<	simError();
1430	<	}
1585	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1586
1587	<	if( globals->haveTauBarostat() )
1588	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1589	<	else{
1590	<	sprintf( painCave.errMsg,
1591	<	"SimSetup error: If you use an NPT\n"
1592	<	"    ensemble, you must set tauBarostat.\n");
1593	<	painCave.isFatal = 1;
1594	<	simError();
1595	<	}
1441	<	break;
1587	>	if (globals->haveTargetPressure())
1588	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1589	>	else{
1590	>	sprintf(painCave.errMsg,
1591	>	"SimSetup error: If you use a constant pressure\n"
1592	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1593	>	painCave.isFatal = 1;
1594	>	simError();
1595	>	}
1596
1597	<	case NPTfm_ENS:
1598	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1445	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1597	>	if (globals->haveTauThermostat())
1598	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1599
1600	<	if (globals->haveTargetPressure())
1601	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1602	<	else {
1603	<	sprintf( painCave.errMsg,
1604	<	"SimSetup error: If you use a constant pressure\n"
1605	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1606	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1600	>	else{
1601	>	sprintf(painCave.errMsg,
1602	>	"SimSetup error: If you use an NPT\n"
1603	>	"\tensemble, you must set tauThermostat.\n");
1604	>	painCave.isFatal = 1;
1605	>	simError();
1606	>	}
1607
1608	<	if( globals->haveTauBarostat() )
1609	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NVEZCONS_ENS:
1479	<	{
1608	>	if (globals->haveTauBarostat())
1609	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1610
1611	<	if(globals->haveZConsTime()){
1612	<
1613	<	//add sample time of z-constraint  into SimInfo's property list
1614	<	DoubleData* zconsTimeProp = new DoubleData();
1615	<	zconsTimeProp->setID("zconstime");
1616	<	zconsTimeProp->setData(globals->getZConsTime());
1617	<	info->addProperty(zconsTimeProp);
1488	<	}
1489	<	else{
1490	<	sprintf( painCave.errMsg,
1491	<	"ZConstraint error: If you use an ZConstraint\n"
1492	<	" , you must set sample time.\n");
1493	<	painCave.isFatal = 1;
1494	<	simError();
1495	<	}
1496	<
1497	<	if(globals->haveIndexOfAllZConsMols()){
1498	<
1499	<	//add index of z-constraint molecules into SimInfo's property list
1500	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1501	<	sort(tempIndex.begin(), tempIndex.end());
1502	<
1503	<	IndexData* zconsIndex = new IndexData();
1504	<	zconsIndex->setID("zconsindex");
1505	<	zconsIndex->setIndexData(tempIndex);
1506	<	info->addProperty(zconsIndex);
1507	<	}
1508	<	else{
1509	<	sprintf( painCave.errMsg,
1510	<	"SimSetup error: If you use an ZConstraint\n"
1511	<	" , you must set index of z-constraint molecules.\n");
1512	<	painCave.isFatal = 1;
1513	<	simError();
1514	<
1515	<	}
1611	>	else{
1612	>	sprintf(painCave.errMsg,
1613	>	"SimSetup error: If you use an NPT\n"
1614	>	"\tensemble, you must set tauBarostat.\n");
1615	>	painCave.isFatal = 1;
1616	>	simError();
1617	>	}
1618
1619	<	//Determine the name of ouput file and add it into SimInfo's property list
1620	<	//Be careful, do not use inFileName, since it is a pointer which
1519	<	//point to a string at master node, and slave nodes do not contain that string
1520	<
1521	<	string zconsOutput(info->finalName);
1522	<
1523	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1524	<
1525	<	StringData* zconsFilename = new StringData();
1526	<	zconsFilename->setID("zconsfilename");
1527	<	zconsFilename->setData(zconsOutput);
1619	>	info->the_integrator = myNPTf;
1620	>	break;
1621
1622	<	info->addProperty(zconsFilename);
1623	<
1624	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1625	<
1626	<	break;
1622	>	case NPTxyz_ENS:
1623	>	if (globals->haveZconstraints()){
1624	>	setupZConstraint(info[k]);
1625	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1626	>	}
1627	>	else
1628	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1629	>
1630	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1631	>
1632	>	if (globals->haveTargetPressure())
1633	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1634	>	else{
1635	>	sprintf(painCave.errMsg,
1636	>	"SimSetup error: If you use a constant pressure\n"
1637	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1638	>	painCave.isFatal = 1;
1639	>	simError();
1640	>	}
1641	>
1642	>	if (globals->haveTauThermostat())
1643	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1644	>	else{
1645	>	sprintf(painCave.errMsg,
1646	>	"SimSetup error: If you use an NPT\n"
1647	>	"\tensemble, you must set tauThermostat.\n");
1648	>	painCave.isFatal = 1;
1649	>	simError();
1650	>	}
1651	>
1652	>	if (globals->haveTauBarostat())
1653	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1654	>	else{
1655	>	sprintf(painCave.errMsg,
1656	>	"SimSetup error: If you use an NPT\n"
1657	>	"\tensemble, you must set tauBarostat.\n");
1658	>	painCave.isFatal = 1;
1659	>	simError();
1660	>	}
1661	>
1662	>	info->the_integrator = myNPTxyz;
1663	>	break;
1664	>
1665	>	default:
1666	>	sprintf(painCave.errMsg,
1667	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1668	>	painCave.isFatal = 1;
1669	>	simError();
1670		}
1535	–
1536	–	default:
1537	–	sprintf( painCave.errMsg,
1538	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1539	–	painCave.isFatal = 1;
1540	–	simError();
1671		}
1542	–
1672		}
1673
1674	<	void SimSetup::initFortran( void ){
1674	>	void SimSetup::initFortran(void){
1675	>	info[0].refreshSim();
1676
1677	<	info->refreshSim();
1678	<
1549	<	if( !strcmp( info->mixingRule, "standard") ){
1550	<	the_ff->initForceField( LB_MIXING_RULE );
1677	>	if (!strcmp(info[0].mixingRule, "standard")){
1678	>	the_ff->initForceField(LB_MIXING_RULE);
1679		}
1680	<	else if( !strcmp( info->mixingRule, "explicit") ){
1681	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1680	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1681	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1682		}
1683		else{
1684	<	sprintf( painCave.errMsg,
1685	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1558	<	info->mixingRule );
1684	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1685	>	info[0].mixingRule);
1686		painCave.isFatal = 1;
1687		simError();
1688		}
1689
1690
1691		#ifdef IS_MPI
1692	<	strcpy( checkPointMsg,
1566	<	"Successfully intialized the mixingRule for Fortran." );
1692	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1693		MPIcheckPoint();
1694		#endif // is_mpi
1695	+	}
1696
1697	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1698	+	int nZConstraints;
1699	+	ZconStamp** zconStamp;
1700	+
1701	+	if (globals->haveZconstraintTime()){
1702	+	//add sample time of z-constraint  into SimInfo's property list
1703	+	DoubleData* zconsTimeProp = new DoubleData();
1704	+	zconsTimeProp->setID(ZCONSTIME_ID);
1705	+	zconsTimeProp->setData(globals->getZconsTime());
1706	+	theInfo.addProperty(zconsTimeProp);
1707	+	}
1708	+	else{
1709	+	sprintf(painCave.errMsg,
1710	+	"ZConstraint error: If you use a ZConstraint,\n"
1711	+	"\tyou must set zconsTime.\n");
1712	+	painCave.isFatal = 1;
1713	+	simError();
1714	+	}
1715	+
1716	+	//push zconsTol into siminfo, if user does not specify
1717	+	//value for zconsTol, a default value will be used
1718	+	DoubleData* zconsTol = new DoubleData();
1719	+	zconsTol->setID(ZCONSTOL_ID);
1720	+	if (globals->haveZconsTol()){
1721	+	zconsTol->setData(globals->getZconsTol());
1722	+	}
1723	+	else{
1724	+	double defaultZConsTol = 0.01;
1725	+	sprintf(painCave.errMsg,
1726	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1727	+	"\tOOPSE will use a default value of %f.\n"
1728	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1729	+	defaultZConsTol);
1730	+	painCave.isFatal = 0;
1731	+	simError();
1732	+
1733	+	zconsTol->setData(defaultZConsTol);
1734	+	}
1735	+	theInfo.addProperty(zconsTol);
1736	+
1737	+	//set Force Subtraction Policy
1738	+	StringData* zconsForcePolicy = new StringData();
1739	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1740	+
1741	+	if (globals->haveZconsForcePolicy()){
1742	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1743	+	}
1744	+	else{
1745	+	sprintf(painCave.errMsg,
1746	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1747	+	"\tOOPSE will use PolicyByMass.\n"
1748	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1749	+	painCave.isFatal = 0;
1750	+	simError();
1751	+	zconsForcePolicy->setData("BYMASS");
1752	+	}
1753	+
1754	+	theInfo.addProperty(zconsForcePolicy);
1755	+
1756	+	//set zcons gap
1757	+	DoubleData* zconsGap = new DoubleData();
1758	+	zconsGap->setID(ZCONSGAP_ID);
1759	+
1760	+	if (globals->haveZConsGap()){
1761	+	zconsGap->setData(globals->getZconsGap());
1762	+	theInfo.addProperty(zconsGap);
1763	+	}
1764	+
1765	+	//set zcons fixtime
1766	+	DoubleData* zconsFixtime = new DoubleData();
1767	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1768	+
1769	+	if (globals->haveZConsFixTime()){
1770	+	zconsFixtime->setData(globals->getZconsFixtime());
1771	+	theInfo.addProperty(zconsFixtime);
1772	+	}
1773	+
1774	+	//set zconsUsingSMD
1775	+	IntData* zconsUsingSMD = new IntData();
1776	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1777	+
1778	+	if (globals->haveZConsUsingSMD()){
1779	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1780	+	theInfo.addProperty(zconsUsingSMD);
1781	+	}
1782	+
1783	+	//Determine the name of ouput file and add it into SimInfo's property list
1784	+	//Be careful, do not use inFileName, since it is a pointer which
1785	+	//point to a string at master node, and slave nodes do not contain that string
1786	+
1787	+	string zconsOutput(theInfo.finalName);
1788	+
1789	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1790	+
1791	+	StringData* zconsFilename = new StringData();
1792	+	zconsFilename->setID(ZCONSFILENAME_ID);
1793	+	zconsFilename->setData(zconsOutput);
1794	+
1795	+	theInfo.addProperty(zconsFilename);
1796	+
1797	+	//setup index, pos and other parameters of z-constraint molecules
1798	+	nZConstraints = globals->getNzConstraints();
1799	+	theInfo.nZconstraints = nZConstraints;
1800	+
1801	+	zconStamp = globals->getZconStamp();
1802	+	ZConsParaItem tempParaItem;
1803	+
1804	+	ZConsParaData* zconsParaData = new ZConsParaData();
1805	+	zconsParaData->setID(ZCONSPARADATA_ID);
1806	+
1807	+	for (int i = 0; i < nZConstraints; i++){
1808	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1809	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1810	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1811	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1812	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1813	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1814	+	zconsParaData->addItem(tempParaItem);
1815	+	}
1816	+
1817	+	//check the uniqueness of index
1818	+	if(!zconsParaData->isIndexUnique()){
1819	+	sprintf(painCave.errMsg,
1820	+	"ZConstraint Error: molIndex is not unique!\n");
1821	+	painCave.isFatal = 1;
1822	+	simError();
1823	+	}
1824	+
1825	+	//sort the parameters by index of molecules
1826	+	zconsParaData->sortByIndex();
1827	+
1828	+	//push data into siminfo, therefore, we can retrieve later
1829	+	theInfo.addProperty(zconsParaData);
1830		}
1831	+
1832	+	void SimSetup::makeMinimizer(){
1833	+
1834	+	OOPSEMinimizer* myOOPSEMinimizer;
1835	+	MinimizerParameterSet* param;
1836	+	char minimizerName[100];
1837	+
1838	+	for (int i = 0; i < nInfo; i++){
1839	+
1840	+	//prepare parameter set for minimizer
1841	+	param = new MinimizerParameterSet();
1842	+	param->setDefaultParameter();
1843	+
1844	+	if (globals->haveMinimizer()){
1845	+	param->setFTol(globals->getMinFTol());
1846	+	}
1847	+
1848	+	if (globals->haveMinGTol()){
1849	+	param->setGTol(globals->getMinGTol());
1850	+	}
1851	+
1852	+	if (globals->haveMinMaxIter()){
1853	+	param->setMaxIteration(globals->getMinMaxIter());
1854	+	}
1855	+
1856	+	if (globals->haveMinWriteFrq()){
1857	+	param->setMaxIteration(globals->getMinMaxIter());
1858	+	}
1859	+
1860	+	if (globals->haveMinWriteFrq()){
1861	+	param->setWriteFrq(globals->getMinWriteFrq());
1862	+	}
1863	+
1864	+	if (globals->haveMinStepSize()){
1865	+	param->setStepSize(globals->getMinStepSize());
1866	+	}
1867	+
1868	+	if (globals->haveMinLSMaxIter()){
1869	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinLSTol()){
1873	+	param->setLineSearchTol(globals->getMinLSTol());
1874	+	}
1875	+
1876	+	strcpy(minimizerName, globals->getMinimizer());
1877	+
1878	+	if (!strcasecmp(minimizerName, "CG")){
1879	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1880	+	}
1881	+	else if (!strcasecmp(minimizerName, "SD")){
1882	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1883	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1884	+	}
1885	+	else{
1886	+	sprintf(painCave.errMsg,
1887	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1888	+	painCave.isFatal = 0;
1889	+	simError();
1890	+
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	info[i].the_integrator = myOOPSEMinimizer;
1894	+
1895	+	//store the minimizer into simInfo
1896	+	info[i].the_minimizer = myOOPSEMinimizer;
1897	+	info[i].has_minimizer = true;
1898	+	}
1899	+
1900	+	}

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