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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 20 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
24	<	#define NPTfm_ENS      5
25	<	#define NVEZCONS_ENS   6
26	<	#define NVTZCONS_ENS   7
27	<	#define NPTiZCONS_ENS  8
28	<	#define NPTfZCONS_ENS  9
29	<	#define NPTimZCONS_ENS 10
30	<	#define NPTfmZCONS_ENS 11
27	>	#define NPTxyz_ENS     4
28
32	–	#define FF_DUFF 0
33	–	#define FF_LJ   1
34	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 55 | 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 ){
66	<
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();
94	<	mpiEventLoop();
95	<
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
102	–	int i, j, k, globalAtomIndex;
103	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 110 | 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
127	–	makeIntegrator();
128	–
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
#	Line 133 | Line 162 | void SimSetup::createSim( void ){
162		// initialize the Fortran
163
164		initFortran();
136	–
137	–
138	–
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;
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	>
194		//init the forceField paramters
195
196		the_ff->readParams();
197
163	–
198		// init the atoms
199
200	<	double ux, uy, uz, u, uSqr;
167	<
168	<	atomOffset = 0;
169	<	excludeOffset = 0;
170	<	for(i=0; i<info->n_mol; i++){
171	<
172	<	stampID = the_molecules[i].getStampID();
200	>	int nMembers, nNew, rb1, rb2;
201
202	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
203	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
202	>	for (k = 0; k < nInfo; k++){
203	>	the_ff->setSimInfo(&(info[k]));
204
205	<	molInfo.myAtoms = &the_atoms[atomOffset];
181	<	molInfo.myExcludes = &the_excludes[excludeOffset];
182	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	<	molInfo.myBends = new Bend*[molInfo.nBends];
184	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
205	>	atomOffset = 0;
206
207	<	theBonds = new bond_pair[molInfo.nBonds];
208	<	theBends = new bend_set[molInfo.nBends];
209	<	theTorsions = new torsion_set[molInfo.nTorsions];
210	<
211	<	// make the Atoms
212	<
213	<	for(j=0; j<molInfo.nAtoms; j++){
207	>	for (i = 0; i < info[k].n_mol; i++){
208	>	stampID = info[k].molecules[i].getStampID();
209	>
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215
216	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	if( currentAtom->haveOrientation() ){
196	<
197	<	dAtom = new DirectionalAtom(j + atomOffset);
198	<	info->n_oriented++;
199	<	molInfo.myAtoms[j] = dAtom;
200	<
201	<	ux = currentAtom->getOrntX();
202	<	uy = currentAtom->getOrntY();
203	<	uz = currentAtom->getOrntZ();
204	<
205	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	<
207	<	u = sqrt( uSqr );
208	<	ux = ux / u;
209	<	uy = uy / u;
210	<	uz = uz / u;
211	<
212	<	dAtom->setSUx( ux );
213	<	dAtom->setSUy( uy );
214	<	dAtom->setSUz( uz );
215	<	}
216	<	else{
217	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
218	<	}
219	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	<
221	<	#ifdef IS_MPI
222	<
223	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	<
225	<	#endif // is_mpi
226	<	}
227	<
228	<	// make the bonds
229	<	for(j=0; j<molInfo.nBonds; j++){
230	<
231	<	currentBond = comp_stamps[stampID]->getBond( j );
232	<	theBonds[j].a = currentBond->getA() + atomOffset;
233	<	theBonds[j].b = currentBond->getB() + atomOffset;
216	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
217
218	<	exI = theBonds[j].a;
219	<	exJ = theBonds[j].b;
218	>	if (molInfo.nBonds > 0)
219	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	>	else
221	>	molInfo.myBonds = NULL;
222
223	<	// exclude_I must always be the smaller of the pair
224	<	if( exI > exJ ){
225	<	tempEx = exI;
226	<	exI = exJ;
242	<	exJ = tempEx;
243	<	}
244	<	#ifdef IS_MPI
245	<	tempEx = exI;
246	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
247	<	tempEx = exJ;
248	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
249	<
250	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
251	<	#else  // isn't MPI
223	>	if (molInfo.nBends > 0)
224	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	>	else
226	>	molInfo.myBends = NULL;
227
228	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
229	<	#endif  //is_mpi
230	<	}
231	<	excludeOffset += molInfo.nBonds;
228	>	if (molInfo.nTorsions > 0)
229	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	>	else
231	>	molInfo.myTorsions = NULL;
232
233	<	//make the bends
234	<	for(j=0; j<molInfo.nBends; j++){
233	>	theBonds = new bond_pair[molInfo.nBonds];
234	>	theBends = new bend_set[molInfo.nBends];
235	>	theTorsions = new torsion_set[molInfo.nTorsions];
236
237	<	currentBend = comp_stamps[stampID]->getBend( j );
238	<	theBends[j].a = currentBend->getA() + atomOffset;
239	<	theBends[j].b = currentBend->getB() + atomOffset;
240	<	theBends[j].c = currentBend->getC() + atomOffset;
241	<
242	<	if( currentBend->haveExtras() ){
243	<
244	<	extras = currentBend->getExtras();
245	<	current_extra = extras;
246	<
247	<	while( current_extra != NULL ){
248	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
249	<
250	<	switch( current_extra->getType() ){
251	<
252	<	case 0:
253	<	theBends[j].ghost =
254	<	current_extra->getInt() + atomOffset;
255	<	theBends[j].isGhost = 1;
256	<	break;
257	<
258	<	case 1:
259	<	theBends[j].ghost =
260	<	(int)current_extra->getDouble() + atomOffset;
261	<	theBends[j].isGhost = 1;
262	<	break;
263	<
264	<	default:
265	<	sprintf( painCave.errMsg,
266	<	"SimSetup Error: ghostVectorSource was neither a "
267	<	"double nor an int.\n"
268	<	"-->Bend[%d] in %s\n",
269	<	j, comp_stamps[stampID]->getID() );
270	<	painCave.isFatal = 1;
271	<	simError();
272	<	}
273	<	}
274	<
275	<	else{
276	<
277	<	sprintf( painCave.errMsg,
278	<	"SimSetup Error: unhandled bend assignment:\n"
279	<	"    -->%s in Bend[%d] in %s\n",
280	<	current_extra->getlhs(),
281	<	j, comp_stamps[stampID]->getID() );
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<
286	<	current_extra = current_extra->getNext();
287	<	}
237	>	// make the Atoms
238	>
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241	>
242	>	if (currentAtom->haveOrientation()){
243	>	dAtom = new DirectionalAtom((j + atomOffset),
244	>	info[k].getConfiguration());
245	>	info[k].n_oriented++;
246	>	molInfo.myAtoms[j] = dAtom;
247	>
248	>	// Directional Atoms have standard unit vectors which are oriented
249	>	// in space using the three Euler angles.  We assume the standard
250	>	// unit vector was originally along the z axis below.
251	>
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255	>
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260	>
261	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	>	}
263	>
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265	>
266	>	#ifdef IS_MPI
267	>
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269	>
270	>	#endif // is_mpi
271	>	}
272	>
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278	>
279	>	tempI = theBonds[j].a;
280	>	tempJ = theBonds[j].b;
281	>
282	>	#ifdef IS_MPI
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289	>
290	>	info[k].excludes->addPair(exI, exJ);
291		}
292	<
293	<	if( !theBends[j].isGhost ){
294	<
295	<	exI = theBends[j].a;
296	<	exJ = theBends[j].c;
297	<	}
298	<	else{
299	<
300	<	exI = theBends[j].a;
301	<	exJ = theBends[j].b;
302	<	}
303	<
304	<	// exclude_I must always be the smaller of the pair
305	<	if( exI > exJ ){
306	<	tempEx = exI;
307	<	exI = exJ;
308	<	exJ = tempEx;
309	<	}
292	>
293	>	//make the bends
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299	>
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303	>
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311	>
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317	>
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336	>
337	>	current_extra = current_extra->getNext();
338	>	}
339	>	}
340	>
341	>	if (theBends[j].isGhost) {
342	>
343	>	tempI = theBends[j].a;
344	>	tempJ = theBends[j].b;
345	>
346		#ifdef IS_MPI
347	<	tempEx = exI;
348	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
349	<	tempEx = exJ;
350	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	<
352	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
353	<	#else  // isn't MPI
339	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	<	#endif  //is_mpi
341	<	}
342	<	excludeOffset += molInfo.nBends;
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354
355	<	for(j=0; j<molInfo.nTorsions; j++){
345	<
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;
355	>	} else {
356
357	<	// exclude_I must always be the smaller of the pair
358	<	if( exI > exJ ){
359	<	tempEx = exI;
360	<	exI = exJ;
361	<	exJ = tempEx;
357	>	tempI = theBends[j].a;
358	>	tempJ = theBends[j].b;
359	>	tempK = theBends[j].c;
360	>
361	>	#ifdef IS_MPI
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375		}
376	+
377	+	for (j = 0; j < molInfo.nTorsions; j++){
378	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383	+
384	+	tempI = theTorsions[j].a;
385	+	tempJ = theTorsions[j].b;
386	+	tempK = theTorsions[j].c;
387	+	tempL = theTorsions[j].d;
388	+
389		#ifdef IS_MPI
390	<	tempEx = exI;
391	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
392	<	tempEx = exJ;
393	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
394	<
395	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
396	<	#else  // isn't MPI
397	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
398	<	#endif  //is_mpi
399	<	}
372	<	excludeOffset += molInfo.nTorsions;
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399	>	#endif
400
401	<
402	<	// send the arrays off to the forceField for init.
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407	>	}
408
409	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410
411	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	+	nMembers = currentRigidBody->getNMembers();
413
414	<	the_molecules[i].initialize( molInfo );
414	>	// Create the Rigid Body:
415
416	+	myRB = new RigidBody();
417	+
418	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
419
420	<	atomOffset += molInfo.nAtoms;
421	<	delete[] theBonds;
422	<	delete[] theBends;
423	<	delete[] theTorsions;
420	>	// molI is atom numbering inside this molecule
421	>	molI = currentRigidBody->getMember(rb1);
422	>
423	>	// tempI is atom numbering on local processor
424	>	tempI = molI + atomOffset;
425	>
426	>	// currentAtom is the AtomStamp (which we need for
427	>	// rigid body reference positions)
428	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
429	>
430	>	// When we add to the rigid body, add the atom itself and
431	>	// the stamp info:
432	>
433	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	>
435	>	// Add this atom to the Skip List for the integrators
436	>	#ifdef IS_MPI
437	>	slI = info[k].atoms[tempI]->getGlobalIndex();
438	>	#else
439	>	slI = tempI;
440	>	#endif
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468	>	}
469	>
470	>	// send the arrays off to the forceField for init.
471	>
472	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
473	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
474	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
475	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
476	>	theTorsions);
477	>
478	>	info[k].molecules[i].initialize(molInfo);
479	>
480	>
481	>	atomOffset += molInfo.nAtoms;
482	>	delete[] theBonds;
483	>	delete[] theBends;
484	>	delete[] theTorsions;
485	>	}
486	>
487	>	// build up the integrableObjects vector:
488	>
489	>	for (i = 0; i < info[k].n_atoms; i++) {
490	>
491	>	#ifdef IS_MPI
492	>	slI = info[k].atoms[i]->getGlobalIndex();
493	>	#else
494	>	slI = i;
495	>	#endif
496	>
497	>	if (skipList.find(slI) == skipList.end()) {
498	>	mySD = (StuntDouble *) info[k].atoms[i];
499	>	info[k].integrableObjects.push_back(mySD);
500	>	}
501	>	}
502	>	for (i = 0; i < info[k].rigidBodies.size(); i++) {
503	>	mySD = (StuntDouble *) info[k].rigidBodies[i];
504	>	info[k].integrableObjects.push_back(mySD);
505	>	}
506	>
507		}
508
509		#ifdef IS_MPI
510	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
510	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
511		MPIcheckPoint();
512		#endif // is_mpi
513
514		// clean up the forcefield
398	–	the_ff->calcRcut();
399	–	the_ff->cleanMe();
515
516	<	}
516	>	if (!globals->haveLJrcut()){
517
518	<	void SimSetup::initFromBass( void ){
518	>	the_ff->calcRcut();
519
520	+	} else {
521	+
522	+	the_ff->setRcut( globals->getLJrcut() );
523	+	}
524	+
525	+	the_ff->cleanMe();
526	+	}
527	+
528	+	void SimSetup::initFromBass(void){
529		int i, j, k;
530		int n_cells;
531		double cellx, celly, cellz;
#	Line 410 | Line 534 | void SimSetup::initFromBass( void ){
534		int n_extra;
535		int have_extra, done;
536
537	<	temp1 = (double)tot_nmol / 4.0;
538	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
539	<	temp3 = ceil( temp2 );
537	>	double vel[3];
538	>	vel[0] = 0.0;
539	>	vel[1] = 0.0;
540	>	vel[2] = 0.0;
541
542	<	have_extra =0;
543	<	if( temp2 < temp3 ){ // we have a non-complete lattice
544	<	have_extra =1;
542	>	temp1 = (double) tot_nmol / 4.0;
543	>	temp2 = pow(temp1, (1.0 / 3.0));
544	>	temp3 = ceil(temp2);
545
546	<	n_cells = (int)temp3 - 1;
547	<	cellx = info->boxL[0] / temp3;
548	<	celly = info->boxL[1] / temp3;
549	<	cellz = info->boxL[2] / temp3;
425	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
426	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
427	<	n_per_extra = (int)ceil( temp1 );
546	>	have_extra = 0;
547	>	if (temp2 < temp3){
548	>	// we have a non-complete lattice
549	>	have_extra = 1;
550
551	<	if( n_per_extra > 4){
552	<	sprintf( painCave.errMsg,
553	<	"SimSetup error. There has been an error in constructing"
554	<	" the non-complete lattice.\n" );
551	>	n_cells = (int) temp3 - 1;
552	>	cellx = info[0].boxL[0] / temp3;
553	>	celly = info[0].boxL[1] / temp3;
554	>	cellz = info[0].boxL[2] / temp3;
555	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
556	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
557	>	n_per_extra = (int) ceil(temp1);
558	>
559	>	if (n_per_extra > 4){
560	>	sprintf(painCave.errMsg,
561	>	"SimSetup error. There has been an error in constructing"
562	>	" the non-complete lattice.\n");
563		painCave.isFatal = 1;
564		simError();
565		}
566		}
567		else{
568	<	n_cells = (int)temp3;
569	<	cellx = info->boxL[0] / temp3;
570	<	celly = info->boxL[1] / temp3;
571	<	cellz = info->boxL[2] / temp3;
568	>	n_cells = (int) temp3;
569	>	cellx = info[0].boxL[0] / temp3;
570	>	celly = info[0].boxL[1] / temp3;
571	>	cellz = info[0].boxL[2] / temp3;
572		}
573
574		current_mol = 0;
#	Line 446 | Line 576 | void SimSetup::initFromBass( void ){
576		current_comp = 0;
577		current_atom_ndx = 0;
578
579	<	for( i=0; i < n_cells ; i++ ){
580	<	for( j=0; j < n_cells; j++ ){
581	<	for( k=0; k < n_cells; k++ ){
579	>	for (i = 0; i < n_cells ; i++){
580	>	for (j = 0; j < n_cells; j++){
581	>	for (k = 0; k < n_cells; k++){
582	>	makeElement(i * cellx, j * celly, k * cellz);
583
584	<	makeElement( i * cellx,
454	<	j * celly,
455	<	k * cellz );
584	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
585
586	<	makeElement( i * cellx + 0.5 * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz );
586	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
587
588	<	makeElement( i * cellx,
462	<	j * celly + 0.5 * celly,
463	<	k * cellz + 0.5 * cellz );
464	<
465	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly,
467	<	k * cellz + 0.5 * cellz );
588	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
589		}
590		}
591		}
592
593	<	if( have_extra ){
593	>	if (have_extra){
594		done = 0;
595
596		int start_ndx;
597	<	for( i=0; i < (n_cells+1) && !done; i++ ){
598	<	for( j=0; j < (n_cells+1) && !done; j++ ){
597	>	for (i = 0; i < (n_cells + 1) && !done; i++){
598	>	for (j = 0; j < (n_cells + 1) && !done; j++){
599	>	if (i < n_cells){
600	>	if (j < n_cells){
601	>	start_ndx = n_cells;
602	>	}
603	>	else
604	>	start_ndx = 0;
605	>	}
606	>	else
607	>	start_ndx = 0;
608
609	<	if( i < n_cells ){
609	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
610	>	makeElement(i * cellx, j * celly, k * cellz);
611	>	done = (current_mol >= tot_nmol);
612
613	<	if( j < n_cells ){
614	<	start_ndx = n_cells;
615	<	}
616	<	else start_ndx = 0;
617	<	}
486	<	else start_ndx = 0;
613	>	if (!done && n_per_extra > 1){
614	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
615	>	k * cellz);
616	>	done = (current_mol >= tot_nmol);
617	>	}
618
619	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
619	>	if (!done && n_per_extra > 2){
620	>	makeElement(i * cellx, j * celly + 0.5 * celly,
621	>	k * cellz + 0.5 * cellz);
622	>	done = (current_mol >= tot_nmol);
623	>	}
624
625	<	makeElement( i * cellx,
626	<	j * celly,
627	<	k * cellz );
628	<	done = ( current_mol >= tot_nmol );
629	<
630	<	if( !done && n_per_extra > 1 ){
496	<	makeElement( i * cellx + 0.5 * cellx,
497	<	j * celly + 0.5 * celly,
498	<	k * cellz );
499	<	done = ( current_mol >= tot_nmol );
500	<	}
501	<
502	<	if( !done && n_per_extra > 2){
503	<	makeElement( i * cellx,
504	<	j * celly + 0.5 * celly,
505	<	k * cellz + 0.5 * cellz );
506	<	done = ( current_mol >= tot_nmol );
507	<	}
508	<
509	<	if( !done && n_per_extra > 3){
510	<	makeElement( i * cellx + 0.5 * cellx,
511	<	j * celly,
512	<	k * cellz + 0.5 * cellz );
513	<	done = ( current_mol >= tot_nmol );
514	<	}
515	<	}
625	>	if (!done && n_per_extra > 3){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
627	>	k * cellz + 0.5 * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630	>	}
631		}
632		}
633		}
634
635	<
636	<	for( i=0; i<info->n_atoms; i++ ){
522	<	info->atoms[i]->set_vx( 0.0 );
523	<	info->atoms[i]->set_vy( 0.0 );
524	<	info->atoms[i]->set_vz( 0.0 );
635	>	for (i = 0; i < info[0].n_atoms; i++){
636	>	info[0].atoms[i]->setVel(vel);
637		}
638		}
527	–
528	–	void SimSetup::makeElement( double x, double y, double z ){
639
640	+	void SimSetup::makeElement(double x, double y, double z){
641		int k;
642		AtomStamp* current_atom;
643		DirectionalAtom* dAtom;
644		double rotMat[3][3];
645	+	double pos[3];
646
647	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
648	<
649	<	current_atom = comp_stamps[current_comp]->getAtom( k );
650	<	if( !current_atom->havePosition() ){
651	<	sprintf( painCave.errMsg,
652	<	"SimSetup:initFromBass error.\n"
653	<	"\tComponent %s, atom %s does not have a position specified.\n"
654	<	"\tThe initialization routine is unable to give a start"
655	<	" position.\n",
544	<	comp_stamps[current_comp]->getID(),
545	<	current_atom->getType() );
647	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
648	>	current_atom = comp_stamps[current_comp]->getAtom(k);
649	>	if (!current_atom->havePosition()){
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup:initFromBass error.\n"
652	>	"\tComponent %s, atom %s does not have a position specified.\n"
653	>	"\tThe initialization routine is unable to give a start"
654	>	" position.\n",
655	>	comp_stamps[current_comp]->getID(), current_atom->getType());
656		painCave.isFatal = 1;
657		simError();
658		}
659
660	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
661	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
662	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
660	>	pos[0] = x + current_atom->getPosX();
661	>	pos[1] = y + current_atom->getPosY();
662	>	pos[2] = z + current_atom->getPosZ();
663
664	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
664	>	info[0].atoms[current_atom_ndx]->setPos(pos);
665
666	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
666	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
667	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
668
669		rotMat[0][0] = 1.0;
670		rotMat[0][1] = 0.0;
#	Line 567 | Line 678 | void SimSetup::makeElement( double x, double y, double
678		rotMat[2][1] = 0.0;
679		rotMat[2][2] = 1.0;
680
681	<	dAtom->setA( rotMat );
681	>	dAtom->setA(rotMat);
682		}
683
684		current_atom_ndx++;
#	Line 576 | Line 687 | void SimSetup::makeElement( double x, double y, double
687		current_mol++;
688		current_comp_mol++;
689
690	<	if( current_comp_mol >= components_nmol[current_comp] ){
580	<
690	>	if (current_comp_mol >= components_nmol[current_comp]){
691		current_comp_mol = 0;
692		current_comp++;
693		}
694		}
695
696
697	<	void SimSetup::gatherInfo( void ){
698	<	int i,j,k;
697	>	void SimSetup::gatherInfo(void){
698	>	int i;
699
700		ensembleCase = -1;
701		ffCase = -1;
702
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
703		// set the easy ones first
704	<	info->target_temp = globals->getTargetTemp();
705	<	info->dt = globals->getDt();
706	<	info->run_time = globals->getRunTime();
704	>
705	>	for (i = 0; i < nInfo; i++){
706	>	info[i].target_temp = globals->getTargetTemp();
707	>	info[i].dt = globals->getDt();
708	>	info[i].run_time = globals->getRunTime();
709	>	}
710		n_components = globals->getNComponents();
711
712
713		// get the forceField
714
715	<	strcpy( force_field, globals->getForceField() );
715	>	strcpy(force_field, globals->getForceField());
716
717	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
718	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
719	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
717	>	if (!strcasecmp(force_field, "DUFF")){
718	>	ffCase = FF_DUFF;
719	>	}
720	>	else if (!strcasecmp(force_field, "LJ")){
721	>	ffCase = FF_LJ;
722	>	}
723	>	else if (!strcasecmp(force_field, "EAM")){
724	>	ffCase = FF_EAM;
725	>	}
726	>	else if (!strcasecmp(force_field, "WATER")){
727	>	ffCase = FF_H2O;
728	>	}
729		else{
730	<	sprintf( painCave.errMsg,
731	<	"SimSetup Error. Unrecognized force field -> %s\n",
732	<	force_field );
733	<	painCave.isFatal = 1;
616	<	simError();
730	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
731	>	force_field);
732	>	painCave.isFatal = 1;
733	>	simError();
734		}
735
736	<	// get the ensemble
736	>	// get the ensemble
737
738	<	strcpy( ensemble, globals->getEnsemble() );
738	>	strcpy(ensemble, globals->getEnsemble());
739
740	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
741	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
742	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
740	>	if (!strcasecmp(ensemble, "NVE")){
741	>	ensembleCase = NVE_ENS;
742	>	}
743	>	else if (!strcasecmp(ensemble, "NVT")){
744	>	ensembleCase = NVT_ENS;
745	>	}
746	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
747		ensembleCase = NPTi_ENS;
748	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
749	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
750	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
751	<
752	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
753	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
754	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634	<	ensembleCase = NPTiZCONS_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	<	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	<
748	>	}
749	>	else if (!strcasecmp(ensemble, "NPTf")){
750	>	ensembleCase = NPTf_ENS;
751	>	}
752	>	else if (!strcasecmp(ensemble, "NPTxyz")){
753	>	ensembleCase = NPTxyz_ENS;
754	>	}
755		else{
756	<	sprintf( painCave.errMsg,
757	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
758	<	"reverting to NVE for this simulation.\n",
759	<	ensemble );
760	<	painCave.isFatal = 0;
761	<	simError();
762	<	strcpy( ensemble, "NVE" );
763	<	ensembleCase = NVE_ENS;
756	>	sprintf(painCave.errMsg,
757	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
758	>	"\treverting to NVE for this simulation.\n",
759	>	ensemble);
760	>	painCave.isFatal = 0;
761	>	simError();
762	>	strcpy(ensemble, "NVE");
763	>	ensembleCase = NVE_ENS;
764		}
649	–	strcpy( info->ensemble, ensemble );
765
766	<	// get the mixing rule
766	>	for (i = 0; i < nInfo; i++){
767	>	strcpy(info[i].ensemble, ensemble);
768
769	<	strcpy( info->mixingRule, globals->getMixingRule() );
770	<	info->usePBC = globals->getPBC();
771	<
772	<
769	>	// get the mixing rule
770	>
771	>	strcpy(info[i].mixingRule, globals->getMixingRule());
772	>	info[i].usePBC = globals->getPBC();
773	>	}
774	>
775		// get the components and calculate the tot_nMol and indvidual n_mol
776	<
776	>
777		the_components = globals->getComponents();
778		components_nmol = new int[n_components];
779
780
781	<	if( !globals->haveNMol() ){
781	>	if (!globals->haveNMol()){
782		// we don't have the total number of molecules, so we assume it is
783		// given in each component
784
785		tot_nmol = 0;
786	<	for( i=0; i<n_components; i++ ){
787	<
788	<	if( !the_components[i]->haveNMol() ){
789	<	// we have a problem
790	<	sprintf( painCave.errMsg,
791	<	"SimSetup Error. No global NMol or component NMol"
792	<	" given. Cannot calculate the number of atoms.\n" );
793	<	painCave.isFatal = 1;
676	<	simError();
786	>	for (i = 0; i < n_components; i++){
787	>	if (!the_components[i]->haveNMol()){
788	>	// we have a problem
789	>	sprintf(painCave.errMsg,
790	>	"SimSetup Error. No global NMol or component NMol given.\n"
791	>	"\tCannot calculate the number of atoms.\n");
792	>	painCave.isFatal = 1;
793	>	simError();
794		}
795
796		tot_nmol += the_components[i]->getNMol();
#	Line 681 | Line 798 | void SimSetup::gatherInfo( void ){
798		}
799		}
800		else{
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup error.\n"
803	<	"\tSorry, the ability to specify total"
804	<	" nMols and then give molfractions in the components\n"
805	<	"\tis not currently supported."
806	<	" Please give nMol in the components.\n" );
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup error.\n"
803	>	"\tSorry, the ability to specify total"
804	>	" nMols and then give molfractions in the components\n"
805	>	"\tis not currently supported."
806	>	" Please give nMol in the components.\n");
807		painCave.isFatal = 1;
808		simError();
809		}
810
811	<	// set the status, sample, and thermal kick times
812	<
813	<	if( globals->haveSampleTime() ){
814	<	info->sampleTime = globals->getSampleTime();
815	<	info->statusTime = info->sampleTime;
816	<	info->thermalTime = info->sampleTime;
811	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
812	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
813	>	sprintf(painCave.errMsg,
814	>	"Sample time is not divisible by dt.\n"
815	>	"\tThis will result in samples that are not uniformly\n"
816	>	"\tdistributed in time.  If this is a problem, change\n"
817	>	"\tyour sampleTime variable.\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820		}
701	–	else{
702	–	info->sampleTime = globals->getRunTime();
703	–	info->statusTime = info->sampleTime;
704	–	info->thermalTime = info->sampleTime;
705	–	}
821
822	<	if( globals->haveStatusTime() ){
823	<	info->statusTime = globals->getStatusTime();
822	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
823	>	sprintf(painCave.errMsg,
824	>	"Status time is not divisible by dt.\n"
825	>	"\tThis will result in status reports that are not uniformly\n"
826	>	"\tdistributed in time.  If this is a problem, change \n"
827	>	"\tyour statusTime variable.\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830		}
831
832	<	if( globals->haveThermalTime() ){
833	<	info->thermalTime = globals->getThermalTime();
834	<	}
832	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
833	>	sprintf(painCave.errMsg,
834	>	"Thermal time is not divisible by dt.\n"
835	>	"\tThis will result in thermalizations that are not uniformly\n"
836	>	"\tdistributed in time.  If this is a problem, change \n"
837	>	"\tyour thermalTime variable.\n");
838	>	painCave.isFatal = 0;
839	>	simError();
840	>	}
841
842	<	// check for the temperature set flag
842	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
843	>	sprintf(painCave.errMsg,
844	>	"Reset time is not divisible by dt.\n"
845	>	"\tThis will result in integrator resets that are not uniformly\n"
846	>	"\tdistributed in time.  If this is a problem, change\n"
847	>	"\tyour resetTime variable.\n");
848	>	painCave.isFatal = 0;
849	>	simError();
850	>	}
851
852	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
852	>	// set the status, sample, and thermal kick times
853
854	<	// get some of the tricky things that may still be in the globals
854	>	for (i = 0; i < nInfo; i++){
855	>	if (globals->haveSampleTime()){
856	>	info[i].sampleTime = globals->getSampleTime();
857	>	info[i].statusTime = info[i].sampleTime;
858	>	info[i].thermalTime = info[i].sampleTime;
859	>	}
860	>	else{
861	>	info[i].sampleTime = globals->getRunTime();
862	>	info[i].statusTime = info[i].sampleTime;
863	>	info[i].thermalTime = info[i].sampleTime;
864	>	}
865
866	<	double boxVector[3];
867	<	if( globals->haveBox() ){
723	<	boxVector[0] = globals->getBox();
724	<	boxVector[1] = globals->getBox();
725	<	boxVector[2] = globals->getBox();
726	<
727	<	info->setBox( boxVector );
728	<	}
729	<	else if( globals->haveDensity() ){
730	<
731	<	double vol;
732	<	vol = (double)tot_nmol / globals->getDensity();
733	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	<	boxVector[1] = boxVector[0];
735	<	boxVector[2] = boxVector[0];
736	<
737	<	info->setBox( boxVector );
738	<	}
739	<	else{
740	<	if( !globals->haveBoxX() ){
741	<	sprintf( painCave.errMsg,
742	<	"SimSetup error, no periodic BoxX size given.\n" );
743	<	painCave.isFatal = 1;
744	<	simError();
866	>	if (globals->haveStatusTime()){
867	>	info[i].statusTime = globals->getStatusTime();
868		}
746	–	boxVector[0] = globals->getBoxX();
869
870	<	if( !globals->haveBoxY() ){
871	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
870	>	if (globals->haveThermalTime()){
871	>	info[i].thermalTime = globals->getThermalTime();
872		}
754	–	boxVector[1] = globals->getBoxY();
873
874	<	if( !globals->haveBoxZ() ){
875	<	sprintf( painCave.errMsg,
876	<	"SimSetup error, no periodic BoxZ size given.\n" );
877	<	painCave.isFatal = 1;
760	<	simError();
874	>	info[i].resetIntegrator = 0;
875	>	if( globals->haveResetTime() ){
876	>	info[i].resetTime = globals->getResetTime();
877	>	info[i].resetIntegrator = 1;
878		}
762	–	boxVector[2] = globals->getBoxZ();
879
880	<	info->setBox( boxVector );
880	>	// check for the temperature set flag
881	>
882	>	if (globals->haveTempSet())
883	>	info[i].setTemp = globals->getTempSet();
884	>
885	>	// check for the extended State init
886	>
887	>	info[i].useInitXSstate = globals->getUseInitXSstate();
888	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
889	>
890		}
891	+
892	+	//setup seed for random number generator
893	+	int seedValue;
894
895	+	if (globals->haveSeed()){
896	+	seedValue = globals->getSeed();
897
898	+	if(seedValue / 1E9 == 0){
899	+	sprintf(painCave.errMsg,
900	+	"Seed for sprng library should contain at least 9 digits\n"
901	+	"OOPSE will generate a seed for user\n");
902	+	painCave.isFatal = 0;
903	+	simError();
904	+
905	+	//using seed generated by system instead of invalid seed set by user
906	+	#ifndef IS_MPI
907	+	seedValue = make_sprng_seed();
908	+	#else
909	+	if (worldRank == 0){
910	+	seedValue = make_sprng_seed();
911	+	}
912	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
913	+	#endif
914	+	}
915	+	}//end of if branch of globals->haveSeed()
916	+	else{
917
918	+	#ifndef IS_MPI
919	+	seedValue = make_sprng_seed();
920	+	#else
921	+	if (worldRank == 0){
922	+	seedValue = make_sprng_seed();
923	+	}
924	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	+	#endif
926	+	}//end of globals->haveSeed()
927	+
928	+	for (int i = 0; i < nInfo; i++){
929	+	info[i].setSeed(seedValue);
930	+	}
931	+
932		#ifdef IS_MPI
933	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
933	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
934		MPIcheckPoint();
935		#endif // is_mpi
773	–
936		}
937
938
939	<	void SimSetup::finalInfoCheck( void ){
939	>	void SimSetup::finalInfoCheck(void){
940		int index;
941		int usesDipoles;
942	<
942	>	int i;
943
944	<	// check electrostatic parameters
945	<
946	<	index = 0;
947	<	usesDipoles = 0;
948	<	while( (index < info->n_atoms) && !usesDipoles ){
949	<	usesDipoles = ((info->atoms)[index])->hasDipole();
950	<	index++;
951	<	}
952	<
944	>	for (i = 0; i < nInfo; i++){
945	>	// check electrostatic parameters
946	>
947	>	index = 0;
948	>	usesDipoles = 0;
949	>	while ((index < info[i].n_atoms) && !usesDipoles){
950	>	usesDipoles = (info[i].atoms[index])->hasDipole();
951	>	index++;
952	>	}
953	>
954		#ifdef IS_MPI
955	<	int myUse = usesDipoles;
956	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
955	>	int myUse = usesDipoles;
956	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
957		#endif //is_mpi
958
959	<	double theEcr, theEst;
959	>	double theEcr, theEst;
960
961	<	if (globals->getUseRF() ) {
962	<	info->useReactionField = 1;
800	<
801	<	if( !globals->haveECR() ){
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Warning: using default value of 1/2 the smallest "
804	<	"box length for the electrostaticCutoffRadius.\n"
805	<	"I hope you have a very fast processor!\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	double smallest;
809	<	smallest = info->boxL[0];
810	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	<	theEcr = 0.5 * smallest;
813	<	} else {
814	<	theEcr = globals->getECR();
815	<	}
961	>	if (globals->getUseRF()){
962	>	info[i].useReactionField = 1;
963
964	<	if( !globals->haveEST() ){
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Warning: using default value of 0.05 * the "
967	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
968	<	);
969	<	painCave.isFatal = 0;
970	<	simError();
971	<	theEst = 0.05 * theEcr;
972	<	} else {
973	<	theEst= globals->getEST();
974	<	}
964	>	if (!globals->haveECR()){
965	>	sprintf(painCave.errMsg,
966	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
967	>	"\tOOPSE will use a default value of 15.0 angstroms"
968	>	"\tfor the electrostaticCutoffRadius.\n");
969	>	painCave.isFatal = 0;
970	>	simError();
971	>	theEcr = 15.0;
972	>	}
973	>	else{
974	>	theEcr = globals->getECR();
975	>	}
976
977	<	info->setEcr( theEcr, theEst );
978	<
979	<	if(!globals->haveDielectric() ){
980	<	sprintf( painCave.errMsg,
981	<	"SimSetup Error: You are trying to use Reaction Field without"
982	<	"setting a dielectric constant!\n"
983	<	);
984	<	painCave.isFatal = 1;
985	<	simError();
838	<	}
839	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	else {
842	<	if (usesDipoles) {
843	<
844	<	if( !globals->haveECR() ){
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Warning: using default value of 1/2 the smallest "
847	<	"box length for the electrostaticCutoffRadius.\n"
848	<	"I hope you have a very fast processor!\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	double smallest;
852	<	smallest = info->boxL[0];
853	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
854	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
855	<	theEcr = 0.5 * smallest;
856	<	} else {
857	<	theEcr = globals->getECR();
977	>	if (!globals->haveEST()){
978	>	sprintf(painCave.errMsg,
979	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
980	>	"\tOOPSE will use a default value of\n"
981	>	"\t0.05 * electrostaticCutoffRadius\n"
982	>	"\tfor the electrostaticSkinThickness\n");
983	>	painCave.isFatal = 0;
984	>	simError();
985	>	theEst = 0.05 * theEcr;
986		}
987	<
988	<	if( !globals->haveEST() ){
861	<	sprintf( painCave.errMsg,
862	<	"SimSetup Warning: using default value of 0.05 * the "
863	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
865	<	);
866	<	painCave.isFatal = 0;
867	<	simError();
868	<	theEst = 0.05 * theEcr;
869	<	} else {
870	<	theEst= globals->getEST();
987	>	else{
988	>	theEst = globals->getEST();
989		}
990
991	<	info->setEcr( theEcr, theEst );
874	<	}
875	<	}
991	>	info[i].setDefaultEcr(theEcr, theEst);
992
993	+	if (!globals->haveDielectric()){
994	+	sprintf(painCave.errMsg,
995	+	"SimSetup Error: No Dielectric constant was set.\n"
996	+	"\tYou are trying to use Reaction Field without"
997	+	"\tsetting a dielectric constant!\n");
998	+	painCave.isFatal = 1;
999	+	simError();
1000	+	}
1001	+	info[i].dielectric = globals->getDielectric();
1002	+	}
1003	+	else{
1004	+	if (usesDipoles){
1005	+	if (!globals->haveECR()){
1006	+	sprintf(painCave.errMsg,
1007	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1008	+	"\tOOPSE will use a default value of 15.0 angstroms"
1009	+	"\tfor the electrostaticCutoffRadius.\n");
1010	+	painCave.isFatal = 0;
1011	+	simError();
1012	+	theEcr = 15.0;
1013	+	}
1014	+	else{
1015	+	theEcr = globals->getECR();
1016	+	}
1017	+
1018	+	if (!globals->haveEST()){
1019	+	sprintf(painCave.errMsg,
1020	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1021	+	"\tOOPSE will use a default value of\n"
1022	+	"\t0.05 * electrostaticCutoffRadius\n"
1023	+	"\tfor the electrostaticSkinThickness\n");
1024	+	painCave.isFatal = 0;
1025	+	simError();
1026	+	theEst = 0.05 * theEcr;
1027	+	}
1028	+	else{
1029	+	theEst = globals->getEST();
1030	+	}
1031	+
1032	+	info[i].setDefaultEcr(theEcr, theEst);
1033	+	}
1034	+	}
1035	+	}
1036		#ifdef IS_MPI
1037	<	strcpy( checkPointMsg, "post processing checks out" );
1037	>	strcpy(checkPointMsg, "post processing checks out");
1038		MPIcheckPoint();
1039		#endif // is_mpi
881	–
1040		}
1041	+
1042	+	void SimSetup::initSystemCoords(void){
1043	+	int i;
1044
1045	<	void SimSetup::initSystemCoords( void ){
1045	>	char* inName;
1046
1047	<	if( globals->haveInitialConfig() ){
1048	<
1049	<	InitializeFromFile* fileInit;
1047	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1048	>
1049	>	for (i = 0; i < info[0].n_atoms; i++)
1050	>	info[0].atoms[i]->setCoords();
1051	>
1052	>	if (globals->haveInitialConfig()){
1053	>	InitializeFromFile* fileInit;
1054		#ifdef IS_MPI // is_mpi
1055	<	if( worldRank == 0 ){
1055	>	if (worldRank == 0){
1056		#endif //is_mpi
1057	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1057	>	inName = globals->getInitialConfig();
1058	>	fileInit = new InitializeFromFile(inName);
1059		#ifdef IS_MPI
1060	<	}else fileInit = new InitializeFromFile( NULL );
1060	>	}
1061	>	else
1062	>	fileInit = new InitializeFromFile(NULL);
1063		#endif
1064	<	fileInit->readInit( info ); // default velocities on
1064	>	fileInit->readInit(info); // default velocities on
1065
1066	<	delete fileInit;
1067	<	}
1068	<	else{
1066	>	delete fileInit;
1067	>	}
1068	>	else{
1069	>
1070	>	// no init from bass
1071	>
1072	>	sprintf(painCave.errMsg,
1073	>	"Cannot intialize a simulation without an initial configuration file.\n");
1074	>	painCave.isFatal = 1;;
1075	>	simError();
1076	>
1077	>	}
1078
902	–	#ifdef IS_MPI
903	–
904	–	// no init from bass
905	–
906	–	sprintf( painCave.errMsg,
907	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
908	–	painCave.isFatal;
909	–	simError();
910	–
911	–	#else
912	–
913	–	initFromBass();
914	–
915	–
916	–	#endif
917	–	}
918	–
1079		#ifdef IS_MPI
1080	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1080	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1081		MPIcheckPoint();
1082		#endif // is_mpi
923	–
1083		}
1084
1085
1086	<	void SimSetup::makeOutNames( void ){
1086	>	void SimSetup::makeOutNames(void){
1087	>	int k;
1088
1089	+
1090	+	for (k = 0; k < nInfo; k++){
1091		#ifdef IS_MPI
1092	<	if( worldRank == 0 ){
1092	>	if (worldRank == 0){
1093		#endif // is_mpi
1094	<
1095	<	if( globals->haveFinalConfig() ){
1096	<	strcpy( info->finalName, globals->getFinalConfig() );
935	<	}
936	<	else{
937	<	strcpy( info->finalName, inFileName );
938	<	char* endTest;
939	<	int nameLength = strlen( info->finalName );
940	<	endTest = &(info->finalName[nameLength - 5]);
941	<	if( !strcmp( endTest, ".bass" ) ){
942	<	strcpy( endTest, ".eor" );
1094	>
1095	>	if (globals->haveFinalConfig()){
1096	>	strcpy(info[k].finalName, globals->getFinalConfig());
1097		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
1098		else{
1099	<	endTest = &(info->finalName[nameLength - 4]);
1100	<	if( !strcmp( endTest, ".bss" ) ){
1101	<	strcpy( endTest, ".eor" );
1102	<	}
1103	<	else if( !strcmp( endTest, ".mdl" ) ){
1104	<	strcpy( endTest, ".eor" );
1105	<	}
1106	<	else{
1107	<	strcat( info->finalName, ".eor" );
1108	<	}
1099	>	strcpy(info[k].finalName, inFileName);
1100	>	char* endTest;
1101	>	int nameLength = strlen(info[k].finalName);
1102	>	endTest = &(info[k].finalName[nameLength - 5]);
1103	>	if (!strcmp(endTest, ".bass")){
1104	>	strcpy(endTest, ".eor");
1105	>	}
1106	>	else if (!strcmp(endTest, ".BASS")){
1107	>	strcpy(endTest, ".eor");
1108	>	}
1109	>	else{
1110	>	endTest = &(info[k].finalName[nameLength - 4]);
1111	>	if (!strcmp(endTest, ".bss")){
1112	>	strcpy(endTest, ".eor");
1113	>	}
1114	>	else if (!strcmp(endTest, ".mdl")){
1115	>	strcpy(endTest, ".eor");
1116	>	}
1117	>	else{
1118	>	strcat(info[k].finalName, ".eor");
1119	>	}
1120	>	}
1121		}
1122	<	}
1123	<
1124	<	// make the sample and status out names
1125	<
1126	<	strcpy( info->sampleName, inFileName );
1127	<	char* endTest;
1128	<	int nameLength = strlen( info->sampleName );
1129	<	endTest = &(info->sampleName[nameLength - 5]);
1130	<	if( !strcmp( endTest, ".bass" ) ){
968	<	strcpy( endTest, ".dump" );
969	<	}
970	<	else if( !strcmp( endTest, ".BASS" ) ){
971	<	strcpy( endTest, ".dump" );
972	<	}
973	<	else{
974	<	endTest = &(info->sampleName[nameLength - 4]);
975	<	if( !strcmp( endTest, ".bss" ) ){
976	<	strcpy( endTest, ".dump" );
1122	>
1123	>	// make the sample and status out names
1124	>
1125	>	strcpy(info[k].sampleName, inFileName);
1126	>	char* endTest;
1127	>	int nameLength = strlen(info[k].sampleName);
1128	>	endTest = &(info[k].sampleName[nameLength - 5]);
1129	>	if (!strcmp(endTest, ".bass")){
1130	>	strcpy(endTest, ".dump");
1131		}
1132	<	else if( !strcmp( endTest, ".mdl" ) ){
1133	<	strcpy( endTest, ".dump" );
1132	>	else if (!strcmp(endTest, ".BASS")){
1133	>	strcpy(endTest, ".dump");
1134		}
1135		else{
1136	<	strcat( info->sampleName, ".dump" );
1136	>	endTest = &(info[k].sampleName[nameLength - 4]);
1137	>	if (!strcmp(endTest, ".bss")){
1138	>	strcpy(endTest, ".dump");
1139	>	}
1140	>	else if (!strcmp(endTest, ".mdl")){
1141	>	strcpy(endTest, ".dump");
1142	>	}
1143	>	else{
1144	>	strcat(info[k].sampleName, ".dump");
1145	>	}
1146		}
1147	<	}
1148	<
1149	<	strcpy( info->statusName, inFileName );
1150	<	nameLength = strlen( info->statusName );
1151	<	endTest = &(info->statusName[nameLength - 5]);
1152	<	if( !strcmp( endTest, ".bass" ) ){
990	<	strcpy( endTest, ".stat" );
991	<	}
992	<	else if( !strcmp( endTest, ".BASS" ) ){
993	<	strcpy( endTest, ".stat" );
994	<	}
995	<	else{
996	<	endTest = &(info->statusName[nameLength - 4]);
997	<	if( !strcmp( endTest, ".bss" ) ){
998	<	strcpy( endTest, ".stat" );
1147	>
1148	>	strcpy(info[k].statusName, inFileName);
1149	>	nameLength = strlen(info[k].statusName);
1150	>	endTest = &(info[k].statusName[nameLength - 5]);
1151	>	if (!strcmp(endTest, ".bass")){
1152	>	strcpy(endTest, ".stat");
1153		}
1154	<	else if( !strcmp( endTest, ".mdl" ) ){
1155	<	strcpy( endTest, ".stat" );
1154	>	else if (!strcmp(endTest, ".BASS")){
1155	>	strcpy(endTest, ".stat");
1156		}
1157		else{
1158	<	strcat( info->statusName, ".stat" );
1158	>	endTest = &(info[k].statusName[nameLength - 4]);
1159	>	if (!strcmp(endTest, ".bss")){
1160	>	strcpy(endTest, ".stat");
1161	>	}
1162	>	else if (!strcmp(endTest, ".mdl")){
1163	>	strcpy(endTest, ".stat");
1164	>	}
1165	>	else{
1166	>	strcat(info[k].statusName, ".stat");
1167	>	}
1168		}
1169	<	}
1007	<
1169	>
1170		#ifdef IS_MPI
1009	–	}
1010	–	#endif // is_mpi
1171
1172	+	}
1173	+	#endif // is_mpi
1174	+	}
1175		}
1176
1177
1178	<	void SimSetup::sysObjectsCreation( void ){
1178	>	void SimSetup::sysObjectsCreation(void){
1179	>	int i, k;
1180
1017	–	int i;
1018	–
1181		// create the forceField
1182
1183		createFF();
#	Line 1030 | Line 1192 | void SimSetup::sysObjectsCreation( void ){
1192
1193		#ifdef IS_MPI
1194		// divide the molecules among the processors
1195	<
1195	>
1196		mpiMolDivide();
1197		#endif //is_mpi
1198	<
1198	>
1199		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1200	<
1200	>
1201		makeSysArrays();
1202
1203		// make and initialize the molecules (all but atomic coordinates)
1204	<
1204	>
1205		makeMolecules();
1044	–	info->identArray = new int[info->n_atoms];
1045	–	for(i=0; i<info->n_atoms; i++){
1046	–	info->identArray[i] = the_atoms[i]->getIdent();
1047	–	}
1048	–
1206
1207	<
1207	>	for (k = 0; k < nInfo; k++){
1208	>	info[k].identArray = new int[info[k].n_atoms];
1209	>	for (i = 0; i < info[k].n_atoms; i++){
1210	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1211	>	}
1212	>	}
1213		}
1214
1215
1216	<	void SimSetup::createFF( void ){
1216	>	void SimSetup::createFF(void){
1217	>	switch (ffCase){
1218	>	case FF_DUFF:
1219	>	the_ff = new DUFF();
1220	>	break;
1221
1222	<	switch( ffCase ){
1222	>	case FF_LJ:
1223	>	the_ff = new LJFF();
1224	>	break;
1225
1226	<	case FF_DUFF:
1227	<	the_ff = new DUFF();
1228	<	break;
1226	>	case FF_EAM:
1227	>	the_ff = new EAM_FF();
1228	>	break;
1229
1230	<	case FF_LJ:
1231	<	the_ff = new LJFF();
1232	<	break;
1230	>	case FF_H2O:
1231	>	the_ff = new WATER();
1232	>	break;
1233
1234	<	case FF_EAM:
1235	<	the_ff = new EAM_FF();
1236	<	break;
1237	<
1238	<	default:
1071	<	sprintf( painCave.errMsg,
1072	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1073	<	painCave.isFatal = 1;
1074	<	simError();
1234	>	default:
1235	>	sprintf(painCave.errMsg,
1236	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1237	>	painCave.isFatal = 1;
1238	>	simError();
1239		}
1240
1241		#ifdef IS_MPI
1242	<	strcpy( checkPointMsg, "ForceField creation successful" );
1242	>	strcpy(checkPointMsg, "ForceField creation successful");
1243		MPIcheckPoint();
1244		#endif // is_mpi
1081	–
1245		}
1246
1247
1248	<	void SimSetup::compList( void ){
1086	<
1248	>	void SimSetup::compList(void){
1249		int i;
1250	+	char* id;
1251	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1252	+	LinkedMolStamp* currentStamp = NULL;
1253	+	comp_stamps = new MoleculeStamp * [n_components];
1254
1089	–	comp_stamps = new MoleculeStamp*[n_components];
1090	–
1255		// make an array of molecule stamps that match the components used.
1256		// also extract the used stamps out into a separate linked list
1257
1258	<	info->nComponents = n_components;
1259	<	info->componentsNmol = components_nmol;
1260	<	info->compStamps = comp_stamps;
1261	<	info->headStamp = new LinkedMolStamp();
1262	<
1263	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1102	<	for( i=0; i<n_components; i++ ){
1258	>	for (i = 0; i < nInfo; i++){
1259	>	info[i].nComponents = n_components;
1260	>	info[i].componentsNmol = components_nmol;
1261	>	info[i].compStamps = comp_stamps;
1262	>	info[i].headStamp = headStamp;
1263	>	}
1264
1265	+
1266	+	for (i = 0; i < n_components; i++){
1267		id = the_components[i]->getType();
1268		comp_stamps[i] = NULL;
1269	<
1269	>
1270		// check to make sure the component isn't already in the list
1271
1272	<	comp_stamps[i] = headStamp->match( id );
1273	<	if( comp_stamps[i] == NULL ){
1111	<
1272	>	comp_stamps[i] = headStamp->match(id);
1273	>	if (comp_stamps[i] == NULL){
1274		// extract the component from the list;
1275	<
1276	<	currentStamp = stamps->extractMolStamp( id );
1277	<	if( currentStamp == NULL ){
1278	<	sprintf( painCave.errMsg,
1279	<	"SimSetup error: Component \"%s\" was not found in the "
1280	<	"list of declared molecules\n",
1281	<	id );
1282	<	painCave.isFatal = 1;
1283	<	simError();
1275	>
1276	>	currentStamp = stamps->extractMolStamp(id);
1277	>	if (currentStamp == NULL){
1278	>	sprintf(painCave.errMsg,
1279	>	"SimSetup error: Component \"%s\" was not found in the "
1280	>	"list of declared molecules\n",
1281	>	id);
1282	>	painCave.isFatal = 1;
1283	>	simError();
1284		}
1285	<
1286	<	headStamp->add( currentStamp );
1287	<	comp_stamps[i] = headStamp->match( id );
1285	>
1286	>	headStamp->add(currentStamp);
1287	>	comp_stamps[i] = headStamp->match(id);
1288		}
1289		}
1290
1291		#ifdef IS_MPI
1292	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1292	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1293		MPIcheckPoint();
1294		#endif // is_mpi
1133	–
1134	–
1295		}
1296
1297	<	void SimSetup::calcSysValues( void ){
1298	<	int i, j, k;
1297	>	void SimSetup::calcSysValues(void){
1298	>	int i;
1299
1300	+	int* molMembershipArray;
1301
1302		tot_atoms = 0;
1303		tot_bonds = 0;
1304		tot_bends = 0;
1305		tot_torsions = 0;
1306	<	for( i=0; i<n_components; i++ ){
1307	<
1308	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1309	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1310	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1306	>	tot_rigid = 0;
1307	>	for (i = 0; i < n_components; i++){
1308	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1309	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1310	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1311		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1312	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1313		}
1314	<
1314	>
1315		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1316	+	molMembershipArray = new int[tot_atoms];
1317
1318	<	info->n_atoms = tot_atoms;
1319	<	info->n_bonds = tot_bonds;
1320	<	info->n_bends = tot_bends;
1321	<	info->n_torsions = tot_torsions;
1322	<	info->n_SRI = tot_SRI;
1323	<	info->n_mol = tot_nmol;
1324	<
1162	<	info->molMembershipArray = new int[tot_atoms];
1163	<	}
1318	>	for (i = 0; i < nInfo; i++){
1319	>	info[i].n_atoms = tot_atoms;
1320	>	info[i].n_bonds = tot_bonds;
1321	>	info[i].n_bends = tot_bends;
1322	>	info[i].n_torsions = tot_torsions;
1323	>	info[i].n_SRI = tot_SRI;
1324	>	info[i].n_mol = tot_nmol;
1325
1326	+	info[i].molMembershipArray = molMembershipArray;
1327	+	}
1328	+	}
1329
1330		#ifdef IS_MPI
1331
1332	<	void SimSetup::mpiMolDivide( void ){
1169	<
1332	>	void SimSetup::mpiMolDivide(void){
1333		int i, j, k;
1334		int localMol, allMol;
1335		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1336	+	int local_rigid;
1337
1338	<	mpiSim = new mpiSimulation( info );
1339	<
1338	>	mpiSim = new mpiSimulation(info);
1339	>
1340		globalIndex = mpiSim->divideLabor();
1341
1342		// set up the local variables
1343	<
1343	>
1344		mol2proc = mpiSim->getMolToProcMap();
1345		molCompType = mpiSim->getMolComponentType();
1346	<
1346	>
1347		allMol = 0;
1348		localMol = 0;
1349		local_atoms = 0;
1350		local_bonds = 0;
1351		local_bends = 0;
1352		local_torsions = 0;
1353	+	local_rigid = 0;
1354		globalAtomIndex = 0;
1355
1356	<
1357	<	for( i=0; i<n_components; i++ ){
1358	<
1359	<	for( j=0; j<components_nmol[i]; j++ ){
1360	<
1361	<	if( mol2proc[allMol] == worldRank ){
1362	<
1363	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1364	<	local_bonds +=    comp_stamps[i]->getNBonds();
1200	<	local_bends +=    comp_stamps[i]->getNBends();
1201	<	local_torsions += comp_stamps[i]->getNTorsions();
1202	<	localMol++;
1356	>	for (i = 0; i < n_components; i++){
1357	>	for (j = 0; j < components_nmol[i]; j++){
1358	>	if (mol2proc[allMol] == worldRank){
1359	>	local_atoms += comp_stamps[i]->getNAtoms();
1360	>	local_bonds += comp_stamps[i]->getNBonds();
1361	>	local_bends += comp_stamps[i]->getNBends();
1362	>	local_torsions += comp_stamps[i]->getNTorsions();
1363	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1364	>	localMol++;
1365		}
1366	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1367	<	info->molMembershipArray[globalAtomIndex] = allMol;
1366	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1367	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1368		globalAtomIndex++;
1369		}
1370
1371	<	allMol++;
1371	>	allMol++;
1372		}
1373		}
1374		local_SRI = local_bonds + local_bends + local_torsions;
1375	+
1376	+	info[0].n_atoms = mpiSim->getMyNlocal();
1377
1378	<	info->n_atoms = mpiSim->getMyNlocal();
1379	<
1380	<	if( local_atoms != info->n_atoms ){
1381	<	sprintf( painCave.errMsg,
1382	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1383	<	" localAtom (%d) are not equal.\n",
1220	<	info->n_atoms,
1221	<	local_atoms );
1378	>
1379	>	if (local_atoms != info[0].n_atoms){
1380	>	sprintf(painCave.errMsg,
1381	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1382	>	"\tlocalAtom (%d) are not equal.\n",
1383	>	info[0].n_atoms, local_atoms);
1384		painCave.isFatal = 1;
1385		simError();
1386		}
1387
1388	<	info->n_bonds = local_bonds;
1389	<	info->n_bends = local_bends;
1390	<	info->n_torsions = local_torsions;
1391	<	info->n_SRI = local_SRI;
1392	<	info->n_mol = localMol;
1388	>	info[0].n_bonds = local_bonds;
1389	>	info[0].n_bends = local_bends;
1390	>	info[0].n_torsions = local_torsions;
1391	>	info[0].n_SRI = local_SRI;
1392	>	info[0].n_mol = localMol;
1393
1394	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1394	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1395		MPIcheckPoint();
1396		}
1397	<
1397	>
1398		#endif // is_mpi
1399
1400
1401	<	void SimSetup::makeSysArrays( void ){
1402	<	int i, j, k;
1401	>	void SimSetup::makeSysArrays(void){
1402	>
1403	>	#ifndef IS_MPI
1404	>	int k, j;
1405	>	#endif // is_mpi
1406	>	int i, l;
1407
1408	+	Atom** the_atoms;
1409	+	Molecule* the_molecules;
1410
1411	<	// create the atom and short range interaction arrays
1411	>	for (l = 0; l < nInfo; l++){
1412	>	// create the atom and short range interaction arrays
1413
1414	<	Atom::createArrays(info->n_atoms);
1415	<	the_atoms = new Atom*[info->n_atoms];
1416	<	the_molecules = new Molecule[info->n_mol];
1248	<	int molIndex;
1414	>	the_atoms = new Atom * [info[l].n_atoms];
1415	>	the_molecules = new Molecule[info[l].n_mol];
1416	>	int molIndex;
1417
1418	<	// initialize the molecule's stampID's
1418	>	// initialize the molecule's stampID's
1419
1420		#ifdef IS_MPI
1253	–
1421
1422	<	molIndex = 0;
1423	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1424	<
1425	<	if(mol2proc[i] == worldRank ){
1426	<	the_molecules[molIndex].setStampID( molCompType[i] );
1427	<	the_molecules[molIndex].setMyIndex( molIndex );
1428	<	the_molecules[molIndex].setGlobalIndex( i );
1429	<	molIndex++;
1422	>
1423	>	molIndex = 0;
1424	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1425	>	if (mol2proc[i] == worldRank){
1426	>	the_molecules[molIndex].setStampID(molCompType[i]);
1427	>	the_molecules[molIndex].setMyIndex(molIndex);
1428	>	the_molecules[molIndex].setGlobalIndex(i);
1429	>	molIndex++;
1430	>	}
1431		}
1264	–	}
1432
1433		#else // is_mpi
1434	<
1435	<	molIndex = 0;
1436	<	globalAtomIndex = 0;
1437	<	for(i=0; i<n_components; i++){
1438	<	for(j=0; j<components_nmol[i]; j++ ){
1439	<	the_molecules[molIndex].setStampID( i );
1440	<	the_molecules[molIndex].setMyIndex( molIndex );
1441	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1442	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1443	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1444	<	globalAtomIndex++;
1434	>
1435	>	molIndex = 0;
1436	>	globalAtomIndex = 0;
1437	>	for (i = 0; i < n_components; i++){
1438	>	for (j = 0; j < components_nmol[i]; j++){
1439	>	the_molecules[molIndex].setStampID(i);
1440	>	the_molecules[molIndex].setMyIndex(molIndex);
1441	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1442	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1443	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1444	>	globalAtomIndex++;
1445	>	}
1446	>	molIndex++;
1447		}
1279	–	molIndex++;
1448		}
1281	–	}
1282	–
1449
1450	+
1451		#endif // is_mpi
1452
1453	<
1454	<	if( info->n_SRI ){
1453	>	info[l].globalExcludes = new int;
1454	>	info[l].globalExcludes[0] = 0;
1455
1456	<	Exclude::createArray(info->n_SRI);
1290	<	the_excludes = new Exclude*[info->n_SRI];
1291	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1292	<	info->globalExcludes = new int;
1293	<	info->n_exclude = info->n_SRI;
1294	<	}
1295	<	else{
1296	<
1297	<	Exclude::createArray( 1 );
1298	<	the_excludes = new Exclude*;
1299	<	the_excludes[0] = new Exclude(0);
1300	<	the_excludes[0]->setPair( 0,0 );
1301	<	info->globalExcludes = new int;
1302	<	info->globalExcludes[0] = 0;
1303	<	info->n_exclude = 0;
1304	<	}
1456	>	// set the arrays into the SimInfo object
1457
1458	<	// set the arrays into the SimInfo object
1459	<
1460	<	info->atoms = the_atoms;
1309	<	info->molecules = the_molecules;
1310	<	info->nGlobalExcludes = 0;
1311	<	info->excludes = the_excludes;
1312	<
1313	<	the_ff->setSimInfo( info );
1458	>	info[l].atoms = the_atoms;
1459	>	info[l].molecules = the_molecules;
1460	>	info[l].nGlobalExcludes = 0;
1461
1462	+	the_ff->setSimInfo(info);
1463	+	}
1464		}
1465
1466	<	void SimSetup::makeIntegrator( void ){
1466	>	void SimSetup::makeIntegrator(void){
1467	>	int k;
1468
1469	<	NVT<RealIntegrator>*  myNVT = NULL;
1470	<	NPTi<RealIntegrator>* myNPTi = NULL;
1471	<	NPTf<RealIntegrator>* myNPTf = NULL;
1472	<	NPTim<RealIntegrator>* myNPTim = NULL;
1473	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1324	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330	<
1331	<	cerr << "setting integrator" <<endl;
1469	>	NVE<RealIntegrator>* myNVE = NULL;
1470	>	NVT<RealIntegrator>* myNVT = NULL;
1471	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1472	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1473	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1474
1475	<	switch( ensembleCase ){
1475	>	for (k = 0; k < nInfo; k++){
1476	>	switch (ensembleCase){
1477	>	case NVE_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1481	>	}
1482	>	else{
1483	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1484	>	}
1485	>
1486	>	info->the_integrator = myNVE;
1487	>	break;
1488
1489	<	case NVE_ENS:
1490	<	new NVE<RealIntegrator>( info, the_ff );
1491	<	break;
1489	>	case NVT_ENS:
1490	>	if (globals->haveZconstraints()){
1491	>	setupZConstraint(info[k]);
1492	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1493	>	}
1494	>	else
1495	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1496
1497	<	case NVT_ENS:
1340	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1341	<	myNVT->setTargetTemp(globals->getTargetTemp());
1497	>	myNVT->setTargetTemp(globals->getTargetTemp());
1498
1499	<	if (globals->haveTauThermostat())
1500	<	myNVT->setTauThermostat(globals->getTauThermostat());
1499	>	if (globals->haveTauThermostat())
1500	>	myNVT->setTauThermostat(globals->getTauThermostat());
1501	>	else{
1502	>	sprintf(painCave.errMsg,
1503	>	"SimSetup error: If you use the NVT\n"
1504	>	"\tensemble, you must set tauThermostat.\n");
1505	>	painCave.isFatal = 1;
1506	>	simError();
1507	>	}
1508
1509	<	else {
1510	<	sprintf( painCave.errMsg,
1348	<	"SimSetup error: If you use the NVT\n"
1349	<	"    ensemble, you must set tauThermostat.\n");
1350	<	painCave.isFatal = 1;
1351	<	simError();
1352	<	}
1353	<	break;
1509	>	info->the_integrator = myNVT;
1510	>	break;
1511
1512	<	case NPTi_ENS:
1513	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1514	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1512	>	case NPTi_ENS:
1513	>	if (globals->haveZconstraints()){
1514	>	setupZConstraint(info[k]);
1515	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1516	>	}
1517	>	else
1518	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1519
1520	<	if (globals->haveTargetPressure())
1360	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1361	<	else {
1362	<	sprintf( painCave.errMsg,
1363	<	"SimSetup error: If you use a constant pressure\n"
1364	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1365	<	painCave.isFatal = 1;
1366	<	simError();
1367	<	}
1368	<
1369	<	if( globals->haveTauThermostat() )
1370	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1371	<	else{
1372	<	sprintf( painCave.errMsg,
1373	<	"SimSetup error: If you use an NPT\n"
1374	<	"    ensemble, you must set tauThermostat.\n");
1375	<	painCave.isFatal = 1;
1376	<	simError();
1377	<	}
1520	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1521
1522	<	if( globals->haveTauBarostat() )
1523	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1524	<	else{
1525	<	sprintf( painCave.errMsg,
1526	<	"SimSetup error: If you use an NPT\n"
1527	<	"    ensemble, you must set tauBarostat.\n");
1528	<	painCave.isFatal = 1;
1529	<	simError();
1530	<	}
1388	<	break;
1522	>	if (globals->haveTargetPressure())
1523	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1524	>	else{
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup error: If you use a constant pressure\n"
1527	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1528	>	painCave.isFatal = 1;
1529	>	simError();
1530	>	}
1531
1532	<	case NPTf_ENS:
1533	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1534	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1532	>	if (globals->haveTauThermostat())
1533	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1534	>	else{
1535	>	sprintf(painCave.errMsg,
1536	>	"SimSetup error: If you use an NPT\n"
1537	>	"\tensemble, you must set tauThermostat.\n");
1538	>	painCave.isFatal = 1;
1539	>	simError();
1540	>	}
1541
1542	<	if (globals->haveTargetPressure())
1543	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1544	<	else {
1545	<	sprintf( painCave.errMsg,
1546	<	"SimSetup error: If you use a constant pressure\n"
1547	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1548	<	painCave.isFatal = 1;
1549	<	simError();
1550	<	}
1542	>	if (globals->haveTauBarostat())
1543	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1544	>	else{
1545	>	sprintf(painCave.errMsg,
1546	>	"SimSetup error: If you use an NPT\n"
1547	>	"\tensemble, you must set tauBarostat.\n");
1548	>	painCave.isFatal = 1;
1549	>	simError();
1550	>	}
1551
1552	<	if( globals->haveTauThermostat() )
1553	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1406	<	else{
1407	<	sprintf( painCave.errMsg,
1408	<	"SimSetup error: If you use an NPT\n"
1409	<	"    ensemble, you must set tauThermostat.\n");
1410	<	painCave.isFatal = 1;
1411	<	simError();
1412	<	}
1552	>	info->the_integrator = myNPTi;
1553	>	break;
1554
1555	<	if( globals->haveTauBarostat() )
1556	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1557	<	else{
1558	<	sprintf( painCave.errMsg,
1559	<	"SimSetup error: If you use an NPT\n"
1560	<	"    ensemble, you must set tauBarostat.\n");
1561	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1423	<	break;
1424	<
1425	<	case NPTim_ENS:
1426	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1555	>	case NPTf_ENS:
1556	>	if (globals->haveZconstraints()){
1557	>	setupZConstraint(info[k]);
1558	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1559	>	}
1560	>	else
1561	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1562
1563	<	if (globals->haveTargetPressure())
1430	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1431	<	else {
1432	<	sprintf( painCave.errMsg,
1433	<	"SimSetup error: If you use a constant pressure\n"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1437	<	}
1438	<
1439	<	if( globals->haveTauThermostat() )
1440	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1441	<	else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1447	<	}
1563	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1564
1565	<	if( globals->haveTauBarostat() )
1566	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1567	<	else{
1568	<	sprintf( painCave.errMsg,
1569	<	"SimSetup error: If you use an NPT\n"
1570	<	"    ensemble, you must set tauBarostat.\n");
1571	<	painCave.isFatal = 1;
1572	<	simError();
1573	<	}
1458	<	break;
1565	>	if (globals->haveTargetPressure())
1566	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1567	>	else{
1568	>	sprintf(painCave.errMsg,
1569	>	"SimSetup error: If you use a constant pressure\n"
1570	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1571	>	painCave.isFatal = 1;
1572	>	simError();
1573	>	}
1574
1575	<	case NPTfm_ENS:
1576	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1462	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1575	>	if (globals->haveTauThermostat())
1576	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1577
1578	<	if (globals->haveTargetPressure())
1579	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1580	<	else {
1581	<	sprintf( painCave.errMsg,
1582	<	"SimSetup error: If you use a constant pressure\n"
1583	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1584	<	painCave.isFatal = 1;
1471	<	simError();
1472	<	}
1473	<
1474	<	if( globals->haveTauThermostat() )
1475	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1476	<	else{
1477	<	sprintf( painCave.errMsg,
1478	<	"SimSetup error: If you use an NPT\n"
1479	<	"    ensemble, you must set tauThermostat.\n");
1480	<	painCave.isFatal = 1;
1481	<	simError();
1482	<	}
1578	>	else{
1579	>	sprintf(painCave.errMsg,
1580	>	"SimSetup error: If you use an NPT\n"
1581	>	"\tensemble, you must set tauThermostat.\n");
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585
1586	<	if( globals->haveTauBarostat() )
1587	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	<	else{
1487	<	sprintf( painCave.errMsg,
1488	<	"SimSetup error: If you use an NPT\n"
1489	<	"    ensemble, you must set tauBarostat.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<	break;
1494	<
1495	<	case NVEZCONS_ENS:
1586	>	if (globals->haveTauBarostat())
1587	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1588
1589	+	else{
1590	+	sprintf(painCave.errMsg,
1591	+	"SimSetup error: If you use an NPT\n"
1592	+	"\tensemble, you must set tauBarostat.\n");
1593	+	painCave.isFatal = 1;
1594	+	simError();
1595	+	}
1596
1597	<	//setup index of z-constraint molecules, z-constraint sampel time
1598	<	//and z-constraint force output name. These parameter should be known
1500	<	//before constructing the z-constraint integrator
1501	<	setupZConstraint();
1502	<
1503	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1504	<
1505	<	break;
1506	<
1507	<
1508	<	case NVTZCONS_ENS:
1509	<
1510	<	setupZConstraint();
1511	<
1512	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1597	>	info->the_integrator = myNPTf;
1598	>	break;
1599
1600	<	if (globals->haveTauThermostat())
1601	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1600	>	case NPTxyz_ENS:
1601	>	if (globals->haveZconstraints()){
1602	>	setupZConstraint(info[k]);
1603	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1604	>	}
1605	>	else
1606	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1607
1608	<	else {
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use the NVT\n"
1521	<	"    ensemble, you must set tauThermostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1525	<	break;
1526	<
1527	<	case NPTiZCONS_ENS:
1528	<
1529	<	setupZConstraint();
1530	<
1531	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1608	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1609
1610	<	if (globals->haveTargetPressure())
1611	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1612	<	else {
1613	<	sprintf( painCave.errMsg,
1614	<	"SimSetup error: If you use a constant pressure\n"
1615	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1616	<	painCave.isFatal = 1;
1617	<	simError();
1618	<	}
1543	<
1544	<	if( globals->haveTauThermostat() )
1545	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546	<	else{
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use an NPT\n"
1549	<	"    ensemble, you must set tauThermostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1610	>	if (globals->haveTargetPressure())
1611	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1612	>	else{
1613	>	sprintf(painCave.errMsg,
1614	>	"SimSetup error: If you use a constant pressure\n"
1615	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1616	>	painCave.isFatal = 1;
1617	>	simError();
1618	>	}
1619
1620	<	if( globals->haveTauBarostat() )
1621	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1622	<	else{
1623	<	sprintf( painCave.errMsg,
1624	<	"SimSetup error: If you use an NPT\n"
1625	<	"    ensemble, you must set tauBarostat.\n");
1626	<	painCave.isFatal = 1;
1627	<	simError();
1628	<	}
1563	<
1564	<	break;
1565	<
1566	<	case NPTfZCONS_ENS:
1567	<
1568	<	setupZConstraint();
1569	<
1570	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1620	>	if (globals->haveTauThermostat())
1621	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1622	>	else{
1623	>	sprintf(painCave.errMsg,
1624	>	"SimSetup error: If you use an NPT\n"
1625	>	"\tensemble, you must set tauThermostat.\n");
1626	>	painCave.isFatal = 1;
1627	>	simError();
1628	>	}
1629
1630	<	if (globals->haveTargetPressure())
1631	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1632	<	else {
1633	<	sprintf( painCave.errMsg,
1634	<	"SimSetup error: If you use a constant pressure\n"
1635	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1636	<	painCave.isFatal = 1;
1637	<	simError();
1638	<	}
1630	>	if (globals->haveTauBarostat())
1631	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1632	>	else{
1633	>	sprintf(painCave.errMsg,
1634	>	"SimSetup error: If you use an NPT\n"
1635	>	"\tensemble, you must set tauBarostat.\n");
1636	>	painCave.isFatal = 1;
1637	>	simError();
1638	>	}
1639
1640	<	if( globals->haveTauThermostat() )
1641	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585	<	else{
1586	<	sprintf( painCave.errMsg,
1587	<	"SimSetup error: If you use an NPT\n"
1588	<	"    ensemble, you must set tauThermostat.\n");
1589	<	painCave.isFatal = 1;
1590	<	simError();
1591	<	}
1640	>	info->the_integrator = myNPTxyz;
1641	>	break;
1642
1643	<	if( globals->haveTauBarostat() )
1644	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1645	<	else{
1646	<	sprintf( painCave.errMsg,
1647	<	"SimSetup error: If you use an NPT\n"
1598	<	"    ensemble, you must set tauBarostat.\n");
1599	<	painCave.isFatal = 1;
1600	<	simError();
1601	<	}
1602	<
1603	<	break;
1604	<
1605	<	case NPTimZCONS_ENS:
1606	<
1607	<	setupZConstraint();
1608	<
1609	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1610	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1611	<
1612	<	if (globals->haveTargetPressure())
1613	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1614	<	else {
1615	<	sprintf( painCave.errMsg,
1616	<	"SimSetup error: If you use a constant pressure\n"
1617	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1618	<	painCave.isFatal = 1;
1619	<	simError();
1643	>	default:
1644	>	sprintf(painCave.errMsg,
1645	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1646	>	painCave.isFatal = 1;
1647	>	simError();
1648		}
1621	–
1622	–	if( globals->haveTauThermostat() )
1623	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624	–	else{
1625	–	sprintf( painCave.errMsg,
1626	–	"SimSetup error: If you use an NPT\n"
1627	–	"    ensemble, you must set tauThermostat.\n");
1628	–	painCave.isFatal = 1;
1629	–	simError();
1630	–	}
1631	–
1632	–	if( globals->haveTauBarostat() )
1633	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634	–	else{
1635	–	sprintf( painCave.errMsg,
1636	–	"SimSetup error: If you use an NPT\n"
1637	–	"    ensemble, you must set tauBarostat.\n");
1638	–	painCave.isFatal = 1;
1639	–	simError();
1640	–	}
1641	–
1642	–	break;
1643	–
1644	–	case NPTfmZCONS_ENS:
1645	–
1646	–	setupZConstraint();
1647	–
1648	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650	–
1651	–	if (globals->haveTargetPressure())
1652	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653	–	else {
1654	–	sprintf( painCave.errMsg,
1655	–	"SimSetup error: If you use a constant pressure\n"
1656	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1657	–	painCave.isFatal = 1;
1658	–	simError();
1659	–	}
1660	–
1661	–	if( globals->haveTauThermostat() )
1662	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663	–	else{
1664	–	sprintf( painCave.errMsg,
1665	–	"SimSetup error: If you use an NPT\n"
1666	–	"    ensemble, you must set tauThermostat.\n");
1667	–	painCave.isFatal = 1;
1668	–	simError();
1669	–	}
1670	–
1671	–	if( globals->haveTauBarostat() )
1672	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673	–	else{
1674	–	sprintf( painCave.errMsg,
1675	–	"SimSetup error: If you use an NPT\n"
1676	–	"    ensemble, you must set tauBarostat.\n");
1677	–	painCave.isFatal = 1;
1678	–	simError();
1679	–	}
1680	–	break;
1681	–
1682	–
1683	–
1684	–	default:
1685	–	sprintf( painCave.errMsg,
1686	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1687	–	painCave.isFatal = 1;
1688	–	simError();
1649		}
1690	–
1650		}
1651
1652	<	void SimSetup::initFortran( void ){
1652	>	void SimSetup::initFortran(void){
1653	>	info[0].refreshSim();
1654
1655	<	info->refreshSim();
1656	<
1697	<	if( !strcmp( info->mixingRule, "standard") ){
1698	<	the_ff->initForceField( LB_MIXING_RULE );
1655	>	if (!strcmp(info[0].mixingRule, "standard")){
1656	>	the_ff->initForceField(LB_MIXING_RULE);
1657		}
1658	<	else if( !strcmp( info->mixingRule, "explicit") ){
1659	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1658	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1659	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1660		}
1661		else{
1662	<	sprintf( painCave.errMsg,
1663	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1706	<	info->mixingRule );
1662	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1663	>	info[0].mixingRule);
1664		painCave.isFatal = 1;
1665		simError();
1666		}
1667
1668
1669		#ifdef IS_MPI
1670	<	strcpy( checkPointMsg,
1714	<	"Successfully intialized the mixingRule for Fortran." );
1670	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1671		MPIcheckPoint();
1672		#endif // is_mpi
1717	–
1673		}
1674
1675	<	void SimSetup::setupZConstraint()
1676	<	{
1677	<	if(globals->haveZConsTime()){
1678	<
1679	<	//add sample time of z-constraint  into SimInfo's property list
1680	<	DoubleData* zconsTimeProp = new DoubleData();
1681	<	zconsTimeProp->setID("zconstime");
1682	<	zconsTimeProp->setData(globals->getZConsTime());
1683	<	info->addProperty(zconsTimeProp);
1675	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1676	>	int nZConstraints;
1677	>	ZconStamp** zconStamp;
1678	>
1679	>	if (globals->haveZconstraintTime()){
1680	>	//add sample time of z-constraint  into SimInfo's property list
1681	>	DoubleData* zconsTimeProp = new DoubleData();
1682	>	zconsTimeProp->setID(ZCONSTIME_ID);
1683	>	zconsTimeProp->setData(globals->getZconsTime());
1684	>	theInfo.addProperty(zconsTimeProp);
1685		}
1686		else{
1687	<	sprintf( painCave.errMsg,
1688	<	"ZConstraint error: If you use an ZConstraint\n"
1689	<	" , you must set sample time.\n");
1687	>	sprintf(painCave.errMsg,
1688	>	"ZConstraint error: If you use a ZConstraint,\n"
1689	>	"\tyou must set zconsTime.\n");
1690		painCave.isFatal = 1;
1691	+	simError();
1692	+	}
1693	+
1694	+	//push zconsTol into siminfo, if user does not specify
1695	+	//value for zconsTol, a default value will be used
1696	+	DoubleData* zconsTol = new DoubleData();
1697	+	zconsTol->setID(ZCONSTOL_ID);
1698	+	if (globals->haveZconsTol()){
1699	+	zconsTol->setData(globals->getZconsTol());
1700	+	}
1701	+	else{
1702	+	double defaultZConsTol = 0.01;
1703	+	sprintf(painCave.errMsg,
1704	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1705	+	"\tOOPSE will use a default value of %f.\n"
1706	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1707	+	defaultZConsTol);
1708	+	painCave.isFatal = 0;
1709		simError();
1710	+
1711	+	zconsTol->setData(defaultZConsTol);
1712		}
1713	<
1714	<	if(globals->haveIndexOfAllZConsMols()){
1715	<
1716	<	//add index of z-constraint molecules into SimInfo's property list
1717	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1718	<
1719	<	//sort the index
1720	<	sort(tempIndex.begin(), tempIndex.end());
1745	<
1746	<	IndexData* zconsIndex = new IndexData();
1747	<	zconsIndex->setID("zconsindex");
1748	<	zconsIndex->setIndexData(tempIndex);
1749	<	info->addProperty(zconsIndex);
1713	>	theInfo.addProperty(zconsTol);
1714	>
1715	>	//set Force Subtraction Policy
1716	>	StringData* zconsForcePolicy = new StringData();
1717	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1718	>
1719	>	if (globals->haveZconsForcePolicy()){
1720	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1721		}
1722		else{
1723	<	sprintf( painCave.errMsg,
1724	<	"SimSetup error: If you use an ZConstraint\n"
1725	<	" , you must set index of z-constraint molecules.\n");
1726	<	painCave.isFatal = 1;
1727	<	simError();
1728	<
1723	>	sprintf(painCave.errMsg,
1724	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1725	>	"\tOOPSE will use PolicyByMass.\n"
1726	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1727	>	painCave.isFatal = 0;
1728	>	simError();
1729	>	zconsForcePolicy->setData("BYMASS");
1730		}
1731
1732	+	theInfo.addProperty(zconsForcePolicy);
1733	+
1734	+	//set zcons gap
1735	+	DoubleData* zconsGap = new DoubleData();
1736	+	zconsGap->setID(ZCONSGAP_ID);
1737	+
1738	+	if (globals->haveZConsGap()){
1739	+	zconsGap->setData(globals->getZconsGap());
1740	+	theInfo.addProperty(zconsGap);
1741	+	}
1742	+
1743	+	//set zcons fixtime
1744	+	DoubleData* zconsFixtime = new DoubleData();
1745	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1746	+
1747	+	if (globals->haveZConsFixTime()){
1748	+	zconsFixtime->setData(globals->getZconsFixtime());
1749	+	theInfo.addProperty(zconsFixtime);
1750	+	}
1751	+
1752	+	//set zconsUsingSMD
1753	+	IntData* zconsUsingSMD = new IntData();
1754	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1755	+
1756	+	if (globals->haveZConsUsingSMD()){
1757	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1758	+	theInfo.addProperty(zconsUsingSMD);
1759	+	}
1760	+
1761		//Determine the name of ouput file and add it into SimInfo's property list
1762		//Be careful, do not use inFileName, since it is a pointer which
1763		//point to a string at master node, and slave nodes do not contain that string
1764	<
1765	<	string zconsOutput(info->finalName);
1766	<
1764	>
1765	>	string zconsOutput(theInfo.finalName);
1766	>
1767		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1768	<
1768	>
1769		StringData* zconsFilename = new StringData();
1770	<	zconsFilename->setID("zconsfilename");
1770	>	zconsFilename->setID(ZCONSFILENAME_ID);
1771		zconsFilename->setData(zconsOutput);
1772
1773	<	info->addProperty(zconsFilename);
1773	>	theInfo.addProperty(zconsFilename);
1774
1775	+	//setup index, pos and other parameters of z-constraint molecules
1776	+	nZConstraints = globals->getNzConstraints();
1777	+	theInfo.nZconstraints = nZConstraints;
1778	+
1779	+	zconStamp = globals->getZconStamp();
1780	+	ZConsParaItem tempParaItem;
1781	+
1782	+	ZConsParaData* zconsParaData = new ZConsParaData();
1783	+	zconsParaData->setID(ZCONSPARADATA_ID);
1784	+
1785	+	for (int i = 0; i < nZConstraints; i++){
1786	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1787	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1788	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1789	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1790	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1791	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1792	+	zconsParaData->addItem(tempParaItem);
1793	+	}
1794	+
1795	+	//check the uniqueness of index
1796	+	if(!zconsParaData->isIndexUnique()){
1797	+	sprintf(painCave.errMsg,
1798	+	"ZConstraint Error: molIndex is not unique!\n");
1799	+	painCave.isFatal = 1;
1800	+	simError();
1801	+	}
1802	+
1803	+	//sort the parameters by index of molecules
1804	+	zconsParaData->sortByIndex();
1805	+
1806	+	//push data into siminfo, therefore, we can retrieve later
1807	+	theInfo.addProperty(zconsParaData);
1808		}
1809	+
1810	+	void SimSetup::makeMinimizer(){
1811	+
1812	+	OOPSEMinimizer* myOOPSEMinimizer;
1813	+	MinimizerParameterSet* param;
1814	+	char minimizerName[100];
1815	+
1816	+	for (int i = 0; i < nInfo; i++){
1817	+
1818	+	//prepare parameter set for minimizer
1819	+	param = new MinimizerParameterSet();
1820	+	param->setDefaultParameter();
1821	+
1822	+	if (globals->haveMinimizer()){
1823	+	param->setFTol(globals->getMinFTol());
1824	+	}
1825	+
1826	+	if (globals->haveMinGTol()){
1827	+	param->setGTol(globals->getMinGTol());
1828	+	}
1829	+
1830	+	if (globals->haveMinMaxIter()){
1831	+	param->setMaxIteration(globals->getMinMaxIter());
1832	+	}
1833	+
1834	+	if (globals->haveMinWriteFrq()){
1835	+	param->setMaxIteration(globals->getMinMaxIter());
1836	+	}
1837	+
1838	+	if (globals->haveMinWriteFrq()){
1839	+	param->setWriteFrq(globals->getMinWriteFrq());
1840	+	}
1841	+
1842	+	if (globals->haveMinStepSize()){
1843	+	param->setStepSize(globals->getMinStepSize());
1844	+	}
1845	+
1846	+	if (globals->haveMinLSMaxIter()){
1847	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinLSTol()){
1851	+	param->setLineSearchTol(globals->getMinLSTol());
1852	+	}
1853	+
1854	+	strcpy(minimizerName, globals->getMinimizer());
1855	+
1856	+	if (!strcasecmp(minimizerName, "CG")){
1857	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1858	+	}
1859	+	else if (!strcasecmp(minimizerName, "SD")){
1860	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1861	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1862	+	}
1863	+	else{
1864	+	sprintf(painCave.errMsg,
1865	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1866	+	painCave.isFatal = 0;
1867	+	simError();
1868	+
1869	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870	+	}
1871	+	info[i].the_integrator = myOOPSEMinimizer;
1872	+
1873	+	//store the minimizer into simInfo
1874	+	info[i].the_minimizer = myOOPSEMinimizer;
1875	+	info[i].has_minimizer = true;
1876	+	}
1877	+
1878	+	}

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