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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 21 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 50 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87		}
88
89
90	<	void SimSetup::parseFile( char* fileName ){
61	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
97	–	int i, j, k, globalAtomIndex;
98	–
126		// gather all of the information from the Bass file
127
128		gatherInfo();
#	Line 110 | Line 137 | void SimSetup::createSim(void){
137
138		// initialize the system coordinates
139
140	<	if( !isInfoArray ) initSystemCoords();
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
118	–
119	–	// make the integrator
150
121	–	makeIntegrator();
122	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 128 | Line 156 | void SimSetup::createSim(void){
156
157		initFortran();
158
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165
132	–
166		}
167
168
169	<	void SimSetup::makeMolecules( void ){
170	<
171	<	int k,l;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	<
195	>	set<int> skipList;
196	>
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200	>
201		//init the forceField paramters
202
203		the_ff->readParams();
204
158	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
162	<
163	<	for(k=0; k<nInfo; k++){
164	<
165	<	the_ff->setSimInfo( &(info[k]) );
207	>	int nMembers, nNew, rb1, rb2;
208
209	+	for (k = 0; k < nInfo; k++){
210	+	the_ff->setSimInfo(&(info[k]));
211	+
212		atomOffset = 0;
213	<	excludeOffset = 0;
214	<	for(i=0; i<info[k].n_mol; i++){
170	<
213	>
214	>	for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
219	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
220	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223	>
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	–	molInfo.myBends = new Bend*[molInfo.nBends];
183	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248	<
249	<	for(j=0; j<molInfo.nAtoms; j++){
250	<
251	<	currentAtom = comp_stamps[stampID]->getAtom( j );
252	<	if( currentAtom->haveOrientation() ){
253	<
254	<	dAtom = new DirectionalAtom( (j + atomOffset),
255	<	info[k].getConfiguration() );
256	<	info[k].n_oriented++;
257	<	molInfo.myAtoms[j] = dAtom;
258	<
259	<	ux = currentAtom->getOrntX();
260	<	uy = currentAtom->getOrntY();
261	<	uz = currentAtom->getOrntZ();
262	<
263	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
264	<
265	<	u = sqrt( uSqr );
266	<	ux = ux / u;
267	<	uy = uy / u;
268	<	uz = uz / u;
269	<
270	<	dAtom->setSUx( ux );
271	<	dAtom->setSUy( uy );
272	<	dAtom->setSUz( uz );
273	<	}
274	<	else{
275	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
248	>
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251	>
252	>	if (currentAtom->haveOrientation()){
253	>	dAtom = new DirectionalAtom((j + atomOffset),
254	>	info[k].getConfiguration());
255	>	info[k].n_oriented++;
256	>	molInfo.myAtoms[j] = dAtom;
257	>
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261	>
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265	>
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270	>
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272	>
273	>	}
274	>
275	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277	<
278	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
279	<
277	>
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279	>
280		#endif // is_mpi
281		}
282	<
283	<	// make the bonds
284	<	for(j=0; j<molInfo.nBonds; j++){
285	<
286	<	currentBond = comp_stamps[stampID]->getBond( j );
287	<	theBonds[j].a = currentBond->getA() + atomOffset;
288	<	theBonds[j].b = currentBond->getB() + atomOffset;
289	<
290	<	exI = theBonds[j].a;
291	<	exJ = theBonds[j].b;
292	<
293	<	// exclude_I must always be the smaller of the pair
294	<	if( exI > exJ ){
295	<	tempEx = exI;
296	<	exI = exJ;
297	<	exJ = tempEx;
298	<	}
299	<	#ifdef IS_MPI
300	<	tempEx = exI;
301	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
302	<	tempEx = exJ;
249	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	<	#else  // isn't MPI
253	<
254	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	<	#endif  //is_mpi
256	<	}
257	<	excludeOffset += molInfo.nBonds;
258	<
282	>
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288	>
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291	>
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299	>
300	>	info[k].excludes->addPair(exI, exJ);
301	>	}
302	>
303		//make the bends
304	<	for(j=0; j<molInfo.nBends; j++){
305	<
306	<	currentBend = comp_stamps[stampID]->getBend( j );
307	<	theBends[j].a = currentBend->getA() + atomOffset;
308	<	theBends[j].b = currentBend->getB() + atomOffset;
309	<	theBends[j].c = currentBend->getC() + atomOffset;
310	<
311	<	if( currentBend->haveExtras() ){
312	<
313	<	extras = currentBend->getExtras();
314	<	current_extra = extras;
315	<
316	<	while( current_extra != NULL ){
317	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
318	<
319	<	switch( current_extra->getType() ){
320	<
321	<	case 0:
322	<	theBends[j].ghost =
323	<	current_extra->getInt() + atomOffset;
324	<	theBends[j].isGhost = 1;
325	<	break;
326	<
327	<	case 1:
328	<	theBends[j].ghost =
329	<	(int)current_extra->getDouble() + atomOffset;
330	<	theBends[j].isGhost = 1;
331	<	break;
332	<
333	<	default:
334	<	sprintf( painCave.errMsg,
335	<	"SimSetup Error: ghostVectorSource was neither a "
336	<	"double nor an int.\n"
337	<	"-->Bend[%d] in %s\n",
338	<	j, comp_stamps[stampID]->getID() );
339	<	painCave.isFatal = 1;
340	<	simError();
341	<	}
342	<	}
343	<
344	<	else{
345	<
346	<	sprintf( painCave.errMsg,
347	<	"SimSetup Error: unhandled bend assignment:\n"
348	<	"    -->%s in Bend[%d] in %s\n",
349	<	current_extra->getlhs(),
350	<	j, comp_stamps[stampID]->getID() );
351	<	painCave.isFatal = 1;
352	<	simError();
353	<	}
354	<
355	<	current_extra = current_extra->getNext();
312	<	}
313	<	}
314	<
315	<	if( !theBends[j].isGhost ){
316	<
317	<	exI = theBends[j].a;
318	<	exJ = theBends[j].c;
319	<	}
320	<	else{
321	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].b;
324	<	}
325	<
326	<	// exclude_I must always be the smaller of the pair
327	<	if( exI > exJ ){
328	<	tempEx = exI;
329	<	exI = exJ;
330	<	exJ = tempEx;
331	<	}
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309	>
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313	>
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321	>
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327	>
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346	>
347	>	current_extra = current_extra->getNext();
348	>	}
349	>	}
350	>
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
361	<
362	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
363	<	#else  // isn't MPI
364	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
365	<	#endif  //is_mpi
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364	>
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
386	<	excludeOffset += molInfo.nBends;
387	<
388	<	for(j=0; j<molInfo.nTorsions; j++){
389	<
390	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
391	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
392	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
393	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
394	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
395	<
396	<	exI = theTorsions[j].a;
397	<	exJ = theTorsions[j].d;
398	<
356	<	// exclude_I must always be the smaller of the pair
357	<	if( exI > exJ ){
358	<	tempEx = exI;
359	<	exI = exJ;
360	<	exJ = tempEx;
361	<	}
386	>
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393	>
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398	>
399		#ifdef IS_MPI
400	<	tempEx = exI;
401	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	<	tempEx = exJ;
403	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
404	<
405	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
406	<	#else  // isn't MPI
407	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
408	<	#endif  //is_mpi
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410	>
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417		}
418	<	excludeOffset += molInfo.nTorsions;
418	>
419
420	+	molInfo.myRigidBodies.clear();
421
422	<	// send the arrays off to the forceField for init.
423	<
424	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
425	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
426	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
427	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423	>
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487	>	}
488
489	+
490	+	//create cutoff group for molecule
491	+
492	+	cutoffAtomSet.clear();
493	+	molInfo.myCutoffGroups.clear();
494
495	<	info[k].molecules[i].initialize( molInfo );
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	+	nMembers = currentCutoffGroup->getNMembers();
499	+
500	+	myCutoffGroup = new CutoffGroup();
501	+
502	+	for (int cg = 0; cg < nMembers; cg++) {
503	+
504	+	// molI is atom numbering inside this molecule
505	+	molI = currentCutoffGroup->getMember(cg);
506	+
507	+	// tempI is atom numbering on local processor
508	+	tempI = molI + atomOffset;
509	+
510	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	+
512	+	cutoffAtomSet.insert(tempI);
513	+	}
514	+
515	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	+
518	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	+
520	+	for(j = 0; j < molInfo.nAtoms; j++){
521	+
522	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	+	myCutoffGroup = new CutoffGroup();
524	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	+	}
527	+
528	+	}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537
538	+
539	+	for (j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	#ifdef IS_MPI
542	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	+	#else
544	+	slJ = j+atomOffset;
545	+	#endif
546	+
547	+	// if they aren't on the skip list, then they can be integrated
548	+
549	+	if (skipList.find(slJ) == skipList.end()) {
550	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	+	info[k].integrableObjects.push_back(mySD);
552	+	molInfo.myIntegrableObjects.push_back(mySD);
553	+	}
554	+	}
555	+
556	+	// all rigid bodies are integrated:
557	+
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	+	theTorsions);
572	+
573	+	info[k].molecules[i].initialize(molInfo);
574	+
575	+
576		atomOffset += molInfo.nAtoms;
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582	<
582	>
583		#ifdef IS_MPI
584	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
398	–
399	–	// clean up the forcefield
587
401	–	the_ff->calcRcut();
402	–	the_ff->cleanMe();
403	–
588		}
589
590	<	void SimSetup::initFromBass( void ){
407	<
590	>	void SimSetup::initFromBass(void){
591		int i, j, k;
592		int n_cells;
593		double cellx, celly, cellz;
#	Line 418 | Line 601 | void SimSetup::initFromBass( void ){
601		vel[1] = 0.0;
602		vel[2] = 0.0;
603
604	<	temp1 = (double)tot_nmol / 4.0;
605	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
606	<	temp3 = ceil( temp2 );
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607
608	<	have_extra =0;
609	<	if( temp2 < temp3 ){ // we have a non-complete lattice
610	<	have_extra =1;
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612
613	<	n_cells = (int)temp3 - 1;
613	>	n_cells = (int) temp3 - 1;
614		cellx = info[0].boxL[0] / temp3;
615		celly = info[0].boxL[1] / temp3;
616		cellz = info[0].boxL[2] / temp3;
617	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
618	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
619	<	n_per_extra = (int)ceil( temp1 );
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620
621	<	if( n_per_extra > 4){
622	<	sprintf( painCave.errMsg,
623	<	"SimSetup error. There has been an error in constructing"
624	<	" the non-complete lattice.\n" );
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625		painCave.isFatal = 1;
626		simError();
627		}
628		}
629		else{
630	<	n_cells = (int)temp3;
630	>	n_cells = (int) temp3;
631		cellx = info[0].boxL[0] / temp3;
632		celly = info[0].boxL[1] / temp3;
633		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 638 | void SimSetup::initFromBass( void ){
638		current_comp = 0;
639		current_atom_ndx = 0;
640
641	<	for( i=0; i < n_cells ; i++ ){
642	<	for( j=0; j < n_cells; j++ ){
643	<	for( k=0; k < n_cells; k++ ){
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645
646	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
472	<
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	k * cellz + 0.5 * cellz );
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651		}
652		}
653		}
654
655	<	if( have_extra ){
655	>	if (have_extra){
656		done = 0;
657
658		int start_ndx;
659	<	for( i=0; i < (n_cells+1) && !done; i++ ){
660	<	for( j=0; j < (n_cells+1) && !done; j++ ){
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	if( i < n_cells ){
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	if( j < n_cells ){
676	<	start_ndx = n_cells;
677	<	}
678	<	else start_ndx = 0;
679	<	}
494	<	else start_ndx = 0;
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	makeElement( i * cellx,
688	<	j * celly,
689	<	k * cellz );
690	<	done = ( current_mol >= tot_nmol );
691	<
692	<	if( !done && n_per_extra > 1 ){
504	<	makeElement( i * cellx + 0.5 * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
509	<
510	<	if( !done && n_per_extra > 2){
511	<	makeElement( i * cellx,
512	<	j * celly + 0.5 * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
516	<
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693		}
694		}
695		}
696
697	<	for( i=0; i<info[0].n_atoms; i++ ){
698	<	info[0].atoms[i]->setVel( vel );
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699		}
700		}
701
702	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
702	>	void SimSetup::makeElement(double x, double y, double z){
703		int k;
704		AtomStamp* current_atom;
705		DirectionalAtom* dAtom;
706		double rotMat[3][3];
707		double pos[3];
708
709	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
710	<
711	<	current_atom = comp_stamps[current_comp]->getAtom( k );
712	<	if( !current_atom->havePosition() ){
713	<	sprintf( painCave.errMsg,
714	<	"SimSetup:initFromBass error.\n"
715	<	"\tComponent %s, atom %s does not have a position specified.\n"
716	<	"\tThe initialization routine is unable to give a start"
717	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
721	<
721	>
722		pos[0] = x + current_atom->getPosX();
723		pos[1] = y + current_atom->getPosY();
724		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
725
726	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731		rotMat[0][0] = 1.0;
732		rotMat[0][1] = 0.0;
#	Line 575 | Line 740 | void SimSetup::makeElement( double x, double y, double
740		rotMat[2][1] = 0.0;
741		rotMat[2][2] = 1.0;
742
743	<	dAtom->setA( rotMat );
743	>	dAtom->setA(rotMat);
744		}
745
746		current_atom_ndx++;
#	Line 584 | Line 749 | void SimSetup::makeElement( double x, double y, double
749		current_mol++;
750		current_comp_mol++;
751
752	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753		current_comp_mol = 0;
754		current_comp++;
755		}
756		}
757
758
759	<	void SimSetup::gatherInfo( void ){
760	<	int i,j,k;
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762		ensembleCase = -1;
763		ffCase = -1;
764
765		// set the easy ones first
766
767	<	for( i=0; i<nInfo; i++){
767	>	for (i = 0; i < nInfo; i++){
768		info[i].target_temp = globals->getTargetTemp();
769		info[i].dt = globals->getDt();
770		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 774 | void SimSetup::gatherInfo( void ){
774
775		// get the forceField
776
777	<	strcpy( force_field, globals->getForceField() );
777	>	strcpy(force_field, globals->getForceField());
778
779	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
780	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
781	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791		else{
792	<	sprintf( painCave.errMsg,
793	<	"SimSetup Error. Unrecognized force field -> %s\n",
794	<	force_field );
795	<	painCave.isFatal = 1;
623	<	simError();
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796		}
797
798	<	// get the ensemble
798	>	// get the ensemble
799
800	<	strcpy( ensemble, globals->getEnsemble() );
800	>	strcpy(ensemble, globals->getEnsemble());
801
802	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
803	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
804	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809		ensembleCase = NPTi_ENS;
810	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
811	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
812	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817		else{
818	<	sprintf( painCave.errMsg,
819	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
820	<	"reverting to NVE for this simulation.\n",
821	<	ensemble );
822	<	painCave.isFatal = 0;
823	<	simError();
824	<	strcpy( ensemble, "NVE" );
825	<	ensembleCase = NVE_ENS;
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
827
828	+	for (i = 0; i < nInfo; i++){
829	+	strcpy(info[i].ensemble, ensemble);
830	+
831		// get the mixing rule
832
833	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834		info[i].usePBC = globals->getPBC();
835		}
836	<
836	>
837		// get the components and calculate the tot_nMol and indvidual n_mol
838	<
838	>
839		the_components = globals->getComponents();
840		components_nmol = new int[n_components];
841
842
843	<	if( !globals->haveNMol() ){
843	>	if (!globals->haveNMol()){
844		// we don't have the total number of molecules, so we assume it is
845		// given in each component
846
847		tot_nmol = 0;
848	<	for( i=0; i<n_components; i++ ){
849	<
850	<	if( !the_components[i]->haveNMol() ){
851	<	// we have a problem
852	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error. No global NMol or component NMol"
854	<	" given. Cannot calculate the number of atoms.\n" );
855	<	painCave.isFatal = 1;
677	<	simError();
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856		}
857
858		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 860 | void SimSetup::gatherInfo( void ){
860		}
861		}
862		else{
863	<	sprintf( painCave.errMsg,
864	<	"SimSetup error.\n"
865	<	"\tSorry, the ability to specify total"
866	<	" nMols and then give molfractions in the components\n"
867	<	"\tis not currently supported."
868	<	" Please give nMol in the components.\n" );
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869		painCave.isFatal = 1;
870		simError();
871		}
872
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903	+
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
915
916	<	if( globals->haveSampleTime() ){
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
924		}
925	<
926	<	if( globals->haveStatusTime() ){
925	>
926	>	if (globals->haveStatusTime()){
927		info[i].statusTime = globals->getStatusTime();
928		}
929	<
930	<	if( globals->haveThermalTime() ){
929	>
930	>	if (globals->haveThermalTime()){
931		info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934		}
935
936	<	// check for the temperature set flag
937	<
938	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941	>
942	>	// check for the temperature set flag
943
944	<	// get some of the tricky things that may still be in the globals
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951
724	–	double boxVector[3];
725	–	if( globals->haveBox() ){
726	–	boxVector[0] = globals->getBox();
727	–	boxVector[1] = globals->getBox();
728	–	boxVector[2] = globals->getBox();
729	–
730	–	info[i].setBox( boxVector );
731	–	}
732	–	else if( globals->haveDensity() ){
733	–
734	–	double vol;
735	–	vol = (double)tot_nmol / globals->getDensity();
736	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	–	boxVector[1] = boxVector[0];
738	–	boxVector[2] = boxVector[0];
739	–
740	–	info[i].setBox( boxVector );
952		}
953	<	else{
954	<	if( !globals->haveBoxX() ){
955	<	sprintf( painCave.errMsg,
956	<	"SimSetup error, no periodic BoxX size given.\n" );
957	<	painCave.isFatal = 1;
958	<	simError();
953	>
954	>	//setup seed for random number generator
955	>	int seedValue;
956	>
957	>	if (globals->haveSeed()){
958	>	seedValue = globals->getSeed();
959	>
960	>	if(seedValue / 1E9 == 0){
961	>	sprintf(painCave.errMsg,
962	>	"Seed for sprng library should contain at least 9 digits\n"
963	>	"OOPSE will generate a seed for user\n");
964	>	painCave.isFatal = 0;
965	>	simError();
966	>
967	>	//using seed generated by system instead of invalid seed set by user
968	>	#ifndef IS_MPI
969	>	seedValue = make_sprng_seed();
970	>	#else
971	>	if (worldRank == 0){
972	>	seedValue = make_sprng_seed();
973		}
974	<	boxVector[0] = globals->getBoxX();
975	<
751	<	if( !globals->haveBoxY() ){
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error, no periodic BoxY size given.\n" );
754	<	painCave.isFatal = 1;
755	<	simError();
756	<	}
757	<	boxVector[1] = globals->getBoxY();
758	<
759	<	if( !globals->haveBoxZ() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxZ size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
765	<	boxVector[2] = globals->getBoxZ();
766	<
767	<	info[i].setBox( boxVector );
974	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
975	>	#endif
976		}
977	+	}//end of if branch of globals->haveSeed()
978	+	else{
979	+
980	+	#ifndef IS_MPI
981	+	seedValue = make_sprng_seed();
982	+	#else
983	+	if (worldRank == 0){
984	+	seedValue = make_sprng_seed();
985	+	}
986	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
987	+	#endif
988	+	}//end of globals->haveSeed()
989
990	+	for (int i = 0; i < nInfo; i++){
991	+	info[i].setSeed(seedValue);
992		}
993	<
993	>
994		#ifdef IS_MPI
995	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
995	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
996		MPIcheckPoint();
997		#endif // is_mpi
776	–
998		}
999
1000
1001	<	void SimSetup::finalInfoCheck( void ){
1001	>	void SimSetup::finalInfoCheck(void){
1002		int index;
1003		int usesDipoles;
1004	+	int usesCharges;
1005		int i;
1006
1007	<	for(i=0; i<nInfo; i++){
1007	>	for (i = 0; i < nInfo; i++){
1008		// check electrostatic parameters
1009	<
1009	>
1010		index = 0;
1011		usesDipoles = 0;
1012	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1012	>	while ((index < info[i].n_atoms) && !usesDipoles){
1013		usesDipoles = (info[i].atoms[index])->hasDipole();
1014		index++;
1015		}
1016	<
1016	>	index = 0;
1017	>	usesCharges = 0;
1018	>	while ((index < info[i].n_atoms) && !usesCharges){
1019	>	usesCharges= (info[i].atoms[index])->hasCharge();
1020	>	index++;
1021	>	}
1022		#ifdef IS_MPI
1023		int myUse = usesDipoles;
1024	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1024	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1025		#endif //is_mpi
1026	<
1027	<	double theEcr, theEst;
1028	<
1029	<	if (globals->getUseRF() ) {
1030	<	info[i].useReactionField = 1;
1026	>
1027	>	double theRcut, theRsw;
1028	>
1029	>	if (globals->haveRcut()) {
1030	>	theRcut = globals->getRcut();
1031	>
1032	>	if (globals->haveRsw())
1033	>	theRsw = globals->getRsw();
1034	>	else
1035	>	theRsw = theRcut;
1036
1037	<	if( !globals->haveECR() ){
1038	<	sprintf( painCave.errMsg,
1039	<	"SimSetup Warning: using default value of 1/2 the smallest "
808	<	"box length for the electrostaticCutoffRadius.\n"
809	<	"I hope you have a very fast processor!\n");
810	<	painCave.isFatal = 0;
811	<	simError();
812	<	double smallest;
813	<	smallest = info[i].boxL[0];
814	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	<	theEcr = 0.5 * smallest;
817	<	} else {
818	<	theEcr = globals->getECR();
819	<	}
1037	>	info[i].setDefaultRcut(theRcut, theRsw);
1038	>
1039	>	} else {
1040
1041	<	if( !globals->haveEST() ){
1042	<	sprintf( painCave.errMsg,
1043	<	"SimSetup Warning: using default value of 0.05 * the "
1044	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1045	<	);
1046	<	painCave.isFatal = 0;
1047	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
831	<	}
1041	>	the_ff->calcRcut();
1042	>	theRcut = info[i].getRcut();
1043	>
1044	>	if (globals->haveRsw())
1045	>	theRsw = globals->getRsw();
1046	>	else
1047	>	theRsw = theRcut;
1048
1049	<	info[i].setEcr( theEcr, theEst );
1049	>	info[i].setDefaultRcut(theRcut, theRsw);
1050	>	}
1051	>
1052	>	if (globals->getUseRF()){
1053	>	info[i].useReactionField = 1;
1054
1055	<	if(!globals->haveDielectric() ){
1056	<	sprintf( painCave.errMsg,
1057	<	"SimSetup Error: You are trying to use Reaction Field without"
1058	<	"setting a dielectric constant!\n"
1059	<	);
1060	<	painCave.isFatal = 1;
1061	<	simError();
1055	>	if (!globals->haveRcut()){
1056	>	sprintf(painCave.errMsg,
1057	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1058	>	"\tOOPSE will use a default value of 15.0 angstroms"
1059	>	"\tfor the cutoffRadius.\n");
1060	>	painCave.isFatal = 0;
1061	>	simError();
1062	>	theRcut = 15.0;
1063		}
1064	<	info[i].dielectric = globals->getDielectric();
1065	<	}
1066	<	else {
1067	<	if (usesDipoles) {
1068	<
1069	<	if( !globals->haveECR() ){
1070	<	sprintf( painCave.errMsg,
1071	<	"SimSetup Warning: using default value of 1/2 the smallest "
1072	<	"box length for the electrostaticCutoffRadius.\n"
1073	<	"I hope you have a very fast processor!\n");
1074	<	painCave.isFatal = 0;
1075	<	simError();
1076	<	double smallest;
1077	<	smallest = info[i].boxL[0];
1078	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
1079	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
1080	<	theEcr = 0.5 * smallest;
1081	<	} else {
1082	<	theEcr = globals->getECR();
1083	<	}
1064	>	else{
1065	>	theRcut = globals->getRcut();
1066	>	}
1067	>
1068	>	if (!globals->haveRsw()){
1069	>	sprintf(painCave.errMsg,
1070	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1071	>	"\tOOPSE will use a default value of\n"
1072	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1073	>	painCave.isFatal = 0;
1074	>	simError();
1075	>	theRsw = 0.95 * theRcut;
1076	>	}
1077	>	else{
1078	>	theRsw = globals->getRsw();
1079	>	}
1080	>
1081	>	info[i].setDefaultRcut(theRcut, theRsw);
1082	>
1083	>	if (!globals->haveDielectric()){
1084	>	sprintf(painCave.errMsg,
1085	>	"SimSetup Error: No Dielectric constant was set.\n"
1086	>	"\tYou are trying to use Reaction Field without"
1087	>	"\tsetting a dielectric constant!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090	>	}
1091	>	info[i].dielectric = globals->getDielectric();
1092	>	}
1093	>	else{
1094	>	if (usesDipoles || usesCharges){
1095	>
1096	>	if (!globals->haveRcut()){
1097	>	sprintf(painCave.errMsg,
1098	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1099	>	"\tOOPSE will use a default value of 15.0 angstroms"
1100	>	"\tfor the cutoffRadius.\n");
1101	>	painCave.isFatal = 0;
1102	>	simError();
1103	>	theRcut = 15.0;
1104	>	}
1105	>	else{
1106	>	theRcut = globals->getRcut();
1107	>	}
1108	>
1109	>	if (!globals->haveRsw()){
1110	>	sprintf(painCave.errMsg,
1111	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1112	>	"\tOOPSE will use a default value of\n"
1113	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1114	>	painCave.isFatal = 0;
1115	>	simError();
1116	>	theRsw = 0.95 * theRcut;
1117	>	}
1118	>	else{
1119	>	theRsw = globals->getRsw();
1120	>	}
1121	>
1122	>	info[i].setDefaultRcut(theRcut, theRsw);
1123
864	–	if( !globals->haveEST() ){
865	–	sprintf( painCave.errMsg,
866	–	"SimSetup Warning: using default value of 0.05 * the "
867	–	"electrostaticCutoffRadius for the "
868	–	"electrostaticSkinThickness\n"
869	–	);
870	–	painCave.isFatal = 0;
871	–	simError();
872	–	theEst = 0.05 * theEcr;
873	–	} else {
874	–	theEst= globals->getEST();
875	–	}
876	–
877	–	info[i].setEcr( theEcr, theEst );
1124		}
1125	<	}
1125	>	}
1126		}
881	–
1127		#ifdef IS_MPI
1128	<	strcpy( checkPointMsg, "post processing checks out" );
1128	>	strcpy(checkPointMsg, "post processing checks out");
1129		MPIcheckPoint();
1130		#endif // is_mpi
1131
1132	+	// clean up the forcefield
1133	+	the_ff->cleanMe();
1134		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
1135
1136	+	void SimSetup::initSystemCoords(void){
1137	+	int i;
1138	+
1139		char* inName;
1140
1141	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1142
1143	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1144	<
1145	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1146	<
899	<	if( globals->haveInitialConfig() ){
900	<
1143	>	for (i = 0; i < info[0].n_atoms; i++)
1144	>	info[0].atoms[i]->setCoords();
1145	>
1146	>	if (globals->haveInitialConfig()){
1147		InitializeFromFile* fileInit;
1148		#ifdef IS_MPI // is_mpi
1149	<	if( worldRank == 0 ){
1149	>	if (worldRank == 0){
1150		#endif //is_mpi
1151		inName = globals->getInitialConfig();
1152	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
1152	>	fileInit = new InitializeFromFile(inName);
1153		#ifdef IS_MPI
1154	<	}else fileInit = new InitializeFromFile( NULL );
1154	>	}
1155	>	else
1156	>	fileInit = new InitializeFromFile(NULL);
1157		#endif
1158	<	fileInit->readInit( info ); // default velocities on
1159	<
1158	>	fileInit->readInit(info); // default velocities on
1159	>
1160		delete fileInit;
1161		}
1162		else{
1163
917	–	#ifdef IS_MPI
918	–
1164		// no init from bass
1165
1166	<	sprintf( painCave.errMsg,
1167	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1168	<	painCave.isFatal;
1166	>	sprintf(painCave.errMsg,
1167	>	"Cannot intialize a simulation without an initial configuration file.\n");
1168	>	painCave.isFatal = 1;;
1169		simError();
1170
926	–	#else
927	–
928	–	initFromBass();
929	–
930	–
931	–	#endif
1171		}
1172	<
1172	>
1173		#ifdef IS_MPI
1174	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1174	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1175		MPIcheckPoint();
1176		#endif // is_mpi
938	–
1177		}
1178
1179
1180	<	void SimSetup::makeOutNames( void ){
943	<
1180	>	void SimSetup::makeOutNames(void){
1181		int k;
1182
946	–
947	–	for(k=0; k<nInfo; k++){
1183
1184	+	for (k = 0; k < nInfo; k++){
1185		#ifdef IS_MPI
1186	<	if( worldRank == 0 ){
1186	>	if (worldRank == 0){
1187		#endif // is_mpi
1188	<
1189	<	if( globals->haveFinalConfig() ){
1190	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1188	>
1189	>	if (globals->haveFinalConfig()){
1190	>	strcpy(info[k].finalName, globals->getFinalConfig());
1191		}
1192		else{
1193	<	strcpy( info[k].finalName, inFileName );
1194	<	char* endTest;
1195	<	int nameLength = strlen( info[k].finalName );
1196	<	endTest = &(info[k].finalName[nameLength - 5]);
1197	<	if( !strcmp( endTest, ".bass" ) ){
1198	<	strcpy( endTest, ".eor" );
1199	<	}
1200	<	else if( !strcmp( endTest, ".BASS" ) ){
1201	<	strcpy( endTest, ".eor" );
1202	<	}
1203	<	else{
1204	<	endTest = &(info[k].finalName[nameLength - 4]);
1205	<	if( !strcmp( endTest, ".bss" ) ){
1206	<	strcpy( endTest, ".eor" );
1207	<	}
1208	<	else if( !strcmp( endTest, ".mdl" ) ){
1209	<	strcpy( endTest, ".eor" );
1210	<	}
1211	<	else{
1212	<	strcat( info[k].finalName, ".eor" );
1213	<	}
1214	<	}
979	<	}
980	<
981	<	// make the sample and status out names
982	<
983	<	strcpy( info[k].sampleName, inFileName );
984	<	char* endTest;
985	<	int nameLength = strlen( info[k].sampleName );
986	<	endTest = &(info[k].sampleName[nameLength - 5]);
987	<	if( !strcmp( endTest, ".bass" ) ){
988	<	strcpy( endTest, ".dump" );
989	<	}
990	<	else if( !strcmp( endTest, ".BASS" ) ){
991	<	strcpy( endTest, ".dump" );
1193	>	strcpy(info[k].finalName, inFileName);
1194	>	char* endTest;
1195	>	int nameLength = strlen(info[k].finalName);
1196	>	endTest = &(info[k].finalName[nameLength - 5]);
1197	>	if (!strcmp(endTest, ".bass")){
1198	>	strcpy(endTest, ".eor");
1199	>	}
1200	>	else if (!strcmp(endTest, ".BASS")){
1201	>	strcpy(endTest, ".eor");
1202	>	}
1203	>	else{
1204	>	endTest = &(info[k].finalName[nameLength - 4]);
1205	>	if (!strcmp(endTest, ".bss")){
1206	>	strcpy(endTest, ".eor");
1207	>	}
1208	>	else if (!strcmp(endTest, ".mdl")){
1209	>	strcpy(endTest, ".eor");
1210	>	}
1211	>	else{
1212	>	strcat(info[k].finalName, ".eor");
1213	>	}
1214	>	}
1215		}
1216	+
1217	+	// make the sample and status out names
1218	+
1219	+	strcpy(info[k].sampleName, inFileName);
1220	+	char* endTest;
1221	+	int nameLength = strlen(info[k].sampleName);
1222	+	endTest = &(info[k].sampleName[nameLength - 5]);
1223	+	if (!strcmp(endTest, ".bass")){
1224	+	strcpy(endTest, ".dump");
1225	+	}
1226	+	else if (!strcmp(endTest, ".BASS")){
1227	+	strcpy(endTest, ".dump");
1228	+	}
1229		else{
1230	<	endTest = &(info[k].sampleName[nameLength - 4]);
1231	<	if( !strcmp( endTest, ".bss" ) ){
1232	<	strcpy( endTest, ".dump" );
1233	<	}
1234	<	else if( !strcmp( endTest, ".mdl" ) ){
1235	<	strcpy( endTest, ".dump" );
1236	<	}
1237	<	else{
1238	<	strcat( info[k].sampleName, ".dump" );
1239	<	}
1230	>	endTest = &(info[k].sampleName[nameLength - 4]);
1231	>	if (!strcmp(endTest, ".bss")){
1232	>	strcpy(endTest, ".dump");
1233	>	}
1234	>	else if (!strcmp(endTest, ".mdl")){
1235	>	strcpy(endTest, ".dump");
1236	>	}
1237	>	else{
1238	>	strcat(info[k].sampleName, ".dump");
1239	>	}
1240		}
1241	<
1242	<	strcpy( info[k].statusName, inFileName );
1243	<	nameLength = strlen( info[k].statusName );
1241	>
1242	>	strcpy(info[k].statusName, inFileName);
1243	>	nameLength = strlen(info[k].statusName);
1244		endTest = &(info[k].statusName[nameLength - 5]);
1245	<	if( !strcmp( endTest, ".bass" ) ){
1246	<	strcpy( endTest, ".stat" );
1245	>	if (!strcmp(endTest, ".bass")){
1246	>	strcpy(endTest, ".stat");
1247		}
1248	<	else if( !strcmp( endTest, ".BASS" ) ){
1249	<	strcpy( endTest, ".stat" );
1248	>	else if (!strcmp(endTest, ".BASS")){
1249	>	strcpy(endTest, ".stat");
1250		}
1251		else{
1252	<	endTest = &(info[k].statusName[nameLength - 4]);
1253	<	if( !strcmp( endTest, ".bss" ) ){
1254	<	strcpy( endTest, ".stat" );
1255	<	}
1256	<	else if( !strcmp( endTest, ".mdl" ) ){
1257	<	strcpy( endTest, ".stat" );
1258	<	}
1259	<	else{
1260	<	strcat( info[k].statusName, ".stat" );
1261	<	}
1252	>	endTest = &(info[k].statusName[nameLength - 4]);
1253	>	if (!strcmp(endTest, ".bss")){
1254	>	strcpy(endTest, ".stat");
1255	>	}
1256	>	else if (!strcmp(endTest, ".mdl")){
1257	>	strcpy(endTest, ".stat");
1258	>	}
1259	>	else{
1260	>	strcat(info[k].statusName, ".stat");
1261	>	}
1262		}
1263	<
1263	>
1264		#ifdef IS_MPI
1265	+
1266		}
1267		#endif // is_mpi
1268		}
1269		}
1270
1271
1272	<	void SimSetup::sysObjectsCreation( void ){
1273	<
1274	<	int i,k;
1038	<
1272	>	void SimSetup::sysObjectsCreation(void){
1273	>	int i, k;
1274	>
1275		// create the forceField
1276
1277		createFF();
#	Line 1050 | Line 1286 | void SimSetup::sysObjectsCreation( void ){
1286
1287		#ifdef IS_MPI
1288		// divide the molecules among the processors
1289	<
1289	>
1290		mpiMolDivide();
1291		#endif //is_mpi
1292	<
1292	>
1293		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1294	<
1294	>
1295		makeSysArrays();
1296
1297		// make and initialize the molecules (all but atomic coordinates)
1298	<
1298	>
1299		makeMolecules();
1300	<
1301	<	for(k=0; k<nInfo; k++){
1300	>
1301	>	for (k = 0; k < nInfo; k++){
1302		info[k].identArray = new int[info[k].n_atoms];
1303	<	for(i=0; i<info[k].n_atoms; i++){
1303	>	for (i = 0; i < info[k].n_atoms; i++){
1304		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1305		}
1306		}
1307		}
1308
1309
1310	<	void SimSetup::createFF( void ){
1310	>	void SimSetup::createFF(void){
1311	>	switch (ffCase){
1312	>	case FF_DUFF:
1313	>	the_ff = new DUFF();
1314	>	break;
1315
1316	<	switch( ffCase ){
1316	>	case FF_LJ:
1317	>	the_ff = new LJFF();
1318	>	break;
1319
1320	<	case FF_DUFF:
1321	<	the_ff = new DUFF();
1322	<	break;
1320	>	case FF_EAM:
1321	>	the_ff = new EAM_FF();
1322	>	break;
1323
1324	<	case FF_LJ:
1325	<	the_ff = new LJFF();
1326	<	break;
1324	>	case FF_H2O:
1325	>	the_ff = new WATER();
1326	>	break;
1327
1328	<	case FF_EAM:
1329	<	the_ff = new EAM_FF();
1330	<	break;
1331	<
1332	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	simError();
1328	>	default:
1329	>	sprintf(painCave.errMsg,
1330	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1331	>	painCave.isFatal = 1;
1332	>	simError();
1333		}
1334
1335		#ifdef IS_MPI
1336	<	strcpy( checkPointMsg, "ForceField creation successful" );
1336	>	strcpy(checkPointMsg, "ForceField creation successful");
1337		MPIcheckPoint();
1338		#endif // is_mpi
1101	–
1339		}
1340
1341
1342	<	void SimSetup::compList( void ){
1106	<
1342	>	void SimSetup::compList(void){
1343		int i;
1344		char* id;
1345		LinkedMolStamp* headStamp = new LinkedMolStamp();
1346		LinkedMolStamp* currentStamp = NULL;
1347	<	comp_stamps = new MoleculeStamp*[n_components];
1347	>	comp_stamps = new MoleculeStamp * [n_components];
1348	>	bool haveCutoffGroups;
1349	>
1350	>	haveCutoffGroups = false;
1351
1352		// make an array of molecule stamps that match the components used.
1353		// also extract the used stamps out into a separate linked list
1354	<
1355	<	for(i=0; i<nInfo; i++){
1354	>
1355	>	for (i = 0; i < nInfo; i++){
1356		info[i].nComponents = n_components;
1357		info[i].componentsNmol = components_nmol;
1358		info[i].compStamps = comp_stamps;
1359		info[i].headStamp = headStamp;
1360		}
1122	–
1361
1124	–	for( i=0; i<n_components; i++ ){
1362
1363	+	for (i = 0; i < n_components; i++){
1364		id = the_components[i]->getType();
1365		comp_stamps[i] = NULL;
1366	<
1366	>
1367		// check to make sure the component isn't already in the list
1368
1369	<	comp_stamps[i] = headStamp->match( id );
1370	<	if( comp_stamps[i] == NULL ){
1133	<
1369	>	comp_stamps[i] = headStamp->match(id);
1370	>	if (comp_stamps[i] == NULL){
1371		// extract the component from the list;
1372	<
1373	<	currentStamp = stamps->extractMolStamp( id );
1374	<	if( currentStamp == NULL ){
1375	<	sprintf( painCave.errMsg,
1376	<	"SimSetup error: Component \"%s\" was not found in the "
1377	<	"list of declared molecules\n",
1378	<	id );
1379	<	painCave.isFatal = 1;
1380	<	simError();
1372	>
1373	>	currentStamp = stamps->extractMolStamp(id);
1374	>	if (currentStamp == NULL){
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: Component \"%s\" was not found in the "
1377	>	"list of declared molecules\n",
1378	>	id);
1379	>	painCave.isFatal = 1;
1380	>	simError();
1381		}
1382	<
1383	<	headStamp->add( currentStamp );
1384	<	comp_stamps[i] = headStamp->match( id );
1382	>
1383	>	headStamp->add(currentStamp);
1384	>	comp_stamps[i] = headStamp->match(id);
1385		}
1386	+
1387	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1388	+	haveCutoffGroups = true;
1389		}
1390	+
1391	+	for (i = 0; i < nInfo; i++)
1392	+	info[i].haveCutoffGroups = haveCutoffGroups;
1393
1394		#ifdef IS_MPI
1395	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1395	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1396		MPIcheckPoint();
1397		#endif // is_mpi
1398	+	}
1399
1400	+	void SimSetup::calcSysValues(void){
1401	+	int i;
1402
1403	<	}
1403	>	int* molMembershipArray;
1404
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1405		tot_atoms = 0;
1406		tot_bonds = 0;
1407		tot_bends = 0;
1408		tot_torsions = 0;
1409	<	for( i=0; i<n_components; i++ ){
1410	<
1411	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1412	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1413	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1409	>	tot_rigid = 0;
1410	>	for (i = 0; i < n_components; i++){
1411	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1412	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1413	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1414		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1415	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1416		}
1417
1418		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1419		molMembershipArray = new int[tot_atoms];
1420	<
1421	<	for(i=0; i<nInfo; i++){
1420	>
1421	>	for (i = 0; i < nInfo; i++){
1422		info[i].n_atoms = tot_atoms;
1423		info[i].n_bonds = tot_bonds;
1424		info[i].n_bends = tot_bends;
1425		info[i].n_torsions = tot_torsions;
1426		info[i].n_SRI = tot_SRI;
1427		info[i].n_mol = tot_nmol;
1428	<
1428	>
1429		info[i].molMembershipArray = molMembershipArray;
1430	<	}
1430	>	}
1431		}
1432
1433		#ifdef IS_MPI
1434
1435	<	void SimSetup::mpiMolDivide( void ){
1194	<
1435	>	void SimSetup::mpiMolDivide(void){
1436		int i, j, k;
1437		int localMol, allMol;
1438		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1439	+	int local_rigid;
1440	+	vector<int> globalMolIndex;
1441
1442	<	mpiSim = new mpiSimulation( info );
1200	<
1201	<	globalIndex = mpiSim->divideLabor();
1442	>	mpiSim = new mpiSimulation(info);
1443
1444	+	mpiSim->divideLabor();
1445	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1446	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1447	+
1448		// set up the local variables
1449	<
1449	>
1450		mol2proc = mpiSim->getMolToProcMap();
1451		molCompType = mpiSim->getMolComponentType();
1452	<
1452	>
1453		allMol = 0;
1454		localMol = 0;
1455		local_atoms = 0;
1456		local_bonds = 0;
1457		local_bends = 0;
1458		local_torsions = 0;
1459	<	globalAtomIndex = 0;
1459	>	local_rigid = 0;
1460	>	globalAtomCounter = 0;
1461
1462	<
1463	<	for( i=0; i<n_components; i++ ){
1464	<
1465	<	for( j=0; j<components_nmol[i]; j++ ){
1466	<
1467	<	if( mol2proc[allMol] == worldRank ){
1468	<
1469	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1470	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1462	>	for (i = 0; i < n_components; i++){
1463	>	for (j = 0; j < components_nmol[i]; j++){
1464	>	if (mol2proc[allMol] == worldRank){
1465	>	local_atoms += comp_stamps[i]->getNAtoms();
1466	>	local_bonds += comp_stamps[i]->getNBonds();
1467	>	local_bends += comp_stamps[i]->getNBends();
1468	>	local_torsions += comp_stamps[i]->getNTorsions();
1469	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1470	>	localMol++;
1471		}
1472	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1473	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1474	<	globalAtomIndex++;
1472	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1473	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1474	>	globalAtomCounter++;
1475		}
1476
1477	<	allMol++;
1477	>	allMol++;
1478		}
1479		}
1480		local_SRI = local_bonds + local_bends + local_torsions;
1481	<
1481	>
1482		info[0].n_atoms = mpiSim->getMyNlocal();
1483
1484	<	if( local_atoms != info[0].n_atoms ){
1485	<	sprintf( painCave.errMsg,
1486	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1487	<	" localAtom (%d) are not equal.\n",
1488	<	info[0].n_atoms,
1489	<	local_atoms );
1484	>
1485	>	if (local_atoms != info[0].n_atoms){
1486	>	sprintf(painCave.errMsg,
1487	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1488	>	"\tlocalAtom (%d) are not equal.\n",
1489	>	info[0].n_atoms, local_atoms);
1490		painCave.isFatal = 1;
1491		simError();
1492		}
#	Line 1254 | Line 1497 | void SimSetup::mpiMolDivide( void ){
1497		info[0].n_SRI = local_SRI;
1498		info[0].n_mol = localMol;
1499
1500	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1500	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1501		MPIcheckPoint();
1502		}
1503	<
1503	>
1504		#endif // is_mpi
1505
1506
1507	<	void SimSetup::makeSysArrays( void ){
1508	<	int i, j, k, l;
1507	>	void SimSetup::makeSysArrays(void){
1508	>
1509	>	#ifndef IS_MPI
1510	>	int k, j;
1511	>	#endif // is_mpi
1512	>	int i, l;
1513
1514		Atom** the_atoms;
1515		Molecule* the_molecules;
1269	–	Exclude** the_excludes;
1516
1517	<
1272	<	for(l=0; l<nInfo; l++){
1273	<
1517	>	for (l = 0; l < nInfo; l++){
1518		// create the atom and short range interaction arrays
1519	<
1520	<	the_atoms = new Atom*[info[l].n_atoms];
1519	>
1520	>	the_atoms = new Atom * [info[l].n_atoms];
1521		the_molecules = new Molecule[info[l].n_mol];
1522		int molIndex;
1523
1524		// initialize the molecule's stampID's
1525	<
1525	>
1526		#ifdef IS_MPI
1527	<
1528	<
1527	>
1528	>
1529		molIndex = 0;
1530	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1531	<
1532	<	if(mol2proc[i] == worldRank ){
1533	<	the_molecules[molIndex].setStampID( molCompType[i] );
1534	<	the_molecules[molIndex].setMyIndex( molIndex );
1535	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
1530	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1531	>	if (mol2proc[i] == worldRank){
1532	>	the_molecules[molIndex].setStampID(molCompType[i]);
1533	>	the_molecules[molIndex].setMyIndex(molIndex);
1534	>	the_molecules[molIndex].setGlobalIndex(i);
1535	>	molIndex++;
1536		}
1537		}
1538	<
1538	>
1539		#else // is_mpi
1540	<
1540	>
1541		molIndex = 0;
1542	<	globalAtomIndex = 0;
1543	<	for(i=0; i<n_components; i++){
1544	<	for(j=0; j<components_nmol[i]; j++ ){
1545	<	the_molecules[molIndex].setStampID( i );
1546	<	the_molecules[molIndex].setMyIndex( molIndex );
1547	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1548	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1549	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1550	<	globalAtomIndex++;
1551	<	}
1552	<	molIndex++;
1542	>	globalAtomCounter = 0;
1543	>	for (i = 0; i < n_components; i++){
1544	>	for (j = 0; j < components_nmol[i]; j++){
1545	>	the_molecules[molIndex].setStampID(i);
1546	>	the_molecules[molIndex].setMyIndex(molIndex);
1547	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1548	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1549	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1550	>	globalAtomCounter++;
1551	>	}
1552	>	molIndex++;
1553		}
1554		}
1312	–
1313	–
1314	–	#endif // is_mpi
1555
1556
1557	<	if( info[l].n_SRI ){
1318	<
1319	<	Exclude::createArray(info[l].n_SRI);
1320	<	the_excludes = new Exclude*[info[l].n_SRI];
1321	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	<	the_excludes[ex] = new Exclude(ex);
1323	<	}
1324	<	info[l].globalExcludes = new int;
1325	<	info[l].n_exclude = info[l].n_SRI;
1326	<	}
1327	<	else{
1328	<
1329	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1331	<	the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair( 0,0 );
1333	<	info[l].globalExcludes = new int;
1334	<	info[l].globalExcludes[0] = 0;
1335	<	info[l].n_exclude = 0;
1336	<	}
1557	>	#endif // is_mpi
1558
1559	+	info[l].globalExcludes = new int;
1560	+	info[l].globalExcludes[0] = 0;
1561	+
1562		// set the arrays into the SimInfo object
1563
1564		info[l].atoms = the_atoms;
1565		info[l].molecules = the_molecules;
1566		info[l].nGlobalExcludes = 0;
1343	–	info[l].excludes = the_excludes;
1344	–
1345	–	the_ff->setSimInfo( info );
1567
1568	+	the_ff->setSimInfo(info);
1569		}
1570		}
1571
1572	<	void SimSetup::makeIntegrator( void ){
1351	<
1572	>	void SimSetup::makeIntegrator(void){
1573		int k;
1574
1575	<	NVT<RealIntegrator>*  myNVT = NULL;
1576	<	NPTi<RealIntegrator>* myNPTi = NULL;
1577	<	NPTf<RealIntegrator>* myNPTf = NULL;
1578	<	NPTim<RealIntegrator>* myNPTim = NULL;
1579	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1580	<
1581	<	for(k=0; k<nInfo; k++){
1582	<
1583	<	switch( ensembleCase ){
1584	<
1585	<	case NVE_ENS:
1586	<	if (globals->haveZconstraints()){
1587	<	setupZConstraint(info[k]);
1588	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1575	>	NVE<RealIntegrator>* myNVE = NULL;
1576	>	NVT<RealIntegrator>* myNVT = NULL;
1577	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1578	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1579	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1580	>
1581	>	for (k = 0; k < nInfo; k++){
1582	>	switch (ensembleCase){
1583	>	case NVE_ENS:
1584	>	if (globals->haveZconstraints()){
1585	>	setupZConstraint(info[k]);
1586	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1587	>	}
1588	>	else{
1589	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1590		}
1591	+
1592	+	info->the_integrator = myNVE;
1593	+	break;
1594
1595	<	else
1596	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1597	<	break;
1598	<
1599	<	case NVT_ENS:
1600	<	if (globals->haveZconstraints()){
1601	<	setupZConstraint(info[k]);
1377	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	<	}
1379	<	else
1380	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1595	>	case NVT_ENS:
1596	>	if (globals->haveZconstraints()){
1597	>	setupZConstraint(info[k]);
1598	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1599	>	}
1600	>	else
1601	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1602
1603	<	myNVT->setTargetTemp(globals->getTargetTemp());
1383	<
1384	<	if (globals->haveTauThermostat())
1385	<	myNVT->setTauThermostat(globals->getTauThermostat());
1386	<
1387	<	else {
1388	<	sprintf( painCave.errMsg,
1389	<	"SimSetup error: If you use the NVT\n"
1390	<	"    ensemble, you must set tauThermostat.\n");
1391	<	painCave.isFatal = 1;
1392	<	simError();
1393	<	}
1394	<	break;
1395	<
1396	<	case NPTi_ENS:
1397	<	if (globals->haveZconstraints()){
1398	<	setupZConstraint(info[k]);
1399	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	<	}
1401	<	else
1402	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1603	>	myNVT->setTargetTemp(globals->getTargetTemp());
1604
1605	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1606	<
1607	<	if (globals->haveTargetPressure())
1608	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1609	<	else {
1610	<	sprintf( painCave.errMsg,
1611	<	"SimSetup error: If you use a constant pressure\n"
1612	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1613	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<
1416	<	if( globals->haveTauThermostat() )
1417	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	<	else{
1419	<	sprintf( painCave.errMsg,
1420	<	"SimSetup error: If you use an NPT\n"
1421	<	"    ensemble, you must set tauThermostat.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauBarostat() )
1427	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauBarostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<	break;
1436	<
1437	<	case NPTf_ENS:
1438	<	if (globals->haveZconstraints()){
1439	<	setupZConstraint(info[k]);
1440	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	<	}
1442	<	else
1443	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1605	>	if (globals->haveTauThermostat())
1606	>	myNVT->setTauThermostat(globals->getTauThermostat());
1607	>	else{
1608	>	sprintf(painCave.errMsg,
1609	>	"SimSetup error: If you use the NVT\n"
1610	>	"\tensemble, you must set tauThermostat.\n");
1611	>	painCave.isFatal = 1;
1612	>	simError();
1613	>	}
1614
1615	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1616	<
1447	<	if (globals->haveTargetPressure())
1448	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	<	else {
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use a constant pressure\n"
1452	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1466	<
1467	<	if( globals->haveTauBarostat() )
1468	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NPTim_ENS:
1479	<	if (globals->haveZconstraints()){
1480	<	setupZConstraint(info[k]);
1481	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	<	}
1483	<	else
1484	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1615	>	info->the_integrator = myNVT;
1616	>	break;
1617
1618	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1619	<
1620	<	if (globals->haveTargetPressure())
1621	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1622	<	else {
1623	<	sprintf( painCave.errMsg,
1624	<	"SimSetup error: If you use a constant pressure\n"
1493	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	<	painCave.isFatal = 1;
1495	<	simError();
1496	<	}
1497	<
1498	<	if( globals->haveTauThermostat() )
1499	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	<	else{
1501	<	sprintf( painCave.errMsg,
1502	<	"SimSetup error: If you use an NPT\n"
1503	<	"    ensemble, you must set tauThermostat.\n");
1504	<	painCave.isFatal = 1;
1505	<	simError();
1506	<	}
1507	<
1508	<	if( globals->haveTauBarostat() )
1509	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	<	else{
1511	<	sprintf( painCave.errMsg,
1512	<	"SimSetup error: If you use an NPT\n"
1513	<	"    ensemble, you must set tauBarostat.\n");
1514	<	painCave.isFatal = 1;
1515	<	simError();
1516	<	}
1517	<	break;
1518	<
1519	<	case NPTfm_ENS:
1520	<	if (globals->haveZconstraints()){
1521	<	setupZConstraint(info[k]);
1522	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	<	}
1524	<	else
1525	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1618	>	case NPTi_ENS:
1619	>	if (globals->haveZconstraints()){
1620	>	setupZConstraint(info[k]);
1621	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1622	>	}
1623	>	else
1624	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1625
1626	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1627	<
1628	<	if (globals->haveTargetPressure())
1629	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1630	<	else {
1631	<	sprintf( painCave.errMsg,
1632	<	"SimSetup error: If you use a constant pressure\n"
1633	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1634	<	painCave.isFatal = 1;
1635	<	simError();
1636	<	}
1637	<
1638	<	if( globals->haveTauThermostat() )
1639	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1640	<	else{
1641	<	sprintf( painCave.errMsg,
1642	<	"SimSetup error: If you use an NPT\n"
1643	<	"    ensemble, you must set tauThermostat.\n");
1644	<	painCave.isFatal = 1;
1645	<	simError();
1646	<	}
1647	<
1648	<	if( globals->haveTauBarostat() )
1649	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1650	<	else{
1651	<	sprintf( painCave.errMsg,
1652	<	"SimSetup error: If you use an NPT\n"
1653	<	"    ensemble, you must set tauBarostat.\n");
1654	<	painCave.isFatal = 1;
1655	<	simError();
1656	<	}
1657	<	break;
1658	<
1659	<	default:
1660	<	sprintf( painCave.errMsg,
1661	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1662	<	painCave.isFatal = 1;
1663	<	simError();
1626	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1627	>
1628	>	if (globals->haveTargetPressure())
1629	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1630	>	else{
1631	>	sprintf(painCave.errMsg,
1632	>	"SimSetup error: If you use a constant pressure\n"
1633	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1634	>	painCave.isFatal = 1;
1635	>	simError();
1636	>	}
1637	>
1638	>	if (globals->haveTauThermostat())
1639	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1640	>	else{
1641	>	sprintf(painCave.errMsg,
1642	>	"SimSetup error: If you use an NPT\n"
1643	>	"\tensemble, you must set tauThermostat.\n");
1644	>	painCave.isFatal = 1;
1645	>	simError();
1646	>	}
1647	>
1648	>	if (globals->haveTauBarostat())
1649	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1650	>	else{
1651	>	sprintf(painCave.errMsg,
1652	>	"SimSetup error: If you use an NPT\n"
1653	>	"\tensemble, you must set tauBarostat.\n");
1654	>	painCave.isFatal = 1;
1655	>	simError();
1656	>	}
1657	>
1658	>	info->the_integrator = myNPTi;
1659	>	break;
1660	>
1661	>	case NPTf_ENS:
1662	>	if (globals->haveZconstraints()){
1663	>	setupZConstraint(info[k]);
1664	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1665	>	}
1666	>	else
1667	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1668	>
1669	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1670	>
1671	>	if (globals->haveTargetPressure())
1672	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1673	>	else{
1674	>	sprintf(painCave.errMsg,
1675	>	"SimSetup error: If you use a constant pressure\n"
1676	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1677	>	painCave.isFatal = 1;
1678	>	simError();
1679	>	}
1680	>
1681	>	if (globals->haveTauThermostat())
1682	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1683	>
1684	>	else{
1685	>	sprintf(painCave.errMsg,
1686	>	"SimSetup error: If you use an NPT\n"
1687	>	"\tensemble, you must set tauThermostat.\n");
1688	>	painCave.isFatal = 1;
1689	>	simError();
1690	>	}
1691	>
1692	>	if (globals->haveTauBarostat())
1693	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1694	>
1695	>	else{
1696	>	sprintf(painCave.errMsg,
1697	>	"SimSetup error: If you use an NPT\n"
1698	>	"\tensemble, you must set tauBarostat.\n");
1699	>	painCave.isFatal = 1;
1700	>	simError();
1701	>	}
1702	>
1703	>	info->the_integrator = myNPTf;
1704	>	break;
1705	>
1706	>	case NPTxyz_ENS:
1707	>	if (globals->haveZconstraints()){
1708	>	setupZConstraint(info[k]);
1709	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1710	>	}
1711	>	else
1712	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1713	>
1714	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1715	>
1716	>	if (globals->haveTargetPressure())
1717	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1718	>	else{
1719	>	sprintf(painCave.errMsg,
1720	>	"SimSetup error: If you use a constant pressure\n"
1721	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>
1726	>	if (globals->haveTauThermostat())
1727	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1728	>	else{
1729	>	sprintf(painCave.errMsg,
1730	>	"SimSetup error: If you use an NPT\n"
1731	>	"\tensemble, you must set tauThermostat.\n");
1732	>	painCave.isFatal = 1;
1733	>	simError();
1734	>	}
1735	>
1736	>	if (globals->haveTauBarostat())
1737	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1738	>	else{
1739	>	sprintf(painCave.errMsg,
1740	>	"SimSetup error: If you use an NPT\n"
1741	>	"\tensemble, you must set tauBarostat.\n");
1742	>	painCave.isFatal = 1;
1743	>	simError();
1744	>	}
1745	>
1746	>	info->the_integrator = myNPTxyz;
1747	>	break;
1748	>
1749	>	default:
1750	>	sprintf(painCave.errMsg,
1751	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1752	>	painCave.isFatal = 1;
1753	>	simError();
1754		}
1755		}
1756		}
1757
1758	<	void SimSetup::initFortran( void ){
1570	<
1758	>	void SimSetup::initFortran(void){
1759		info[0].refreshSim();
1760	<
1761	<	if( !strcmp( info[0].mixingRule, "standard") ){
1762	<	the_ff->initForceField( LB_MIXING_RULE );
1760	>
1761	>	if (!strcmp(info[0].mixingRule, "standard")){
1762	>	the_ff->initForceField(LB_MIXING_RULE);
1763		}
1764	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1765	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1764	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1765	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1766		}
1767		else{
1768	<	sprintf( painCave.errMsg,
1769	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1768	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1769	>	info[0].mixingRule);
1770		painCave.isFatal = 1;
1771		simError();
1772		}
1773
1774
1775		#ifdef IS_MPI
1776	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1776	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1777		MPIcheckPoint();
1778		#endif // is_mpi
1593	–
1779		}
1780
1781	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1782	<	{
1783	<	int nZConstraints;
1599	<	ZconStamp** zconStamp;
1600	<
1601	<	if(globals->haveZconstraintTime()){
1602	<
1603	<	//add sample time of z-constraint  into SimInfo's property list
1604	<	DoubleData* zconsTimeProp = new DoubleData();
1605	<	zconsTimeProp->setID(ZCONSTIME_ID);
1606	<	zconsTimeProp->setData(globals->getZconsTime());
1607	<	theInfo.addProperty(zconsTimeProp);
1608	<	}
1609	<	else{
1610	<	sprintf( painCave.errMsg,
1611	<	"ZConstraint error: If you use an ZConstraint\n"
1612	<	" , you must set sample time.\n");
1613	<	painCave.isFatal = 1;
1614	<	simError();
1615	<	}
1781	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1782	>	int nZConstraints;
1783	>	ZconStamp** zconStamp;
1784
1785	<	//
1786	<	nZConstraints = globals->getNzConstraints();
1787	<	theInfo.nZconstraints = nZConstraints;
1788	<
1789	<	zconStamp = globals->getZconStamp();
1790	<	ZConsParaItem tempParaItem;
1785	>	if (globals->haveZconstraintTime()){
1786	>	//add sample time of z-constraint  into SimInfo's property list
1787	>	DoubleData* zconsTimeProp = new DoubleData();
1788	>	zconsTimeProp->setID(ZCONSTIME_ID);
1789	>	zconsTimeProp->setData(globals->getZconsTime());
1790	>	theInfo.addProperty(zconsTimeProp);
1791	>	}
1792	>	else{
1793	>	sprintf(painCave.errMsg,
1794	>	"ZConstraint error: If you use a ZConstraint,\n"
1795	>	"\tyou must set zconsTime.\n");
1796	>	painCave.isFatal = 1;
1797	>	simError();
1798	>	}
1799
1800	<	ZConsParaData* zconsParaData = new ZConsParaData();
1801	<	zconsParaData->setID(ZCONSPARADATA_ID);
1802	<
1803	<	for(int i = 0; i < nZConstraints; i++){
1800	>	//push zconsTol into siminfo, if user does not specify
1801	>	//value for zconsTol, a default value will be used
1802	>	DoubleData* zconsTol = new DoubleData();
1803	>	zconsTol->setID(ZCONSTOL_ID);
1804	>	if (globals->haveZconsTol()){
1805	>	zconsTol->setData(globals->getZconsTol());
1806	>	}
1807	>	else{
1808	>	double defaultZConsTol = 0.01;
1809	>	sprintf(painCave.errMsg,
1810	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1811	>	"\tOOPSE will use a default value of %f.\n"
1812	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1813	>	defaultZConsTol);
1814	>	painCave.isFatal = 0;
1815	>	simError();
1816	>
1817	>	zconsTol->setData(defaultZConsTol);
1818	>	}
1819	>	theInfo.addProperty(zconsTol);
1820	>
1821	>	//set Force Subtraction Policy
1822	>	StringData* zconsForcePolicy = new StringData();
1823	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1824	>
1825	>	if (globals->haveZconsForcePolicy()){
1826	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1827	>	}
1828	>	else{
1829	>	sprintf(painCave.errMsg,
1830	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1831	>	"\tOOPSE will use PolicyByMass.\n"
1832	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1833	>	painCave.isFatal = 0;
1834	>	simError();
1835	>	zconsForcePolicy->setData("BYMASS");
1836	>	}
1837	>
1838	>	theInfo.addProperty(zconsForcePolicy);
1839	>
1840	>	//set zcons gap
1841	>	DoubleData* zconsGap = new DoubleData();
1842	>	zconsGap->setID(ZCONSGAP_ID);
1843	>
1844	>	if (globals->haveZConsGap()){
1845	>	zconsGap->setData(globals->getZconsGap());
1846	>	theInfo.addProperty(zconsGap);
1847	>	}
1848	>
1849	>	//set zcons fixtime
1850	>	DoubleData* zconsFixtime = new DoubleData();
1851	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
1852	>
1853	>	if (globals->haveZConsFixTime()){
1854	>	zconsFixtime->setData(globals->getZconsFixtime());
1855	>	theInfo.addProperty(zconsFixtime);
1856	>	}
1857	>
1858	>	//set zconsUsingSMD
1859	>	IntData* zconsUsingSMD = new IntData();
1860	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1861	>
1862	>	if (globals->haveZConsUsingSMD()){
1863	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1864	>	theInfo.addProperty(zconsUsingSMD);
1865	>	}
1866	>
1867	>	//Determine the name of ouput file and add it into SimInfo's property list
1868	>	//Be careful, do not use inFileName, since it is a pointer which
1869	>	//point to a string at master node, and slave nodes do not contain that string
1870	>
1871	>	string zconsOutput(theInfo.finalName);
1872	>
1873	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1874	>
1875	>	StringData* zconsFilename = new StringData();
1876	>	zconsFilename->setID(ZCONSFILENAME_ID);
1877	>	zconsFilename->setData(zconsOutput);
1878	>
1879	>	theInfo.addProperty(zconsFilename);
1880	>
1881	>	//setup index, pos and other parameters of z-constraint molecules
1882	>	nZConstraints = globals->getNzConstraints();
1883	>	theInfo.nZconstraints = nZConstraints;
1884	>
1885	>	zconStamp = globals->getZconStamp();
1886	>	ZConsParaItem tempParaItem;
1887	>
1888	>	ZConsParaData* zconsParaData = new ZConsParaData();
1889	>	zconsParaData->setID(ZCONSPARADATA_ID);
1890	>
1891	>	for (int i = 0; i < nZConstraints; i++){
1892		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1893		tempParaItem.zPos = zconStamp[i]->getZpos();
1894		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1895		tempParaItem.kRatio = zconStamp[i]->getKratio();
1896	<
1896	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1897	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1898		zconsParaData->addItem(tempParaItem);
1899	+	}
1900	+
1901	+	//check the uniqueness of index
1902	+	if(!zconsParaData->isIndexUnique()){
1903	+	sprintf(painCave.errMsg,
1904	+	"ZConstraint Error: molIndex is not unique!\n");
1905	+	painCave.isFatal = 1;
1906	+	simError();
1907	+	}
1908	+
1909	+	//sort the parameters by index of molecules
1910	+	zconsParaData->sortByIndex();
1911	+
1912	+	//push data into siminfo, therefore, we can retrieve later
1913	+	theInfo.addProperty(zconsParaData);
1914	+	}
1915	+
1916	+	void SimSetup::makeMinimizer(){
1917	+
1918	+	OOPSEMinimizer* myOOPSEMinimizer;
1919	+	MinimizerParameterSet* param;
1920	+	char minimizerName[100];
1921	+
1922	+	for (int i = 0; i < nInfo; i++){
1923	+
1924	+	//prepare parameter set for minimizer
1925	+	param = new MinimizerParameterSet();
1926	+	param->setDefaultParameter();
1927	+
1928	+	if (globals->haveMinimizer()){
1929	+	param->setFTol(globals->getMinFTol());
1930		}
1931
1932	<	//sort the parameters by index of molecules
1933	<	zconsParaData->sortByIndex();
1934	<
1639	<	//push data into siminfo, therefore, we can retrieve later
1640	<	theInfo.addProperty(zconsParaData);
1932	>	if (globals->haveMinGTol()){
1933	>	param->setGTol(globals->getMinGTol());
1934	>	}
1935
1936	<	//push zconsTol into siminfo, if user does not specify
1937	<	//value for zconsTol, a default value will be used
1644	<	DoubleData* zconsTol = new DoubleData();
1645	<	zconsTol->setID(ZCONSTOL_ID);
1646	<	if(globals->haveZconsTol()){
1647	<	zconsTol->setData(globals->getZconsTol());
1936	>	if (globals->haveMinMaxIter()){
1937	>	param->setMaxIteration(globals->getMinMaxIter());
1938		}
1649	–	else{
1650	–	double defaultZConsTol = 1E-6;
1651	–	sprintf( painCave.errMsg,
1652	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1653	–	" , default value %f is used.\n", defaultZConsTol);
1654	–	painCave.isFatal = 0;
1655	–	simError();
1939
1940	<	zconsTol->setData(defaultZConsTol);
1941	<	}
1942	<	theInfo.addProperty(zconsTol);
1943	<
1944	<	//Determine the name of ouput file and add it into SimInfo's property list
1945	<	//Be careful, do not use inFileName, since it is a pointer which
1946	<	//point to a string at master node, and slave nodes do not contain that string
1940	>	if (globals->haveMinWriteFrq()){
1941	>	param->setMaxIteration(globals->getMinMaxIter());
1942	>	}
1943	>
1944	>	if (globals->haveMinWriteFrq()){
1945	>	param->setWriteFrq(globals->getMinWriteFrq());
1946	>	}
1947
1948	<	string zconsOutput(theInfo.finalName);
1949	<
1950	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1951	<
1952	<	StringData* zconsFilename = new StringData();
1953	<	zconsFilename->setID(ZCONSFILENAME_ID);
1954	<	zconsFilename->setData(zconsOutput);
1955	<
1956	<	theInfo.addProperty(zconsFilename);
1948	>	if (globals->haveMinStepSize()){
1949	>	param->setStepSize(globals->getMinStepSize());
1950	>	}
1951	>
1952	>	if (globals->haveMinLSMaxIter()){
1953	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1954	>	}
1955	>
1956	>	if (globals->haveMinLSTol()){
1957	>	param->setLineSearchTol(globals->getMinLSTol());
1958	>	}
1959	>
1960	>	strcpy(minimizerName, globals->getMinimizer());
1961	>
1962	>	if (!strcasecmp(minimizerName, "CG")){
1963	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1964	>	}
1965	>	else if (!strcasecmp(minimizerName, "SD")){
1966	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1967	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1968	>	}
1969	>	else{
1970	>	sprintf(painCave.errMsg,
1971	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1972	>	painCave.isFatal = 0;
1973	>	simError();
1974	>
1975	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1976	>	}
1977	>	info[i].the_integrator = myOOPSEMinimizer;
1978	>
1979	>	//store the minimizer into simInfo
1980	>	info[i].the_minimizer = myOOPSEMinimizer;
1981	>	info[i].has_minimizer = true;
1982	>	}
1983	>
1984		}

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