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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 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	<	#include <sys/time.h>
7	<
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 22 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
26	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
28	–	#define FF_DUFF 0
29	–	#define FF_LJ   1
30	–	#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 51 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87		}
88
89
90	<	void SimSetup::parseFile( char* fileName ){
62	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
90	<	mpiEventLoop();
91	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
98	–	int i, j, k, globalAtomIndex;
99	–
126		// gather all of the information from the Bass file
127
128		gatherInfo();
#	Line 111 | 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();
119	–
120	–	// make the integrator
150
122	–	makeIntegrator();
123	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 129 | 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
133	–
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
159	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
208	<
209	<	for(k=0; k<nInfo; k++){
210	<
166	<	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++){
171	<
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]);
181	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
182	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	–	molInfo.myBends = new Bend*[molInfo.nBends];
184	–	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),
219	<	info[k].getConfiguration() );
220	<	}
221	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	<
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;
250	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251	<
252	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
253	<	#else  // isn't MPI
254	<
255	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
256	<	#endif  //is_mpi
257	<	}
258	<	excludeOffset += molInfo.nBonds;
259	<
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" )){
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	>	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	>
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	>	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	>
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
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	<	switch( current_extra->getType() ){
435	<
436	<	case 0:
437	<	theBends[j].ghost =
438	<	current_extra->getInt() + atomOffset;
439	<	theBends[j].isGhost = 1;
440	<	break;
441	<
442	<	case 1:
443	<	theBends[j].ghost =
444	<	(int)current_extra->getDouble() + atomOffset;
445	<	theBends[j].isGhost = 1;
446	<	break;
447	<
448	<	default:
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Error: ghostVectorSource was neither a "
451	<	"double nor an int.\n"
452	<	"-->Bend[%d] in %s\n",
453	<	j, comp_stamps[stampID]->getID() );
454	<	painCave.isFatal = 1;
455	<	simError();
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	<	else{
489	>
490	>	//create cutoff group for molecule
491	>
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
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	<	sprintf( painCave.errMsg,
503	<	"SimSetup Error: unhandled bend assignment:\n"
504	<	"    -->%s in Bend[%d] in %s\n",
505	<	current_extra->getlhs(),
506	<	j, comp_stamps[stampID]->getID() );
507	<	painCave.isFatal = 1;
508	<	simError();
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	<	current_extra = current_extra->getNext();
539	<	}
540	<	}
315	<
316	<	if( !theBends[j].isGhost ){
317	<
318	<	exI = theBends[j].a;
319	<	exJ = theBends[j].c;
320	<	}
321	<	else{
322	<
323	<	exI = theBends[j].a;
324	<	exJ = theBends[j].b;
325	<	}
326	<
327	<	// exclude_I must always be the smaller of the pair
328	<	if( exI > exJ ){
329	<	tempEx = exI;
330	<	exI = exJ;
331	<	exJ = tempEx;
332	<	}
538	>
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540	>
541		#ifdef IS_MPI
542	<	tempEx = exI;
543	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
544	<	tempEx = exJ;
545	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
546	<
547	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
548	<	#else  // isn't MPI
549	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
550	<	#endif  //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	<	excludeOffset += molInfo.nBends;
556	<
557	<	for(j=0; j<molInfo.nTorsions; j++){
558	<
559	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
560	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
561	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353	<
354	<	exI = theTorsions[j].a;
355	<	exJ = theTorsions[j].d;
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;
362	<	}
363	<	#ifdef IS_MPI
364	<	tempEx = exI;
365	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	<	tempEx = exJ;
367	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368	<
369	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
370	<	#else  // isn't MPI
371	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
372	<	#endif  //is_mpi
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	<	excludeOffset += molInfo.nTorsions;
563	>
564
376	–
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, theTorsions );
571	<
384	<
385	<	info[k].molecules[i].initialize( molInfo );
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	<
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
399	–
400	–	// clean up the forcefield
587
402	–	the_ff->calcRcut();
403	–	the_ff->cleanMe();
404	–
588		}
589
590	<	void SimSetup::initFromBass( void ){
408	<
590	>	void SimSetup::initFromBass(void){
591		int i, j, k;
592		int n_cells;
593		double cellx, celly, cellz;
#	Line 419 | 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 455 | 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,
463	<	j * celly,
464	<	k * cellz );
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
473	<
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	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	<	}
495	<	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 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
510	<
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
517	<
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
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 ){
535	<
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",
551	<	comp_stamps[current_comp]->getID(),
552	<	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();
560	–
561	–	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 576 | 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 585 | 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] ){
589	<
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 611 | 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;
624	<	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		}
648	–
649	–	for(i=0; i<nInfo; i++){
650	–
651	–	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;
678	<	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 683 | 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
697	–
698	–	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;
703	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
708	–	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
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941
942	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
942	>	// check for the temperature set flag
943
944	<	// get some of the tricky things that may still be in the globals
945	<
946	<	double boxVector[3];
947	<	if( globals->haveBox() ){
948	<	boxVector[0] = globals->getBox();
949	<	boxVector[1] = globals->getBox();
950	<	boxVector[2] = globals->getBox();
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	>
952	>	// check for thermodynamic integration
953	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
954	>	info[i].thermIntLambda = globals->getThermIntLambda();
955	>	info[i].thermIntK = globals->getThermIntK();
956	>	info[i].useThermInt = 1;
957
958	<	info[i].setBox( boxVector );
958	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
959	>	info[i].restraint = myRestraint;
960		}
733	–	else if( globals->haveDensity() ){
734	–
735	–	double vol;
736	–	vol = (double)tot_nmol / globals->getDensity();
737	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
738	–	boxVector[1] = boxVector[0];
739	–	boxVector[2] = boxVector[0];
740	–
741	–	info[i].setBox( boxVector );
961		}
962	<	else{
963	<	if( !globals->haveBoxX() ){
745	<	sprintf( painCave.errMsg,
746	<	"SimSetup error, no periodic BoxX size given.\n" );
747	<	painCave.isFatal = 1;
748	<	simError();
749	<	}
750	<	boxVector[0] = globals->getBoxX();
751	<
752	<	if( !globals->haveBoxY() ){
753	<	sprintf( painCave.errMsg,
754	<	"SimSetup error, no periodic BoxY size given.\n" );
755	<	painCave.isFatal = 1;
756	<	simError();
757	<	}
758	<	boxVector[1] = globals->getBoxY();
759	<
760	<	if( !globals->haveBoxZ() ){
761	<	sprintf( painCave.errMsg,
762	<	"SimSetup error, no periodic BoxZ size given.\n" );
763	<	painCave.isFatal = 1;
764	<	simError();
765	<	}
766	<	boxVector[2] = globals->getBoxZ();
767	<
768	<	info[i].setBox( boxVector );
769	<	}
770	<	}
771	<
962	>
963	>	//setup seed for random number generator
964		int seedValue;
773	–	struct timeval now_time_val;
774	–	struct timezone time_zone;
965
966	<	if(globals->haveSeed()){
966	>	if (globals->haveSeed()){
967		seedValue = globals->getSeed();
968	<	}
968	>
969	>	if(seedValue / 1E9 == 0){
970	>	sprintf(painCave.errMsg,
971	>	"Seed for sprng library should contain at least 9 digits\n"
972	>	"OOPSE will generate a seed for user\n");
973	>	painCave.isFatal = 0;
974	>	simError();
975	>
976	>	//using seed generated by system instead of invalid seed set by user
977	>	#ifndef IS_MPI
978	>	seedValue = make_sprng_seed();
979	>	#else
980	>	if (worldRank == 0){
981	>	seedValue = make_sprng_seed();
982	>	}
983	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
984	>	#endif
985	>	}
986	>	}//end of if branch of globals->haveSeed()
987		else{
988	+
989		#ifndef IS_MPI
990	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
990	>	seedValue = make_sprng_seed();
991		#else
992	<	if(worldRank == 0){
993	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
992	>	if (worldRank == 0){
993	>	seedValue = make_sprng_seed();
994		}
995	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
995	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
996		#endif
997	<	}
997	>	}//end of globals->haveSeed()
998
999	<	for(int i = 0; i < nInfo; i++){
999	>	for (int i = 0; i < nInfo; i++){
1000		info[i].setSeed(seedValue);
1001		}
1002	<
1002	>
1003		#ifdef IS_MPI
1004	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1004	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1005		MPIcheckPoint();
1006		#endif // is_mpi
800	–
1007		}
1008
1009
1010	<	void SimSetup::finalInfoCheck( void ){
1010	>	void SimSetup::finalInfoCheck(void){
1011		int index;
1012		int usesDipoles;
1013	+	int usesCharges;
1014		int i;
1015
1016	<	for(i=0; i<nInfo; i++){
1016	>	for (i = 0; i < nInfo; i++){
1017		// check electrostatic parameters
1018	<
1018	>
1019		index = 0;
1020		usesDipoles = 0;
1021	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1021	>	while ((index < info[i].n_atoms) && !usesDipoles){
1022		usesDipoles = (info[i].atoms[index])->hasDipole();
1023		index++;
1024		}
1025	<
1025	>	index = 0;
1026	>	usesCharges = 0;
1027	>	while ((index < info[i].n_atoms) && !usesCharges){
1028	>	usesCharges= (info[i].atoms[index])->hasCharge();
1029	>	index++;
1030	>	}
1031		#ifdef IS_MPI
1032		int myUse = usesDipoles;
1033	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1033	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1034		#endif //is_mpi
1035	<
1036	<	double theEcr, theEst;
1037	<
1038	<	if (globals->getUseRF() ) {
1039	<	info[i].useReactionField = 1;
1035	>
1036	>	double theRcut, theRsw;
1037	>
1038	>	if (globals->haveRcut()) {
1039	>	theRcut = globals->getRcut();
1040	>
1041	>	if (globals->haveRsw())
1042	>	theRsw = globals->getRsw();
1043	>	else
1044	>	theRsw = theRcut;
1045
1046	<	if( !globals->haveECR() ){
1047	<	sprintf( painCave.errMsg,
1048	<	"SimSetup Warning: using default value of 1/2 the smallest "
832	<	"box length for the electrostaticCutoffRadius.\n"
833	<	"I hope you have a very fast processor!\n");
834	<	painCave.isFatal = 0;
835	<	simError();
836	<	double smallest;
837	<	smallest = info[i].boxL[0];
838	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	<	theEcr = 0.5 * smallest;
841	<	} else {
842	<	theEcr = globals->getECR();
843	<	}
1046	>	info[i].setDefaultRcut(theRcut, theRsw);
1047	>
1048	>	} else {
1049
1050	<	if( !globals->haveEST() ){
1051	<	sprintf( painCave.errMsg,
1052	<	"SimSetup Warning: using default value of 0.05 * the "
1053	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1054	<	);
1055	<	painCave.isFatal = 0;
1056	<	simError();
852	<	theEst = 0.05 * theEcr;
853	<	} else {
854	<	theEst= globals->getEST();
855	<	}
1050	>	the_ff->calcRcut();
1051	>	theRcut = info[i].getRcut();
1052	>
1053	>	if (globals->haveRsw())
1054	>	theRsw = globals->getRsw();
1055	>	else
1056	>	theRsw = theRcut;
1057
1058	<	info[i].setEcr( theEcr, theEst );
1058	>	info[i].setDefaultRcut(theRcut, theRsw);
1059	>	}
1060	>
1061	>	if (globals->getUseRF()){
1062	>	info[i].useReactionField = 1;
1063
1064	<	if(!globals->haveDielectric() ){
1065	<	sprintf( painCave.errMsg,
1066	<	"SimSetup Error: You are trying to use Reaction Field without"
1067	<	"setting a dielectric constant!\n"
1068	<	);
1069	<	painCave.isFatal = 1;
1070	<	simError();
1064	>	if (!globals->haveRcut()){
1065	>	sprintf(painCave.errMsg,
1066	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067	>	"\tOOPSE will use a default value of 15.0 angstroms"
1068	>	"\tfor the cutoffRadius.\n");
1069	>	painCave.isFatal = 0;
1070	>	simError();
1071	>	theRcut = 15.0;
1072		}
1073	<	info[i].dielectric = globals->getDielectric();
1074	<	}
869	<	else {
870	<	if (usesDipoles) {
871	<
872	<	if( !globals->haveECR() ){
873	<	sprintf( painCave.errMsg,
874	<	"SimSetup Warning: using default value of 1/2 the smallest "
875	<	"box length for the electrostaticCutoffRadius.\n"
876	<	"I hope you have a very fast processor!\n");
877	<	painCave.isFatal = 0;
878	<	simError();
879	<	double smallest;
880	<	smallest = info[i].boxL[0];
881	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	<	theEcr = 0.5 * smallest;
884	<	} else {
885	<	theEcr = globals->getECR();
886	<	}
887	<
888	<	if( !globals->haveEST() ){
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Warning: using default value of 0.05 * the "
891	<	"electrostaticCutoffRadius for the "
892	<	"electrostaticSkinThickness\n"
893	<	);
894	<	painCave.isFatal = 0;
895	<	simError();
896	<	theEst = 0.05 * theEcr;
897	<	} else {
898	<	theEst= globals->getEST();
899	<	}
900	<
901	<	info[i].setEcr( theEcr, theEst );
1073	>	else{
1074	>	theRcut = globals->getRcut();
1075		}
903	–	}
904	–	}
1076
1077	+	if (!globals->haveRsw()){
1078	+	sprintf(painCave.errMsg,
1079	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1080	+	"\tOOPSE will use a default value of\n"
1081	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082	+	painCave.isFatal = 0;
1083	+	simError();
1084	+	theRsw = 0.95 * theRcut;
1085	+	}
1086	+	else{
1087	+	theRsw = globals->getRsw();
1088	+	}
1089	+
1090	+	info[i].setDefaultRcut(theRcut, theRsw);
1091	+
1092	+	if (!globals->haveDielectric()){
1093	+	sprintf(painCave.errMsg,
1094	+	"SimSetup Error: No Dielectric constant was set.\n"
1095	+	"\tYou are trying to use Reaction Field without"
1096	+	"\tsetting a dielectric constant!\n");
1097	+	painCave.isFatal = 1;
1098	+	simError();
1099	+	}
1100	+	info[i].dielectric = globals->getDielectric();
1101	+	}
1102	+	else{
1103	+	if (usesDipoles || usesCharges){
1104	+
1105	+	if (!globals->haveRcut()){
1106	+	sprintf(painCave.errMsg,
1107	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1108	+	"\tOOPSE will use a default value of 15.0 angstroms"
1109	+	"\tfor the cutoffRadius.\n");
1110	+	painCave.isFatal = 0;
1111	+	simError();
1112	+	theRcut = 15.0;
1113	+	}
1114	+	else{
1115	+	theRcut = globals->getRcut();
1116	+	}
1117	+
1118	+	if (!globals->haveRsw()){
1119	+	sprintf(painCave.errMsg,
1120	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1121	+	"\tOOPSE will use a default value of\n"
1122	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1123	+	painCave.isFatal = 0;
1124	+	simError();
1125	+	theRsw = 0.95 * theRcut;
1126	+	}
1127	+	else{
1128	+	theRsw = globals->getRsw();
1129	+	}
1130	+
1131	+	info[i].setDefaultRcut(theRcut, theRsw);
1132	+
1133	+	}
1134	+	}
1135	+	}
1136		#ifdef IS_MPI
1137	<	strcpy( checkPointMsg, "post processing checks out" );
1137	>	strcpy(checkPointMsg, "post processing checks out");
1138		MPIcheckPoint();
1139		#endif // is_mpi
1140
1141	+	// clean up the forcefield
1142	+	the_ff->cleanMe();
1143		}
912	–
913	–	void SimSetup::initSystemCoords( void ){
914	–	int i;
1144
1145	+	void SimSetup::initSystemCoords(void){
1146	+	int i;
1147	+
1148		char* inName;
1149
1150	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1150	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1151
1152	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1153	<
1154	<	if( globals->haveInitialConfig() ){
1155	<
1152	>	for (i = 0; i < info[0].n_atoms; i++)
1153	>	info[0].atoms[i]->setCoords();
1154	>
1155	>	if (globals->haveInitialConfig()){
1156		InitializeFromFile* fileInit;
1157		#ifdef IS_MPI // is_mpi
1158	<	if( worldRank == 0 ){
1158	>	if (worldRank == 0){
1159		#endif //is_mpi
1160		inName = globals->getInitialConfig();
1161	<	double* tempDouble = new double[1000000];
930	<	fileInit = new InitializeFromFile( inName );
1161	>	fileInit = new InitializeFromFile(inName);
1162		#ifdef IS_MPI
1163	<	}else fileInit = new InitializeFromFile( NULL );
1163	>	}
1164	>	else
1165	>	fileInit = new InitializeFromFile(NULL);
1166		#endif
1167	<	fileInit->readInit( info ); // default velocities on
1168	<
1167	>	fileInit->readInit(info); // default velocities on
1168	>
1169		delete fileInit;
1170		}
1171		else{
1172
940	–	#ifdef IS_MPI
941	–
1173		// no init from bass
1174
1175	<	sprintf( painCave.errMsg,
1176	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1177	<	painCave.isFatal;
1175	>	sprintf(painCave.errMsg,
1176	>	"Cannot intialize a simulation without an initial configuration file.\n");
1177	>	painCave.isFatal = 1;;
1178		simError();
1179
949	–	#else
950	–
951	–	initFromBass();
952	–
953	–
954	–	#endif
1180		}
1181	<
1181	>
1182		#ifdef IS_MPI
1183	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1183	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1184		MPIcheckPoint();
1185		#endif // is_mpi
961	–
1186		}
1187
1188
1189	<	void SimSetup::makeOutNames( void ){
966	<
1189	>	void SimSetup::makeOutNames(void){
1190		int k;
1191
969	–
970	–	for(k=0; k<nInfo; k++){
1192
1193	+	for (k = 0; k < nInfo; k++){
1194		#ifdef IS_MPI
1195	<	if( worldRank == 0 ){
1195	>	if (worldRank == 0){
1196		#endif // is_mpi
1197	<
1198	<	if( globals->haveFinalConfig() ){
1199	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1197	>
1198	>	if (globals->haveFinalConfig()){
1199	>	strcpy(info[k].finalName, globals->getFinalConfig());
1200		}
1201		else{
1202	<	strcpy( info[k].finalName, inFileName );
1203	<	char* endTest;
1204	<	int nameLength = strlen( info[k].finalName );
1205	<	endTest = &(info[k].finalName[nameLength - 5]);
1206	<	if( !strcmp( endTest, ".bass" ) ){
1207	<	strcpy( endTest, ".eor" );
1208	<	}
1209	<	else if( !strcmp( endTest, ".BASS" ) ){
1210	<	strcpy( endTest, ".eor" );
1211	<	}
1212	<	else{
1213	<	endTest = &(info[k].finalName[nameLength - 4]);
1214	<	if( !strcmp( endTest, ".bss" ) ){
1215	<	strcpy( endTest, ".eor" );
1216	<	}
1217	<	else if( !strcmp( endTest, ".mdl" ) ){
1218	<	strcpy( endTest, ".eor" );
1219	<	}
1220	<	else{
1221	<	strcat( info[k].finalName, ".eor" );
1222	<	}
1223	<	}
1224	<	}
1225	<
1226	<	// make the sample and status out names
1227	<
1228	<	strcpy( info[k].sampleName, inFileName );
1202	>	strcpy(info[k].finalName, inFileName);
1203	>	char* endTest;
1204	>	int nameLength = strlen(info[k].finalName);
1205	>	endTest = &(info[k].finalName[nameLength - 5]);
1206	>	if (!strcmp(endTest, ".bass")){
1207	>	strcpy(endTest, ".eor");
1208	>	}
1209	>	else if (!strcmp(endTest, ".BASS")){
1210	>	strcpy(endTest, ".eor");
1211	>	}
1212	>	else{
1213	>	endTest = &(info[k].finalName[nameLength - 4]);
1214	>	if (!strcmp(endTest, ".bss")){
1215	>	strcpy(endTest, ".eor");
1216	>	}
1217	>	else if (!strcmp(endTest, ".mdl")){
1218	>	strcpy(endTest, ".eor");
1219	>	}
1220	>	else{
1221	>	strcat(info[k].finalName, ".eor");
1222	>	}
1223	>	}
1224	>	}
1225	>
1226	>	// make the sample and status out names
1227	>
1228	>	strcpy(info[k].sampleName, inFileName);
1229		char* endTest;
1230	<	int nameLength = strlen( info[k].sampleName );
1230	>	int nameLength = strlen(info[k].sampleName);
1231		endTest = &(info[k].sampleName[nameLength - 5]);
1232	<	if( !strcmp( endTest, ".bass" ) ){
1233	<	strcpy( endTest, ".dump" );
1232	>	if (!strcmp(endTest, ".bass")){
1233	>	strcpy(endTest, ".dump");
1234		}
1235	<	else if( !strcmp( endTest, ".BASS" ) ){
1236	<	strcpy( endTest, ".dump" );
1235	>	else if (!strcmp(endTest, ".BASS")){
1236	>	strcpy(endTest, ".dump");
1237		}
1238		else{
1239	<	endTest = &(info[k].sampleName[nameLength - 4]);
1240	<	if( !strcmp( endTest, ".bss" ) ){
1241	<	strcpy( endTest, ".dump" );
1242	<	}
1243	<	else if( !strcmp( endTest, ".mdl" ) ){
1244	<	strcpy( endTest, ".dump" );
1245	<	}
1246	<	else{
1247	<	strcat( info[k].sampleName, ".dump" );
1248	<	}
1239	>	endTest = &(info[k].sampleName[nameLength - 4]);
1240	>	if (!strcmp(endTest, ".bss")){
1241	>	strcpy(endTest, ".dump");
1242	>	}
1243	>	else if (!strcmp(endTest, ".mdl")){
1244	>	strcpy(endTest, ".dump");
1245	>	}
1246	>	else{
1247	>	strcat(info[k].sampleName, ".dump");
1248	>	}
1249		}
1250	<
1251	<	strcpy( info[k].statusName, inFileName );
1252	<	nameLength = strlen( info[k].statusName );
1250	>
1251	>	strcpy(info[k].statusName, inFileName);
1252	>	nameLength = strlen(info[k].statusName);
1253		endTest = &(info[k].statusName[nameLength - 5]);
1254	<	if( !strcmp( endTest, ".bass" ) ){
1255	<	strcpy( endTest, ".stat" );
1254	>	if (!strcmp(endTest, ".bass")){
1255	>	strcpy(endTest, ".stat");
1256		}
1257	<	else if( !strcmp( endTest, ".BASS" ) ){
1258	<	strcpy( endTest, ".stat" );
1257	>	else if (!strcmp(endTest, ".BASS")){
1258	>	strcpy(endTest, ".stat");
1259		}
1260		else{
1261	<	endTest = &(info[k].statusName[nameLength - 4]);
1262	<	if( !strcmp( endTest, ".bss" ) ){
1263	<	strcpy( endTest, ".stat" );
1264	<	}
1265	<	else if( !strcmp( endTest, ".mdl" ) ){
1266	<	strcpy( endTest, ".stat" );
1267	<	}
1268	<	else{
1269	<	strcat( info[k].statusName, ".stat" );
1270	<	}
1261	>	endTest = &(info[k].statusName[nameLength - 4]);
1262	>	if (!strcmp(endTest, ".bss")){
1263	>	strcpy(endTest, ".stat");
1264	>	}
1265	>	else if (!strcmp(endTest, ".mdl")){
1266	>	strcpy(endTest, ".stat");
1267	>	}
1268	>	else{
1269	>	strcat(info[k].statusName, ".stat");
1270	>	}
1271		}
1272	<
1272	>
1273	>	strcpy(info[k].rawPotName, inFileName);
1274	>	nameLength = strlen(info[k].rawPotName);
1275	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1276	>	if (!strcmp(endTest, ".bass")){
1277	>	strcpy(endTest, ".raw");
1278	>	}
1279	>	else if (!strcmp(endTest, ".BASS")){
1280	>	strcpy(endTest, ".raw");
1281	>	}
1282	>	else{
1283	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1284	>	if (!strcmp(endTest, ".bss")){
1285	>	strcpy(endTest, ".raw");
1286	>	}
1287	>	else if (!strcmp(endTest, ".mdl")){
1288	>	strcpy(endTest, ".raw");
1289	>	}
1290	>	else{
1291	>	strcat(info[k].rawPotName, ".raw");
1292	>	}
1293	>	}
1294	>
1295		#ifdef IS_MPI
1296	+
1297		}
1298		#endif // is_mpi
1299		}
1300		}
1301
1302
1303	<	void SimSetup::sysObjectsCreation( void ){
1304	<
1305	<	int i,k;
1061	<
1303	>	void SimSetup::sysObjectsCreation(void){
1304	>	int i, k;
1305	>
1306		// create the forceField
1307
1308		createFF();
#	Line 1073 | Line 1317 | void SimSetup::sysObjectsCreation( void ){
1317
1318		#ifdef IS_MPI
1319		// divide the molecules among the processors
1320	<
1320	>
1321		mpiMolDivide();
1322		#endif //is_mpi
1323	<
1323	>
1324		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1325	<
1325	>
1326		makeSysArrays();
1327
1328		// make and initialize the molecules (all but atomic coordinates)
1329	<
1329	>
1330		makeMolecules();
1331	<
1332	<	for(k=0; k<nInfo; k++){
1331	>
1332	>	for (k = 0; k < nInfo; k++){
1333		info[k].identArray = new int[info[k].n_atoms];
1334	<	for(i=0; i<info[k].n_atoms; i++){
1334	>	for (i = 0; i < info[k].n_atoms; i++){
1335		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1336		}
1337		}
1338		}
1339
1340
1341	<	void SimSetup::createFF( void ){
1341	>	void SimSetup::createFF(void){
1342	>	switch (ffCase){
1343	>	case FF_DUFF:
1344	>	the_ff = new DUFF();
1345	>	break;
1346
1347	<	switch( ffCase ){
1347	>	case FF_LJ:
1348	>	the_ff = new LJFF();
1349	>	break;
1350
1351	<	case FF_DUFF:
1352	<	the_ff = new DUFF();
1353	<	break;
1351	>	case FF_EAM:
1352	>	the_ff = new EAM_FF();
1353	>	break;
1354
1355	<	case FF_LJ:
1356	<	the_ff = new LJFF();
1357	<	break;
1355	>	case FF_H2O:
1356	>	the_ff = new WATER();
1357	>	break;
1358
1359	<	case FF_EAM:
1360	<	the_ff = new EAM_FF();
1361	<	break;
1362	<
1363	<	default:
1114	<	sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	<	painCave.isFatal = 1;
1117	<	simError();
1359	>	default:
1360	>	sprintf(painCave.errMsg,
1361	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1362	>	painCave.isFatal = 1;
1363	>	simError();
1364		}
1365
1366		#ifdef IS_MPI
1367	<	strcpy( checkPointMsg, "ForceField creation successful" );
1367	>	strcpy(checkPointMsg, "ForceField creation successful");
1368		MPIcheckPoint();
1369		#endif // is_mpi
1124	–
1370		}
1371
1372
1373	<	void SimSetup::compList( void ){
1129	<
1373	>	void SimSetup::compList(void){
1374		int i;
1375		char* id;
1376		LinkedMolStamp* headStamp = new LinkedMolStamp();
1377		LinkedMolStamp* currentStamp = NULL;
1378	<	comp_stamps = new MoleculeStamp*[n_components];
1378	>	comp_stamps = new MoleculeStamp * [n_components];
1379	>	bool haveCutoffGroups;
1380	>
1381	>	haveCutoffGroups = false;
1382
1383		// make an array of molecule stamps that match the components used.
1384		// also extract the used stamps out into a separate linked list
1385	<
1386	<	for(i=0; i<nInfo; i++){
1385	>
1386	>	for (i = 0; i < nInfo; i++){
1387		info[i].nComponents = n_components;
1388		info[i].componentsNmol = components_nmol;
1389		info[i].compStamps = comp_stamps;
1390		info[i].headStamp = headStamp;
1391		}
1145	–
1392
1147	–	for( i=0; i<n_components; i++ ){
1393
1394	+	for (i = 0; i < n_components; i++){
1395		id = the_components[i]->getType();
1396		comp_stamps[i] = NULL;
1397	<
1397	>
1398		// check to make sure the component isn't already in the list
1399
1400	<	comp_stamps[i] = headStamp->match( id );
1401	<	if( comp_stamps[i] == NULL ){
1156	<
1400	>	comp_stamps[i] = headStamp->match(id);
1401	>	if (comp_stamps[i] == NULL){
1402		// extract the component from the list;
1403	<
1404	<	currentStamp = stamps->extractMolStamp( id );
1405	<	if( currentStamp == NULL ){
1406	<	sprintf( painCave.errMsg,
1407	<	"SimSetup error: Component \"%s\" was not found in the "
1408	<	"list of declared molecules\n",
1409	<	id );
1410	<	painCave.isFatal = 1;
1411	<	simError();
1403	>
1404	>	currentStamp = stamps->extractMolStamp(id);
1405	>	if (currentStamp == NULL){
1406	>	sprintf(painCave.errMsg,
1407	>	"SimSetup error: Component \"%s\" was not found in the "
1408	>	"list of declared molecules\n",
1409	>	id);
1410	>	painCave.isFatal = 1;
1411	>	simError();
1412		}
1413	<
1414	<	headStamp->add( currentStamp );
1415	<	comp_stamps[i] = headStamp->match( id );
1413	>
1414	>	headStamp->add(currentStamp);
1415	>	comp_stamps[i] = headStamp->match(id);
1416		}
1417	+
1418	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1419	+	haveCutoffGroups = true;
1420		}
1421	+
1422	+	for (i = 0; i < nInfo; i++)
1423	+	info[i].haveCutoffGroups = haveCutoffGroups;
1424
1425		#ifdef IS_MPI
1426	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1426	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1427		MPIcheckPoint();
1428		#endif // is_mpi
1429	+	}
1430
1431	+	void SimSetup::calcSysValues(void){
1432	+	int i;
1433
1434	<	}
1434	>	int* molMembershipArray;
1435
1182	–	void SimSetup::calcSysValues( void ){
1183	–	int i, j, k;
1184	–
1185	–	int *molMembershipArray;
1186	–
1436		tot_atoms = 0;
1437		tot_bonds = 0;
1438		tot_bends = 0;
1439		tot_torsions = 0;
1440	<	for( i=0; i<n_components; i++ ){
1441	<
1442	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1443	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1444	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1440	>	tot_rigid = 0;
1441	>	for (i = 0; i < n_components; i++){
1442	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1443	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1444	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1445		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1446	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1447		}
1448
1449		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1450		molMembershipArray = new int[tot_atoms];
1451	<
1452	<	for(i=0; i<nInfo; i++){
1451	>
1452	>	for (i = 0; i < nInfo; i++){
1453		info[i].n_atoms = tot_atoms;
1454		info[i].n_bonds = tot_bonds;
1455		info[i].n_bends = tot_bends;
1456		info[i].n_torsions = tot_torsions;
1457		info[i].n_SRI = tot_SRI;
1458		info[i].n_mol = tot_nmol;
1459	<
1459	>
1460		info[i].molMembershipArray = molMembershipArray;
1461	<	}
1461	>	}
1462		}
1463
1464		#ifdef IS_MPI
1465
1466	<	void SimSetup::mpiMolDivide( void ){
1217	<
1466	>	void SimSetup::mpiMolDivide(void){
1467		int i, j, k;
1468		int localMol, allMol;
1469		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1470	+	int local_rigid;
1471	+	vector<int> globalMolIndex;
1472
1473	<	mpiSim = new mpiSimulation( info );
1223	<
1224	<	globalIndex = mpiSim->divideLabor();
1473	>	mpiSim = new mpiSimulation(info);
1474
1475	+	mpiSim->divideLabor();
1476	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1477	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1478	+
1479		// set up the local variables
1480	<
1480	>
1481		mol2proc = mpiSim->getMolToProcMap();
1482		molCompType = mpiSim->getMolComponentType();
1483	<
1483	>
1484		allMol = 0;
1485		localMol = 0;
1486		local_atoms = 0;
1487		local_bonds = 0;
1488		local_bends = 0;
1489		local_torsions = 0;
1490	<	globalAtomIndex = 0;
1490	>	local_rigid = 0;
1491	>	globalAtomCounter = 0;
1492
1493	<
1494	<	for( i=0; i<n_components; i++ ){
1495	<
1496	<	for( j=0; j<components_nmol[i]; j++ ){
1497	<
1498	<	if( mol2proc[allMol] == worldRank ){
1499	<
1500	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1501	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1493	>	for (i = 0; i < n_components; i++){
1494	>	for (j = 0; j < components_nmol[i]; j++){
1495	>	if (mol2proc[allMol] == worldRank){
1496	>	local_atoms += comp_stamps[i]->getNAtoms();
1497	>	local_bonds += comp_stamps[i]->getNBonds();
1498	>	local_bends += comp_stamps[i]->getNBends();
1499	>	local_torsions += comp_stamps[i]->getNTorsions();
1500	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1501	>	localMol++;
1502		}
1503	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1504	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1505	<	globalAtomIndex++;
1503	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1504	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1505	>	globalAtomCounter++;
1506		}
1507
1508	<	allMol++;
1508	>	allMol++;
1509		}
1510		}
1511		local_SRI = local_bonds + local_bends + local_torsions;
1512	<
1512	>
1513		info[0].n_atoms = mpiSim->getMyNlocal();
1514
1515	<	if( local_atoms != info[0].n_atoms ){
1516	<	sprintf( painCave.errMsg,
1517	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1518	<	" localAtom (%d) are not equal.\n",
1519	<	info[0].n_atoms,
1520	<	local_atoms );
1515	>
1516	>	if (local_atoms != info[0].n_atoms){
1517	>	sprintf(painCave.errMsg,
1518	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1519	>	"\tlocalAtom (%d) are not equal.\n",
1520	>	info[0].n_atoms, local_atoms);
1521		painCave.isFatal = 1;
1522		simError();
1523		}
#	Line 1277 | Line 1528 | void SimSetup::mpiMolDivide( void ){
1528		info[0].n_SRI = local_SRI;
1529		info[0].n_mol = localMol;
1530
1531	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1531	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1532		MPIcheckPoint();
1533		}
1534	<
1534	>
1535		#endif // is_mpi
1536
1537
1538	<	void SimSetup::makeSysArrays( void ){
1539	<	int i, j, k, l;
1538	>	void SimSetup::makeSysArrays(void){
1539	>
1540	>	#ifndef IS_MPI
1541	>	int k, j;
1542	>	#endif // is_mpi
1543	>	int i, l;
1544
1545		Atom** the_atoms;
1546		Molecule* the_molecules;
1292	–	Exclude** the_excludes;
1547
1548	<
1295	<	for(l=0; l<nInfo; l++){
1296	<
1548	>	for (l = 0; l < nInfo; l++){
1549		// create the atom and short range interaction arrays
1550	<
1551	<	the_atoms = new Atom*[info[l].n_atoms];
1550	>
1551	>	the_atoms = new Atom * [info[l].n_atoms];
1552		the_molecules = new Molecule[info[l].n_mol];
1553		int molIndex;
1554
1555		// initialize the molecule's stampID's
1556	<
1556	>
1557		#ifdef IS_MPI
1558	<
1559	<
1558	>
1559	>
1560		molIndex = 0;
1561	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1562	<
1563	<	if(mol2proc[i] == worldRank ){
1564	<	the_molecules[molIndex].setStampID( molCompType[i] );
1565	<	the_molecules[molIndex].setMyIndex( molIndex );
1566	<	the_molecules[molIndex].setGlobalIndex( i );
1315	<	molIndex++;
1561	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1562	>	if (mol2proc[i] == worldRank){
1563	>	the_molecules[molIndex].setStampID(molCompType[i]);
1564	>	the_molecules[molIndex].setMyIndex(molIndex);
1565	>	the_molecules[molIndex].setGlobalIndex(i);
1566	>	molIndex++;
1567		}
1568		}
1569	<
1569	>
1570		#else // is_mpi
1571	<
1571	>
1572		molIndex = 0;
1573	<	globalAtomIndex = 0;
1574	<	for(i=0; i<n_components; i++){
1575	<	for(j=0; j<components_nmol[i]; j++ ){
1576	<	the_molecules[molIndex].setStampID( i );
1577	<	the_molecules[molIndex].setMyIndex( molIndex );
1578	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1579	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1580	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1581	<	globalAtomIndex++;
1582	<	}
1583	<	molIndex++;
1573	>	globalAtomCounter = 0;
1574	>	for (i = 0; i < n_components; i++){
1575	>	for (j = 0; j < components_nmol[i]; j++){
1576	>	the_molecules[molIndex].setStampID(i);
1577	>	the_molecules[molIndex].setMyIndex(molIndex);
1578	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1579	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1580	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1581	>	globalAtomCounter++;
1582	>	}
1583	>	molIndex++;
1584		}
1585		}
1335	–
1336	–
1337	–	#endif // is_mpi
1586
1587
1588	<	if( info[l].n_SRI ){
1341	<
1342	<	Exclude::createArray(info[l].n_SRI);
1343	<	the_excludes = new Exclude*[info[l].n_SRI];
1344	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1345	<	the_excludes[ex] = new Exclude(ex);
1346	<	}
1347	<	info[l].globalExcludes = new int;
1348	<	info[l].n_exclude = info[l].n_SRI;
1349	<	}
1350	<	else{
1351	<
1352	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1354	<	the_excludes[0] = new Exclude(0);
1355	<	the_excludes[0]->setPair( 0,0 );
1356	<	info[l].globalExcludes = new int;
1357	<	info[l].globalExcludes[0] = 0;
1358	<	info[l].n_exclude = 0;
1359	<	}
1588	>	#endif // is_mpi
1589
1590	+	info[l].globalExcludes = new int;
1591	+	info[l].globalExcludes[0] = 0;
1592	+
1593		// set the arrays into the SimInfo object
1594
1595		info[l].atoms = the_atoms;
1596		info[l].molecules = the_molecules;
1597		info[l].nGlobalExcludes = 0;
1366	–	info[l].excludes = the_excludes;
1367	–
1368	–	the_ff->setSimInfo( info );
1598
1599	+	the_ff->setSimInfo(info);
1600		}
1601		}
1602
1603	<	void SimSetup::makeIntegrator( void ){
1374	<
1603	>	void SimSetup::makeIntegrator(void){
1604		int k;
1605
1606	<	NVT<RealIntegrator>*  myNVT = NULL;
1607	<	NPTi<RealIntegrator>* myNPTi = NULL;
1608	<	NPTf<RealIntegrator>* myNPTf = NULL;
1609	<	NPTim<RealIntegrator>* myNPTim = NULL;
1610	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1611	<
1612	<	for(k=0; k<nInfo; k++){
1613	<
1614	<	switch( ensembleCase ){
1615	<
1616	<	case NVE_ENS:
1617	<	if (globals->haveZconstraints()){
1618	<	setupZConstraint(info[k]);
1619	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1620	<	}
1606	>	NVE<RealIntegrator>* myNVE = NULL;
1607	>	NVT<RealIntegrator>* myNVT = NULL;
1608	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1609	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1610	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1611	>
1612	>	for (k = 0; k < nInfo; k++){
1613	>	switch (ensembleCase){
1614	>	case NVE_ENS:
1615	>	if (globals->haveZconstraints()){
1616	>	setupZConstraint(info[k]);
1617	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1618	>	}
1619	>	else{
1620	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1621	>	}
1622	>
1623	>	info->the_integrator = myNVE;
1624	>	break;
1625
1626	<	else
1627	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1628	<	break;
1629	<
1630	<	case NVT_ENS:
1631	<	if (globals->haveZconstraints()){
1632	<	setupZConstraint(info[k]);
1400	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	<	}
1402	<	else
1403	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1626	>	case NVT_ENS:
1627	>	if (globals->haveZconstraints()){
1628	>	setupZConstraint(info[k]);
1629	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1630	>	}
1631	>	else
1632	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1633
1634		myNVT->setTargetTemp(globals->getTargetTemp());
1635	<
1636	<	if (globals->haveTauThermostat())
1635	>
1636	>	if (globals->haveTauThermostat())
1637		myNVT->setTauThermostat(globals->getTauThermostat());
1638	<
1639	<	else {
1640	<	sprintf( painCave.errMsg,
1641	<	"SimSetup error: If you use the NVT\n"
1413	<	"    ensemble, you must set tauThermostat.\n");
1638	>	else{
1639	>	sprintf(painCave.errMsg,
1640	>	"SimSetup error: If you use the NVT\n"
1641	>	"\tensemble, you must set tauThermostat.\n");
1642		painCave.isFatal = 1;
1643		simError();
1644		}
1645	+
1646	+	info->the_integrator = myNVT;
1647		break;
1418	–
1419	–	case NPTi_ENS:
1420	–	if (globals->haveZconstraints()){
1421	–	setupZConstraint(info[k]);
1422	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	–	}
1424	–	else
1425	–	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1648
1649	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1650	<
1651	<	if (globals->haveTargetPressure())
1652	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1653	<	else {
1654	<	sprintf( painCave.errMsg,
1655	<	"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	<	myNPTi->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	<	}
1448	<
1449	<	if( globals->haveTauBarostat() )
1450	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	<	else{
1452	<	sprintf( painCave.errMsg,
1453	<	"SimSetup error: If you use an NPT\n"
1454	<	"    ensemble, you must set tauBarostat.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1458	<	break;
1459	<
1460	<	case NPTf_ENS:
1461	<	if (globals->haveZconstraints()){
1462	<	setupZConstraint(info[k]);
1463	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	<	}
1465	<	else
1466	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1649	>	case NPTi_ENS:
1650	>	if (globals->haveZconstraints()){
1651	>	setupZConstraint(info[k]);
1652	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1653	>	}
1654	>	else
1655	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1656
1657	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1658	<
1659	<	if (globals->haveTargetPressure())
1660	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1661	<	else {
1662	<	sprintf( painCave.errMsg,
1657	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1658	>
1659	>	if (globals->haveTargetPressure())
1660	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1661	>	else{
1662	>	sprintf(painCave.errMsg,
1663		"SimSetup error: If you use a constant pressure\n"
1664	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1665	<	painCave.isFatal = 1;
1666	<	simError();
1667	<	}
1668	<
1669	<	if( globals->haveTauThermostat() )
1670	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1671	<	else{
1672	<	sprintf( painCave.errMsg,
1484	<	"SimSetup error: If you use an NPT\n"
1485	<	"    ensemble, you must set tauThermostat.\n");
1486	<	painCave.isFatal = 1;
1487	<	simError();
1488	<	}
1489	<
1490	<	if( globals->haveTauBarostat() )
1491	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	<	else{
1493	<	sprintf( painCave.errMsg,
1664	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1665	>	painCave.isFatal = 1;
1666	>	simError();
1667	>	}
1668	>
1669	>	if (globals->haveTauThermostat())
1670	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1671	>	else{
1672	>	sprintf(painCave.errMsg,
1673		"SimSetup error: If you use an NPT\n"
1674	<	"    ensemble, you must set tauBarostat.\n");
1675	<	painCave.isFatal = 1;
1676	<	simError();
1677	<	}
1499	<	break;
1500	<
1501	<	case NPTim_ENS:
1502	<	if (globals->haveZconstraints()){
1503	<	setupZConstraint(info[k]);
1504	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	<	}
1506	<	else
1507	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1674	>	"\tensemble, you must set tauThermostat.\n");
1675	>	painCave.isFatal = 1;
1676	>	simError();
1677	>	}
1678
1679	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1680	<
1681	<	if (globals->haveTargetPressure())
1682	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	<	else {
1514	<	sprintf( painCave.errMsg,
1515	<	"SimSetup error: If you use a constant pressure\n"
1516	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	<	painCave.isFatal = 1;
1518	<	simError();
1519	<	}
1520	<
1521	<	if( globals->haveTauThermostat() )
1522	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	<	else{
1524	<	sprintf( painCave.errMsg,
1679	>	if (globals->haveTauBarostat())
1680	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1681	>	else{
1682	>	sprintf(painCave.errMsg,
1683		"SimSetup error: If you use an NPT\n"
1684	<	"    ensemble, you must set tauThermostat.\n");
1685	<	painCave.isFatal = 1;
1686	<	simError();
1687	<	}
1530	<
1531	<	if( globals->haveTauBarostat() )
1532	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	<	else{
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use an NPT\n"
1536	<	"    ensemble, you must set tauBarostat.\n");
1537	<	painCave.isFatal = 1;
1538	<	simError();
1539	<	}
1540	<	break;
1541	<
1542	<	case NPTfm_ENS:
1543	<	if (globals->haveZconstraints()){
1544	<	setupZConstraint(info[k]);
1545	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	<	}
1547	<	else
1548	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1684	>	"\tensemble, you must set tauBarostat.\n");
1685	>	painCave.isFatal = 1;
1686	>	simError();
1687	>	}
1688
1689	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1689	>	info->the_integrator = myNPTi;
1690	>	break;
1691
1692	<	if (globals->haveTargetPressure())
1693	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1694	<	else {
1695	<	sprintf( painCave.errMsg,
1696	<	"SimSetup error: If you use a constant pressure\n"
1697	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1698	<	painCave.isFatal = 1;
1559	<	simError();
1560	<	}
1692	>	case NPTf_ENS:
1693	>	if (globals->haveZconstraints()){
1694	>	setupZConstraint(info[k]);
1695	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1696	>	}
1697	>	else
1698	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1699
1700	<	if( globals->haveTauThermostat() )
1701	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1702	<	else{
1703	<	sprintf( painCave.errMsg,
1700	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1701	>
1702	>	if (globals->haveTargetPressure())
1703	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1704	>	else{
1705	>	sprintf(painCave.errMsg,
1706	>	"SimSetup error: If you use a constant pressure\n"
1707	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1708	>	painCave.isFatal = 1;
1709	>	simError();
1710	>	}
1711	>
1712	>	if (globals->haveTauThermostat())
1713	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1714	>
1715	>	else{
1716	>	sprintf(painCave.errMsg,
1717		"SimSetup error: If you use an NPT\n"
1718	<	"    ensemble, you must set tauThermostat.\n");
1719	<	painCave.isFatal = 1;
1720	<	simError();
1721	<	}
1718	>	"\tensemble, you must set tauThermostat.\n");
1719	>	painCave.isFatal = 1;
1720	>	simError();
1721	>	}
1722
1723	<	if( globals->haveTauBarostat() )
1724	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1725	<	else{
1726	<	sprintf( painCave.errMsg,
1723	>	if (globals->haveTauBarostat())
1724	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1725	>
1726	>	else{
1727	>	sprintf(painCave.errMsg,
1728		"SimSetup error: If you use an NPT\n"
1729	<	"    ensemble, you must set tauBarostat.\n");
1729	>	"\tensemble, you must set tauBarostat.\n");
1730	>	painCave.isFatal = 1;
1731	>	simError();
1732	>	}
1733	>
1734	>	info->the_integrator = myNPTf;
1735	>	break;
1736	>
1737	>	case NPTxyz_ENS:
1738	>	if (globals->haveZconstraints()){
1739	>	setupZConstraint(info[k]);
1740	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1741	>	}
1742	>	else
1743	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1744	>
1745	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1746	>
1747	>	if (globals->haveTargetPressure())
1748	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1749	>	else{
1750	>	sprintf(painCave.errMsg,
1751	>	"SimSetup error: If you use a constant pressure\n"
1752	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1753	>	painCave.isFatal = 1;
1754	>	simError();
1755	>	}
1756	>
1757	>	if (globals->haveTauThermostat())
1758	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1759	>	else{
1760	>	sprintf(painCave.errMsg,
1761	>	"SimSetup error: If you use an NPT\n"
1762	>	"\tensemble, you must set tauThermostat.\n");
1763	>	painCave.isFatal = 1;
1764	>	simError();
1765	>	}
1766	>
1767	>	if (globals->haveTauBarostat())
1768	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1769	>	else{
1770	>	sprintf(painCave.errMsg,
1771	>	"SimSetup error: If you use an NPT\n"
1772	>	"\tensemble, you must set tauBarostat.\n");
1773	>	painCave.isFatal = 1;
1774	>	simError();
1775	>	}
1776	>
1777	>	info->the_integrator = myNPTxyz;
1778	>	break;
1779	>
1780	>	default:
1781	>	sprintf(painCave.errMsg,
1782	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1783		painCave.isFatal = 1;
1784		simError();
1580	–	}
1581	–	break;
1582	–
1583	–	default:
1584	–	sprintf( painCave.errMsg,
1585	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586	–	painCave.isFatal = 1;
1587	–	simError();
1785		}
1786		}
1787		}
1788
1789	<	void SimSetup::initFortran( void ){
1593	<
1789	>	void SimSetup::initFortran(void){
1790		info[0].refreshSim();
1791	<
1792	<	if( !strcmp( info[0].mixingRule, "standard") ){
1793	<	the_ff->initForceField( LB_MIXING_RULE );
1791	>
1792	>	if (!strcmp(info[0].mixingRule, "standard")){
1793	>	the_ff->initForceField(LB_MIXING_RULE);
1794		}
1795	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1796	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1795	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1796	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1797		}
1798		else{
1799	<	sprintf( painCave.errMsg,
1800	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info[0].mixingRule );
1799	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1800	>	info[0].mixingRule);
1801		painCave.isFatal = 1;
1802		simError();
1803		}
1804
1805
1806		#ifdef IS_MPI
1807	<	strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1807	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1808		MPIcheckPoint();
1809		#endif // is_mpi
1616	–
1810		}
1811
1812	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	<	{
1812	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1813		int nZConstraints;
1814		ZconStamp** zconStamp;
1815
1816	<	if(globals->haveZconstraintTime()){
1625	<
1816	>	if (globals->haveZconstraintTime()){
1817		//add sample time of z-constraint  into SimInfo's property list
1818		DoubleData* zconsTimeProp = new DoubleData();
1819		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1630 | Line 1821 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1821		theInfo.addProperty(zconsTimeProp);
1822		}
1823		else{
1824	<	sprintf( painCave.errMsg,
1825	<	"ZConstraint error: If you use an ZConstraint\n"
1826	<	" , you must set sample time.\n");
1824	>	sprintf(painCave.errMsg,
1825	>	"ZConstraint error: If you use a ZConstraint,\n"
1826	>	"\tyou must set zconsTime.\n");
1827		painCave.isFatal = 1;
1828	<	simError();
1828	>	simError();
1829		}
1830
1831		//push zconsTol into siminfo, if user does not specify
1832		//value for zconsTol, a default value will be used
1833		DoubleData* zconsTol = new DoubleData();
1834		zconsTol->setID(ZCONSTOL_ID);
1835	<	if(globals->haveZconsTol()){
1835	>	if (globals->haveZconsTol()){
1836		zconsTol->setData(globals->getZconsTol());
1837		}
1838		else{
1839	<	double defaultZConsTol = 0.01;
1840	<	sprintf( painCave.errMsg,
1841	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1842	<	" , default value %f is used.\n", defaultZConsTol);
1839	>	double defaultZConsTol = 0.01;
1840	>	sprintf(painCave.errMsg,
1841	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1842	>	"\tOOPSE will use a default value of %f.\n"
1843	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1844	>	defaultZConsTol);
1845		painCave.isFatal = 0;
1846		simError();
1847
#	Line 1656 | Line 1849 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1849		}
1850		theInfo.addProperty(zconsTol);
1851
1852	<	//set Force Substraction Policy
1853	<	StringData* zconsForcePolicy =  new StringData();
1852	>	//set Force Subtraction Policy
1853	>	StringData* zconsForcePolicy = new StringData();
1854		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1855	<
1856	<	if(globals->haveZconsForcePolicy()){
1855	>
1856	>	if (globals->haveZconsForcePolicy()){
1857		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1858	<	}
1858	>	}
1859		else{
1860	<	sprintf( painCave.errMsg,
1861	<	"ZConstraint Warning: User does not set force substraction policy, "
1862	<	"average force substraction policy is used\n");
1863	<	painCave.isFatal = 0;
1864	<	simError();
1865	<	zconsForcePolicy->setData("BYNUMBER");
1860	>	sprintf(painCave.errMsg,
1861	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1862	>	"\tOOPSE will use PolicyByMass.\n"
1863	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1864	>	painCave.isFatal = 0;
1865	>	simError();
1866	>	zconsForcePolicy->setData("BYMASS");
1867		}
1868	<
1869	<	theInfo.addProperty(zconsForcePolicy);
1870	<
1868	>
1869	>	theInfo.addProperty(zconsForcePolicy);
1870	>
1871	>	//set zcons gap
1872	>	DoubleData* zconsGap = new DoubleData();
1873	>	zconsGap->setID(ZCONSGAP_ID);
1874	>
1875	>	if (globals->haveZConsGap()){
1876	>	zconsGap->setData(globals->getZconsGap());
1877	>	theInfo.addProperty(zconsGap);
1878	>	}
1879	>
1880	>	//set zcons fixtime
1881	>	DoubleData* zconsFixtime = new DoubleData();
1882	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
1883	>
1884	>	if (globals->haveZConsFixTime()){
1885	>	zconsFixtime->setData(globals->getZconsFixtime());
1886	>	theInfo.addProperty(zconsFixtime);
1887	>	}
1888	>
1889	>	//set zconsUsingSMD
1890	>	IntData* zconsUsingSMD = new IntData();
1891	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1892	>
1893	>	if (globals->haveZConsUsingSMD()){
1894	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1895	>	theInfo.addProperty(zconsUsingSMD);
1896	>	}
1897	>
1898		//Determine the name of ouput file and add it into SimInfo's property list
1899		//Be careful, do not use inFileName, since it is a pointer which
1900		//point to a string at master node, and slave nodes do not contain that string
1901	<
1901	>
1902		string zconsOutput(theInfo.finalName);
1903	<
1903	>
1904		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1905	<
1905	>
1906		StringData* zconsFilename = new StringData();
1907		zconsFilename->setID(ZCONSFILENAME_ID);
1908		zconsFilename->setData(zconsOutput);
1909	<
1909	>
1910		theInfo.addProperty(zconsFilename);
1911	<
1911	>
1912		//setup index, pos and other parameters of z-constraint molecules
1913		nZConstraints = globals->getNzConstraints();
1914		theInfo.nZconstraints = nZConstraints;
#	Line 1697 | Line 1918 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1918
1919		ZConsParaData* zconsParaData = new ZConsParaData();
1920		zconsParaData->setID(ZCONSPARADATA_ID);
1921	<
1922	<	for(int i = 0; i < nZConstraints; i++){
1921	>
1922	>	for (int i = 0; i < nZConstraints; i++){
1923		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1924		tempParaItem.zPos = zconStamp[i]->getZpos();
1925		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1926		tempParaItem.kRatio = zconStamp[i]->getKratio();
1927	<
1927	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1928	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1929		zconsParaData->addItem(tempParaItem);
1930		}
1931
1932	+	//check the uniqueness of index
1933	+	if(!zconsParaData->isIndexUnique()){
1934	+	sprintf(painCave.errMsg,
1935	+	"ZConstraint Error: molIndex is not unique!\n");
1936	+	painCave.isFatal = 1;
1937	+	simError();
1938	+	}
1939	+
1940		//sort the parameters by index of molecules
1941		zconsParaData->sortByIndex();
1942
1943		//push data into siminfo, therefore, we can retrieve later
1944		theInfo.addProperty(zconsParaData);
1715	–
1945		}
1946	+
1947	+	void SimSetup::makeMinimizer(){
1948	+
1949	+	OOPSEMinimizer* myOOPSEMinimizer;
1950	+	MinimizerParameterSet* param;
1951	+	char minimizerName[100];
1952	+
1953	+	for (int i = 0; i < nInfo; i++){
1954	+
1955	+	//prepare parameter set for minimizer
1956	+	param = new MinimizerParameterSet();
1957	+	param->setDefaultParameter();
1958	+
1959	+	if (globals->haveMinimizer()){
1960	+	param->setFTol(globals->getMinFTol());
1961	+	}
1962	+
1963	+	if (globals->haveMinGTol()){
1964	+	param->setGTol(globals->getMinGTol());
1965	+	}
1966	+
1967	+	if (globals->haveMinMaxIter()){
1968	+	param->setMaxIteration(globals->getMinMaxIter());
1969	+	}
1970	+
1971	+	if (globals->haveMinWriteFrq()){
1972	+	param->setMaxIteration(globals->getMinMaxIter());
1973	+	}
1974	+
1975	+	if (globals->haveMinWriteFrq()){
1976	+	param->setWriteFrq(globals->getMinWriteFrq());
1977	+	}
1978	+
1979	+	if (globals->haveMinStepSize()){
1980	+	param->setStepSize(globals->getMinStepSize());
1981	+	}
1982	+
1983	+	if (globals->haveMinLSMaxIter()){
1984	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1985	+	}
1986	+
1987	+	if (globals->haveMinLSTol()){
1988	+	param->setLineSearchTol(globals->getMinLSTol());
1989	+	}
1990	+
1991	+	strcpy(minimizerName, globals->getMinimizer());
1992	+
1993	+	if (!strcasecmp(minimizerName, "CG")){
1994	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1995	+	}
1996	+	else if (!strcasecmp(minimizerName, "SD")){
1997	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1998	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1999	+	}
2000	+	else{
2001	+	sprintf(painCave.errMsg,
2002	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2003	+	painCave.isFatal = 0;
2004	+	simError();
2005	+
2006	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2007	+	}
2008	+	info[i].the_integrator = myOOPSEMinimizer;
2009	+
2010	+	//store the minimizer into simInfo
2011	+	info[i].the_minimizer = myOOPSEMinimizer;
2012	+	info[i].has_minimizer = true;
2013	+	}
2014	+
2015	+	}

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