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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 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	<
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>
189		bond_pair* theBonds;
190		bend_set* theBends;
191		torsion_set* theTorsions;
192
193	<
193	>	set<int> skipList;
194	>
195	>	double phi, theta, psi;
196	>	char* molName;
197	>	char rbName[100];
198	>
199		//init the forceField paramters
200
201		the_ff->readParams();
202
158	–
203		// init the atoms
204
205	<	double ux, uy, uz, u, uSqr;
206	<
207	<	for(k=0; k<nInfo; k++){
208	<
165	<	the_ff->setSimInfo( &(info[k]) );
205	>	int nMembers, nNew, rb1, rb2;
206	>
207	>	for (k = 0; k < nInfo; k++){
208	>	the_ff->setSimInfo(&(info[k]));
209
210		atomOffset = 0;
211	<	excludeOffset = 0;
212	<	for(i=0; i<info[k].n_mol; i++){
170	<
211	>
212	>	for (i = 0; i < info[k].n_mol; i++){
213		stampID = info[k].molecules[i].getStampID();
214	+	molName = comp_stamps[stampID]->getID();
215
216	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
217	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
218	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
216	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
219		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222
223		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];
224
225	+	if (molInfo.nBonds > 0)
226	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	+	else
228	+	molInfo.myBonds = NULL;
229	+
230	+	if (molInfo.nBends > 0)
231	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	+	else
233	+	molInfo.myBends = NULL;
234	+
235	+	if (molInfo.nTorsions > 0)
236	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	+	else
238	+	molInfo.myTorsions = NULL;
239	+
240		theBonds = new bond_pair[molInfo.nBonds];
241		theBends = new bend_set[molInfo.nBends];
242		theTorsions = new torsion_set[molInfo.nTorsions];
243	<
243	>
244		// make the Atoms
245	<
246	<	for(j=0; j<molInfo.nAtoms; j++){
247	<
248	<	currentAtom = comp_stamps[stampID]->getAtom( j );
249	<	if( currentAtom->haveOrientation() ){
250	<
251	<	dAtom = new DirectionalAtom( (j + atomOffset),
252	<	info[k].getConfiguration() );
253	<	info[k].n_oriented++;
254	<	molInfo.myAtoms[j] = dAtom;
255	<
256	<	ux = currentAtom->getOrntX();
257	<	uy = currentAtom->getOrntY();
258	<	uz = currentAtom->getOrntZ();
259	<
260	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
261	<
262	<	u = sqrt( uSqr );
263	<	ux = ux / u;
264	<	uy = uy / u;
265	<	uz = uz / u;
266	<
267	<	dAtom->setSUx( ux );
268	<	dAtom->setSUy( uy );
269	<	dAtom->setSUz( uz );
270	<	}
271	<	else{
272	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
245	>
246	>	for (j = 0; j < molInfo.nAtoms; j++){
247	>	currentAtom = comp_stamps[stampID]->getAtom(j);
248	>
249	>	if (currentAtom->haveOrientation()){
250	>	dAtom = new DirectionalAtom((j + atomOffset),
251	>	info[k].getConfiguration());
252	>	info[k].n_oriented++;
253	>	molInfo.myAtoms[j] = dAtom;
254	>
255	>	// Directional Atoms have standard unit vectors which are oriented
256	>	// in space using the three Euler angles.  We assume the standard
257	>	// unit vector was originally along the z axis below.
258	>
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262	>
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267	>
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269	>
270	>	}
271	>
272	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
274	<
275	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
276	<
274	>
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276	>
277		#endif // is_mpi
278		}
279	<
280	<	// make the bonds
281	<	for(j=0; j<molInfo.nBonds; j++){
282	<
283	<	currentBond = comp_stamps[stampID]->getBond( j );
284	<	theBonds[j].a = currentBond->getA() + atomOffset;
285	<	theBonds[j].b = currentBond->getB() + atomOffset;
286	<
287	<	exI = theBonds[j].a;
288	<	exJ = theBonds[j].b;
289	<
290	<	// exclude_I must always be the smaller of the pair
291	<	if( exI > exJ ){
292	<	tempEx = exI;
293	<	exI = exJ;
294	<	exJ = tempEx;
295	<	}
296	<	#ifdef IS_MPI
297	<	tempEx = exI;
298	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	<	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	<
279	>
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285	>
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288	>
289	>	#ifdef IS_MPI
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296	>
297	>	info[k].excludes->addPair(exI, exJ);
298	>	}
299	>
300		//make the bends
301	<	for(j=0; j<molInfo.nBends; j++){
302	<
303	<	currentBend = comp_stamps[stampID]->getBend( j );
304	<	theBends[j].a = currentBend->getA() + atomOffset;
305	<	theBends[j].b = currentBend->getB() + atomOffset;
306	<	theBends[j].c = currentBend->getC() + atomOffset;
307	<
308	<	if( currentBend->haveExtras() ){
309	<
310	<	extras = currentBend->getExtras();
311	<	current_extra = extras;
312	<
313	<	while( current_extra != NULL ){
314	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
315	<
316	<	switch( current_extra->getType() ){
317	<
318	<	case 0:
319	<	theBends[j].ghost =
320	<	current_extra->getInt() + atomOffset;
321	<	theBends[j].isGhost = 1;
322	<	break;
323	<
324	<	case 1:
325	<	theBends[j].ghost =
326	<	(int)current_extra->getDouble() + atomOffset;
327	<	theBends[j].isGhost = 1;
328	<	break;
329	<
330	<	default:
331	<	sprintf( painCave.errMsg,
332	<	"SimSetup Error: ghostVectorSource was neither a "
333	<	"double nor an int.\n"
334	<	"-->Bend[%d] in %s\n",
335	<	j, comp_stamps[stampID]->getID() );
336	<	painCave.isFatal = 1;
337	<	simError();
338	<	}
339	<	}
340	<
341	<	else{
342	<
343	<	sprintf( painCave.errMsg,
344	<	"SimSetup Error: unhandled bend assignment:\n"
345	<	"    -->%s in Bend[%d] in %s\n",
346	<	current_extra->getlhs(),
347	<	j, comp_stamps[stampID]->getID() );
348	<	painCave.isFatal = 1;
349	<	simError();
350	<	}
351	<
352	<	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	<	}
301	>	for (j = 0; j < molInfo.nBends; j++){
302	>	currentBend = comp_stamps[stampID]->getBend(j);
303	>	theBends[j].a = currentBend->getA() + atomOffset;
304	>	theBends[j].b = currentBend->getB() + atomOffset;
305	>	theBends[j].c = currentBend->getC() + atomOffset;
306	>
307	>	if (currentBend->haveExtras()){
308	>	extras = currentBend->getExtras();
309	>	current_extra = extras;
310	>
311	>	while (current_extra != NULL){
312	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
313	>	switch (current_extra->getType()){
314	>	case 0:
315	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
316	>	theBends[j].isGhost = 1;
317	>	break;
318	>
319	>	case 1:
320	>	theBends[j].ghost = (int) current_extra->getDouble() +
321	>	atomOffset;
322	>	theBends[j].isGhost = 1;
323	>	break;
324	>
325	>	default:
326	>	sprintf(painCave.errMsg,
327	>	"SimSetup Error: ghostVectorSource was neither a "
328	>	"double nor an int.\n"
329	>	"-->Bend[%d] in %s\n",
330	>	j, comp_stamps[stampID]->getID());
331	>	painCave.isFatal = 1;
332	>	simError();
333	>	}
334	>	}
335	>	else{
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: unhandled bend assignment:\n"
338	>	"    -->%s in Bend[%d] in %s\n",
339	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343	>
344	>	current_extra = current_extra->getNext();
345	>	}
346	>	}
347	>
348	>	if (theBends[j].isGhost) {
349	>
350	>	tempI = theBends[j].a;
351	>	tempJ = theBends[j].b;
352	>
353		#ifdef IS_MPI
354	<	tempEx = exI;
355	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
356	<	tempEx = exJ;
357	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
358	<
359	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
360	<	#else  // isn't MPI
361	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
362	<	#endif  //is_mpi
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361	>
362	>	} else {
363	>
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
383	<	excludeOffset += molInfo.nBends;
384	<
385	<	for(j=0; j<molInfo.nTorsions; j++){
386	<
387	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
388	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
389	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
390	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
391	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
392	<
393	<	exI = theTorsions[j].a;
394	<	exJ = theTorsions[j].d;
395	<
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	<	}
383	>
384	>	for (j = 0; j < molInfo.nTorsions; j++){
385	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
386	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
387	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
388	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
389	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
390	>
391	>	tempI = theTorsions[j].a;
392	>	tempJ = theTorsions[j].b;
393	>	tempK = theTorsions[j].c;
394	>	tempL = theTorsions[j].d;
395	>
396		#ifdef IS_MPI
397	<	tempEx = exI;
398	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	<	tempEx = exJ;
400	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
401	<
402	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
403	<	#else  // isn't MPI
404	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
405	<	#endif  //is_mpi
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406	>	#endif
407	>
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414		}
415	<	excludeOffset += molInfo.nTorsions;
415	>
416
417	+	molInfo.myRigidBodies.clear();
418
419	<	// send the arrays off to the forceField for init.
420	<
421	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
422	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
423	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
424	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420	>
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423	>
424	>	// Create the Rigid Body:
425	>
426	>	myRB = new RigidBody();
427	>
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432	>
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435	>
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438	>
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442	>
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445	>
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449	>	#ifdef IS_MPI
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469	>	#ifdef IS_MPI
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481	>
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484	>	}
485
486	+
487	+	//create cutoff group for molecule
488	+	molInfo.myCutoffGroups.clear();
489	+	for (j = 0; j < molInfo.nCutoffGroups; j++){
490	+
491	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	+	nMembers = currentCutoffGroup->getNMembers();
493	+
494	+	myCutoffGroup = new CutoffGroup();
495	+
496	+	for (int cg = 0; cg < nMembers; cg++) {
497	+
498	+	// molI is atom numbering inside this molecule
499	+	molI = currentCutoffGroup->getMember(cg);
500	+
501	+	// tempI is atom numbering on local processor
502	+	tempI = molI + atomOffset;
503	+
504	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	+	}
506	+
507	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509
384	–	info[k].molecules[i].initialize( molInfo );
510
511	+
512	+	// After this is all set up, scan through the atoms to
513	+	// see if they can be added to the integrableObjects:
514	+
515	+	molInfo.myIntegrableObjects.clear();
516
517	+
518	+	for (j = 0; j < molInfo.nAtoms; j++){
519	+
520	+	#ifdef IS_MPI
521	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	+	#else
523	+	slJ = j+atomOffset;
524	+	#endif
525	+
526	+	// if they aren't on the skip list, then they can be integrated
527	+
528	+	if (skipList.find(slJ) == skipList.end()) {
529	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	+	info[k].integrableObjects.push_back(mySD);
531	+	molInfo.myIntegrableObjects.push_back(mySD);
532	+	}
533	+	}
534	+
535	+	// all rigid bodies are integrated:
536	+
537	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	+	info[k].integrableObjects.push_back(mySD);
540	+	molInfo.myIntegrableObjects.push_back(mySD);
541	+	}
542	+
543	+
544	+	// send the arrays off to the forceField for init.
545	+
546	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550	+	theTorsions);
551	+
552	+	info[k].molecules[i].initialize(molInfo);
553	+
554	+
555		atomOffset += molInfo.nAtoms;
556		delete[] theBonds;
557		delete[] theBends;
558		delete[] theTorsions;
559	<	}
559	>	}
560		}
561	<
561	>
562		#ifdef IS_MPI
563	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
563	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
564		MPIcheckPoint();
565		#endif // is_mpi
398	–
399	–	// clean up the forcefield
566
401	–	the_ff->calcRcut();
402	–	the_ff->cleanMe();
403	–
567		}
568
569	<	void SimSetup::initFromBass( void ){
407	<
569	>	void SimSetup::initFromBass(void){
570		int i, j, k;
571		int n_cells;
572		double cellx, celly, cellz;
#	Line 418 | Line 580 | void SimSetup::initFromBass( void ){
580		vel[1] = 0.0;
581		vel[2] = 0.0;
582
583	<	temp1 = (double)tot_nmol / 4.0;
584	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
585	<	temp3 = ceil( temp2 );
583	>	temp1 = (double) tot_nmol / 4.0;
584	>	temp2 = pow(temp1, (1.0 / 3.0));
585	>	temp3 = ceil(temp2);
586
587	<	have_extra =0;
588	<	if( temp2 < temp3 ){ // we have a non-complete lattice
589	<	have_extra =1;
587	>	have_extra = 0;
588	>	if (temp2 < temp3){
589	>	// we have a non-complete lattice
590	>	have_extra = 1;
591
592	<	n_cells = (int)temp3 - 1;
592	>	n_cells = (int) temp3 - 1;
593		cellx = info[0].boxL[0] / temp3;
594		celly = info[0].boxL[1] / temp3;
595		cellz = info[0].boxL[2] / temp3;
596	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
597	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
598	<	n_per_extra = (int)ceil( temp1 );
596	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
597	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
598	>	n_per_extra = (int) ceil(temp1);
599
600	<	if( n_per_extra > 4){
601	<	sprintf( painCave.errMsg,
602	<	"SimSetup error. There has been an error in constructing"
603	<	" the non-complete lattice.\n" );
600	>	if (n_per_extra > 4){
601	>	sprintf(painCave.errMsg,
602	>	"SimSetup error. There has been an error in constructing"
603	>	" the non-complete lattice.\n");
604		painCave.isFatal = 1;
605		simError();
606		}
607		}
608		else{
609	<	n_cells = (int)temp3;
609	>	n_cells = (int) temp3;
610		cellx = info[0].boxL[0] / temp3;
611		celly = info[0].boxL[1] / temp3;
612		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 617 | void SimSetup::initFromBass( void ){
617		current_comp = 0;
618		current_atom_ndx = 0;
619
620	<	for( i=0; i < n_cells ; i++ ){
621	<	for( j=0; j < n_cells; j++ ){
622	<	for( k=0; k < n_cells; k++ ){
620	>	for (i = 0; i < n_cells ; i++){
621	>	for (j = 0; j < n_cells; j++){
622	>	for (k = 0; k < n_cells; k++){
623	>	makeElement(i * cellx, j * celly, k * cellz);
624
625	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
625	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
626
627	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
627	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
628
629	<	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 );
629	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
630		}
631		}
632		}
633
634	<	if( have_extra ){
634	>	if (have_extra){
635		done = 0;
636
637		int start_ndx;
638	<	for( i=0; i < (n_cells+1) && !done; i++ ){
639	<	for( j=0; j < (n_cells+1) && !done; j++ ){
638	>	for (i = 0; i < (n_cells + 1) && !done; i++){
639	>	for (j = 0; j < (n_cells + 1) && !done; j++){
640	>	if (i < n_cells){
641	>	if (j < n_cells){
642	>	start_ndx = n_cells;
643	>	}
644	>	else
645	>	start_ndx = 0;
646	>	}
647	>	else
648	>	start_ndx = 0;
649
650	<	if( i < n_cells ){
650	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
651	>	makeElement(i * cellx, j * celly, k * cellz);
652	>	done = (current_mol >= tot_nmol);
653
654	<	if( j < n_cells ){
655	<	start_ndx = n_cells;
656	<	}
657	<	else start_ndx = 0;
658	<	}
494	<	else start_ndx = 0;
654	>	if (!done && n_per_extra > 1){
655	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
656	>	k * cellz);
657	>	done = (current_mol >= tot_nmol);
658	>	}
659
660	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
660	>	if (!done && n_per_extra > 2){
661	>	makeElement(i * cellx, j * celly + 0.5 * celly,
662	>	k * cellz + 0.5 * cellz);
663	>	done = (current_mol >= tot_nmol);
664	>	}
665
666	<	makeElement( i * cellx,
667	<	j * celly,
668	<	k * cellz );
669	<	done = ( current_mol >= tot_nmol );
670	<
671	<	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	<	}
666	>	if (!done && n_per_extra > 3){
667	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
668	>	k * cellz + 0.5 * cellz);
669	>	done = (current_mol >= tot_nmol);
670	>	}
671	>	}
672		}
673		}
674		}
675
676	<	for( i=0; i<info[0].n_atoms; i++ ){
677	<	info[0].atoms[i]->setVel( vel );
676	>	for (i = 0; i < info[0].n_atoms; i++){
677	>	info[0].atoms[i]->setVel(vel);
678		}
679		}
680
681	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
681	>	void SimSetup::makeElement(double x, double y, double z){
682		int k;
683		AtomStamp* current_atom;
684		DirectionalAtom* dAtom;
685		double rotMat[3][3];
686		double pos[3];
687
688	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
689	<
690	<	current_atom = comp_stamps[current_comp]->getAtom( k );
691	<	if( !current_atom->havePosition() ){
692	<	sprintf( painCave.errMsg,
693	<	"SimSetup:initFromBass error.\n"
694	<	"\tComponent %s, atom %s does not have a position specified.\n"
695	<	"\tThe initialization routine is unable to give a start"
696	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
688	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
689	>	current_atom = comp_stamps[current_comp]->getAtom(k);
690	>	if (!current_atom->havePosition()){
691	>	sprintf(painCave.errMsg,
692	>	"SimSetup:initFromBass error.\n"
693	>	"\tComponent %s, atom %s does not have a position specified.\n"
694	>	"\tThe initialization routine is unable to give a start"
695	>	" position.\n",
696	>	comp_stamps[current_comp]->getID(), current_atom->getType());
697		painCave.isFatal = 1;
698		simError();
699		}
700	<
700	>
701		pos[0] = x + current_atom->getPosX();
702		pos[1] = y + current_atom->getPosY();
703		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
704
705	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
705	>	info[0].atoms[current_atom_ndx]->setPos(pos);
706
707	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
707	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
708	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
709
710		rotMat[0][0] = 1.0;
711		rotMat[0][1] = 0.0;
#	Line 575 | Line 719 | void SimSetup::makeElement( double x, double y, double
719		rotMat[2][1] = 0.0;
720		rotMat[2][2] = 1.0;
721
722	<	dAtom->setA( rotMat );
722	>	dAtom->setA(rotMat);
723		}
724
725		current_atom_ndx++;
#	Line 584 | Line 728 | void SimSetup::makeElement( double x, double y, double
728		current_mol++;
729		current_comp_mol++;
730
731	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
731	>	if (current_comp_mol >= components_nmol[current_comp]){
732		current_comp_mol = 0;
733		current_comp++;
734		}
735		}
736
737
738	<	void SimSetup::gatherInfo( void ){
739	<	int i,j,k;
738	>	void SimSetup::gatherInfo(void){
739	>	int i;
740
741		ensembleCase = -1;
742		ffCase = -1;
743
744		// set the easy ones first
745
746	<	for( i=0; i<nInfo; i++){
746	>	for (i = 0; i < nInfo; i++){
747		info[i].target_temp = globals->getTargetTemp();
748		info[i].dt = globals->getDt();
749		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 753 | void SimSetup::gatherInfo( void ){
753
754		// get the forceField
755
756	<	strcpy( force_field, globals->getForceField() );
756	>	strcpy(force_field, globals->getForceField());
757
758	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
759	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
760	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
758	>	if (!strcasecmp(force_field, "DUFF")){
759	>	ffCase = FF_DUFF;
760	>	}
761	>	else if (!strcasecmp(force_field, "LJ")){
762	>	ffCase = FF_LJ;
763	>	}
764	>	else if (!strcasecmp(force_field, "EAM")){
765	>	ffCase = FF_EAM;
766	>	}
767	>	else if (!strcasecmp(force_field, "WATER")){
768	>	ffCase = FF_H2O;
769	>	}
770		else{
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup Error. Unrecognized force field -> %s\n",
773	<	force_field );
774	<	painCave.isFatal = 1;
623	<	simError();
771	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
772	>	force_field);
773	>	painCave.isFatal = 1;
774	>	simError();
775		}
776
777	<	// get the ensemble
777	>	// get the ensemble
778
779	<	strcpy( ensemble, globals->getEnsemble() );
779	>	strcpy(ensemble, globals->getEnsemble());
780
781	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
782	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
783	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
781	>	if (!strcasecmp(ensemble, "NVE")){
782	>	ensembleCase = NVE_ENS;
783	>	}
784	>	else if (!strcasecmp(ensemble, "NVT")){
785	>	ensembleCase = NVT_ENS;
786	>	}
787	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
788		ensembleCase = NPTi_ENS;
789	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
790	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
791	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
789	>	}
790	>	else if (!strcasecmp(ensemble, "NPTf")){
791	>	ensembleCase = NPTf_ENS;
792	>	}
793	>	else if (!strcasecmp(ensemble, "NPTxyz")){
794	>	ensembleCase = NPTxyz_ENS;
795	>	}
796		else{
797	<	sprintf( painCave.errMsg,
798	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
799	<	"reverting to NVE for this simulation.\n",
800	<	ensemble );
801	<	painCave.isFatal = 0;
802	<	simError();
803	<	strcpy( ensemble, "NVE" );
804	<	ensembleCase = NVE_ENS;
797	>	sprintf(painCave.errMsg,
798	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
799	>	"\treverting to NVE for this simulation.\n",
800	>	ensemble);
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	strcpy(ensemble, "NVE");
804	>	ensembleCase = NVE_ENS;
805		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
806
807	+	for (i = 0; i < nInfo; i++){
808	+	strcpy(info[i].ensemble, ensemble);
809	+
810		// get the mixing rule
811
812	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
812	>	strcpy(info[i].mixingRule, globals->getMixingRule());
813		info[i].usePBC = globals->getPBC();
814		}
815	<
815	>
816		// get the components and calculate the tot_nMol and indvidual n_mol
817	<
817	>
818		the_components = globals->getComponents();
819		components_nmol = new int[n_components];
820
821
822	<	if( !globals->haveNMol() ){
822	>	if (!globals->haveNMol()){
823		// we don't have the total number of molecules, so we assume it is
824		// given in each component
825
826		tot_nmol = 0;
827	<	for( i=0; i<n_components; i++ ){
828	<
829	<	if( !the_components[i]->haveNMol() ){
830	<	// we have a problem
831	<	sprintf( painCave.errMsg,
832	<	"SimSetup Error. No global NMol or component NMol"
833	<	" given. Cannot calculate the number of atoms.\n" );
834	<	painCave.isFatal = 1;
677	<	simError();
827	>	for (i = 0; i < n_components; i++){
828	>	if (!the_components[i]->haveNMol()){
829	>	// we have a problem
830	>	sprintf(painCave.errMsg,
831	>	"SimSetup Error. No global NMol or component NMol given.\n"
832	>	"\tCannot calculate the number of atoms.\n");
833	>	painCave.isFatal = 1;
834	>	simError();
835		}
836
837		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 839 | void SimSetup::gatherInfo( void ){
839		}
840		}
841		else{
842	<	sprintf( painCave.errMsg,
843	<	"SimSetup error.\n"
844	<	"\tSorry, the ability to specify total"
845	<	" nMols and then give molfractions in the components\n"
846	<	"\tis not currently supported."
847	<	" Please give nMol in the components.\n" );
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup error.\n"
844	>	"\tSorry, the ability to specify total"
845	>	" nMols and then give molfractions in the components\n"
846	>	"\tis not currently supported."
847	>	" Please give nMol in the components.\n");
848		painCave.isFatal = 1;
849		simError();
850		}
851
852	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
853	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
854	+	sprintf(painCave.errMsg,
855	+	"Sample time is not divisible by dt.\n"
856	+	"\tThis will result in samples that are not uniformly\n"
857	+	"\tdistributed in time.  If this is a problem, change\n"
858	+	"\tyour sampleTime variable.\n");
859	+	painCave.isFatal = 0;
860	+	simError();
861	+	}
862	+
863	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
864	+	sprintf(painCave.errMsg,
865	+	"Status time is not divisible by dt.\n"
866	+	"\tThis will result in status reports that are not uniformly\n"
867	+	"\tdistributed in time.  If this is a problem, change \n"
868	+	"\tyour statusTime variable.\n");
869	+	painCave.isFatal = 0;
870	+	simError();
871	+	}
872	+
873	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
874	+	sprintf(painCave.errMsg,
875	+	"Thermal time is not divisible by dt.\n"
876	+	"\tThis will result in thermalizations that are not uniformly\n"
877	+	"\tdistributed in time.  If this is a problem, change \n"
878	+	"\tyour thermalTime variable.\n");
879	+	painCave.isFatal = 0;
880	+	simError();
881	+	}
882	+
883	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
884	+	sprintf(painCave.errMsg,
885	+	"Reset time is not divisible by dt.\n"
886	+	"\tThis will result in integrator resets that are not uniformly\n"
887	+	"\tdistributed in time.  If this is a problem, change\n"
888	+	"\tyour resetTime variable.\n");
889	+	painCave.isFatal = 0;
890	+	simError();
891	+	}
892	+
893		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
894
895	<	if( globals->haveSampleTime() ){
895	>	for (i = 0; i < nInfo; i++){
896	>	if (globals->haveSampleTime()){
897		info[i].sampleTime = globals->getSampleTime();
898		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
899		}
900		else{
901		info[i].sampleTime = globals->getRunTime();
902		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
903		}
904	<
905	<	if( globals->haveStatusTime() ){
904	>
905	>	if (globals->haveStatusTime()){
906		info[i].statusTime = globals->getStatusTime();
907		}
908	<
909	<	if( globals->haveThermalTime() ){
908	>
909	>	if (globals->haveThermalTime()){
910		info[i].thermalTime = globals->getThermalTime();
911	+	} else {
912	+	info[i].thermalTime = globals->getRunTime();
913		}
914
915	+	info[i].resetIntegrator = 0;
916	+	if( globals->haveResetTime() ){
917	+	info[i].resetTime = globals->getResetTime();
918	+	info[i].resetIntegrator = 1;
919	+	}
920	+
921		// check for the temperature set flag
922	+
923	+	if (globals->haveTempSet())
924	+	info[i].setTemp = globals->getTempSet();
925
926	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
926	>	// check for the extended State init
927	>
928	>	info[i].useInitXSstate = globals->getUseInitXSstate();
929	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
930
722	–	// get some of the tricky things that may still be in the globals
723	–
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 );
931		}
932	<	else{
933	<	if( !globals->haveBoxX() ){
934	<	sprintf( painCave.errMsg,
935	<	"SimSetup error, no periodic BoxX size given.\n" );
936	<	painCave.isFatal = 1;
937	<	simError();
932	>
933	>	//setup seed for random number generator
934	>	int seedValue;
935	>
936	>	if (globals->haveSeed()){
937	>	seedValue = globals->getSeed();
938	>
939	>	if(seedValue / 1E9 == 0){
940	>	sprintf(painCave.errMsg,
941	>	"Seed for sprng library should contain at least 9 digits\n"
942	>	"OOPSE will generate a seed for user\n");
943	>	painCave.isFatal = 0;
944	>	simError();
945	>
946	>	//using seed generated by system instead of invalid seed set by user
947	>	#ifndef IS_MPI
948	>	seedValue = make_sprng_seed();
949	>	#else
950	>	if (worldRank == 0){
951	>	seedValue = make_sprng_seed();
952		}
953	<	boxVector[0] = globals->getBoxX();
954	<
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 );
953	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
954	>	#endif
955		}
956	+	}//end of if branch of globals->haveSeed()
957	+	else{
958	+
959	+	#ifndef IS_MPI
960	+	seedValue = make_sprng_seed();
961	+	#else
962	+	if (worldRank == 0){
963	+	seedValue = make_sprng_seed();
964	+	}
965	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
966	+	#endif
967	+	}//end of globals->haveSeed()
968
969	+	for (int i = 0; i < nInfo; i++){
970	+	info[i].setSeed(seedValue);
971		}
972	<
972	>
973		#ifdef IS_MPI
974	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
974	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
975		MPIcheckPoint();
976		#endif // is_mpi
776	–
977		}
978
979
980	<	void SimSetup::finalInfoCheck( void ){
980	>	void SimSetup::finalInfoCheck(void){
981		int index;
982		int usesDipoles;
983	+	int usesCharges;
984		int i;
985
986	<	for(i=0; i<nInfo; i++){
986	>	for (i = 0; i < nInfo; i++){
987		// check electrostatic parameters
988	<
988	>
989		index = 0;
990		usesDipoles = 0;
991	<	while( (index < info[i].n_atoms) && !usesDipoles ){
991	>	while ((index < info[i].n_atoms) && !usesDipoles){
992		usesDipoles = (info[i].atoms[index])->hasDipole();
993		index++;
994		}
995	<
995	>	index = 0;
996	>	usesCharges = 0;
997	>	while ((index < info[i].n_atoms) && !usesCharges){
998	>	usesCharges= (info[i].atoms[index])->hasCharge();
999	>	index++;
1000	>	}
1001		#ifdef IS_MPI
1002		int myUse = usesDipoles;
1003	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1003	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1004		#endif //is_mpi
1005	<
1006	<	double theEcr, theEst;
1007	<
1008	<	if (globals->getUseRF() ) {
1009	<	info[i].useReactionField = 1;
1005	>
1006	>	double theRcut, theRsw;
1007	>
1008	>	if (globals->haveRcut()) {
1009	>	theRcut = globals->getRcut();
1010	>
1011	>	if (globals->haveRsw())
1012	>	theRsw = globals->getRsw();
1013	>	else
1014	>	theRsw = theRcut;
1015
1016	<	if( !globals->haveECR() ){
1017	<	sprintf( painCave.errMsg,
1018	<	"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	<	}
1016	>	info[i].setDefaultRcut(theRcut, theRsw);
1017	>
1018	>	} else {
1019
1020	<	if( !globals->haveEST() ){
1021	<	sprintf( painCave.errMsg,
1022	<	"SimSetup Warning: using default value of 0.05 * the "
1023	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1024	<	);
1025	<	painCave.isFatal = 0;
1026	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
831	<	}
1020	>	the_ff->calcRcut();
1021	>	theRcut = info[i].getRcut();
1022	>
1023	>	if (globals->haveRsw())
1024	>	theRsw = globals->getRsw();
1025	>	else
1026	>	theRsw = theRcut;
1027
1028	<	info[i].setEcr( theEcr, theEst );
1028	>	info[i].setDefaultRcut(theRcut, theRsw);
1029	>	}
1030	>
1031	>	if (globals->getUseRF()){
1032	>	info[i].useReactionField = 1;
1033
1034	<	if(!globals->haveDielectric() ){
1035	<	sprintf( painCave.errMsg,
1036	<	"SimSetup Error: You are trying to use Reaction Field without"
1037	<	"setting a dielectric constant!\n"
1038	<	);
1039	<	painCave.isFatal = 1;
1040	<	simError();
1034	>	if (!globals->haveRcut()){
1035	>	sprintf(painCave.errMsg,
1036	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1037	>	"\tOOPSE will use a default value of 15.0 angstroms"
1038	>	"\tfor the cutoffRadius.\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	theRcut = 15.0;
1042		}
1043	<	info[i].dielectric = globals->getDielectric();
1044	<	}
845	<	else {
846	<	if (usesDipoles) {
847	<
848	<	if( !globals->haveECR() ){
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup Warning: using default value of 1/2 the smallest "
851	<	"box length for the electrostaticCutoffRadius.\n"
852	<	"I hope you have a very fast processor!\n");
853	<	painCave.isFatal = 0;
854	<	simError();
855	<	double smallest;
856	<	smallest = info[i].boxL[0];
857	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	<	theEcr = 0.5 * smallest;
860	<	} else {
861	<	theEcr = globals->getECR();
862	<	}
863	<
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 );
1043	>	else{
1044	>	theRcut = globals->getRcut();
1045		}
879	–	}
880	–	}
1046
1047	+	if (!globals->haveRsw()){
1048	+	sprintf(painCave.errMsg,
1049	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1050	+	"\tOOPSE will use a default value of\n"
1051	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1052	+	painCave.isFatal = 0;
1053	+	simError();
1054	+	theRsw = 0.95 * theRcut;
1055	+	}
1056	+	else{
1057	+	theRsw = globals->getRsw();
1058	+	}
1059	+
1060	+	info[i].setDefaultRcut(theRcut, theRsw);
1061	+
1062	+	if (!globals->haveDielectric()){
1063	+	sprintf(painCave.errMsg,
1064	+	"SimSetup Error: No Dielectric constant was set.\n"
1065	+	"\tYou are trying to use Reaction Field without"
1066	+	"\tsetting a dielectric constant!\n");
1067	+	painCave.isFatal = 1;
1068	+	simError();
1069	+	}
1070	+	info[i].dielectric = globals->getDielectric();
1071	+	}
1072	+	else{
1073	+	if (usesDipoles || usesCharges){
1074	+
1075	+	if (!globals->haveRcut()){
1076	+	sprintf(painCave.errMsg,
1077	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1078	+	"\tOOPSE will use a default value of 15.0 angstroms"
1079	+	"\tfor the cutoffRadius.\n");
1080	+	painCave.isFatal = 0;
1081	+	simError();
1082	+	theRcut = 15.0;
1083	+	}
1084	+	else{
1085	+	theRcut = globals->getRcut();
1086	+	}
1087	+
1088	+	if (!globals->haveRsw()){
1089	+	sprintf(painCave.errMsg,
1090	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1091	+	"\tOOPSE will use a default value of\n"
1092	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1093	+	painCave.isFatal = 0;
1094	+	simError();
1095	+	theRsw = 0.95 * theRcut;
1096	+	}
1097	+	else{
1098	+	theRsw = globals->getRsw();
1099	+	}
1100	+
1101	+	info[i].setDefaultRcut(theRcut, theRsw);
1102	+
1103	+	}
1104	+	}
1105	+	}
1106		#ifdef IS_MPI
1107	<	strcpy( checkPointMsg, "post processing checks out" );
1107	>	strcpy(checkPointMsg, "post processing checks out");
1108		MPIcheckPoint();
1109		#endif // is_mpi
1110
1111	+	// clean up the forcefield
1112	+	the_ff->cleanMe();
1113		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
1114
1115	+	void SimSetup::initSystemCoords(void){
1116	+	int i;
1117	+
1118		char* inName;
1119
1120	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1121
1122	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1123	<
1124	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1125	<
899	<	if( globals->haveInitialConfig() ){
900	<
1122	>	for (i = 0; i < info[0].n_atoms; i++)
1123	>	info[0].atoms[i]->setCoords();
1124	>
1125	>	if (globals->haveInitialConfig()){
1126		InitializeFromFile* fileInit;
1127		#ifdef IS_MPI // is_mpi
1128	<	if( worldRank == 0 ){
1128	>	if (worldRank == 0){
1129		#endif //is_mpi
1130		inName = globals->getInitialConfig();
1131	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
1131	>	fileInit = new InitializeFromFile(inName);
1132		#ifdef IS_MPI
1133	<	}else fileInit = new InitializeFromFile( NULL );
1133	>	}
1134	>	else
1135	>	fileInit = new InitializeFromFile(NULL);
1136		#endif
1137	<	fileInit->readInit( info ); // default velocities on
1138	<
1137	>	fileInit->readInit(info); // default velocities on
1138	>
1139		delete fileInit;
1140		}
1141		else{
1142
917	–	#ifdef IS_MPI
918	–
1143		// no init from bass
1144
1145	<	sprintf( painCave.errMsg,
1146	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1147	<	painCave.isFatal;
1145	>	sprintf(painCave.errMsg,
1146	>	"Cannot intialize a simulation without an initial configuration file.\n");
1147	>	painCave.isFatal = 1;;
1148		simError();
1149
926	–	#else
927	–
928	–	initFromBass();
929	–
930	–
931	–	#endif
1150		}
1151	<
1151	>
1152		#ifdef IS_MPI
1153	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1153	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1154		MPIcheckPoint();
1155		#endif // is_mpi
938	–
1156		}
1157
1158
1159	<	void SimSetup::makeOutNames( void ){
943	<
1159	>	void SimSetup::makeOutNames(void){
1160		int k;
1161
946	–
947	–	for(k=0; k<nInfo; k++){
1162
1163	+	for (k = 0; k < nInfo; k++){
1164		#ifdef IS_MPI
1165	<	if( worldRank == 0 ){
1165	>	if (worldRank == 0){
1166		#endif // is_mpi
1167	<
1168	<	if( globals->haveFinalConfig() ){
1169	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1167	>
1168	>	if (globals->haveFinalConfig()){
1169	>	strcpy(info[k].finalName, globals->getFinalConfig());
1170		}
1171		else{
1172	<	strcpy( info[k].finalName, inFileName );
1173	<	char* endTest;
1174	<	int nameLength = strlen( info[k].finalName );
1175	<	endTest = &(info[k].finalName[nameLength - 5]);
1176	<	if( !strcmp( endTest, ".bass" ) ){
1177	<	strcpy( endTest, ".eor" );
1178	<	}
1179	<	else if( !strcmp( endTest, ".BASS" ) ){
1180	<	strcpy( endTest, ".eor" );
1181	<	}
1182	<	else{
1183	<	endTest = &(info[k].finalName[nameLength - 4]);
1184	<	if( !strcmp( endTest, ".bss" ) ){
1185	<	strcpy( endTest, ".eor" );
1186	<	}
1187	<	else if( !strcmp( endTest, ".mdl" ) ){
1188	<	strcpy( endTest, ".eor" );
1189	<	}
1190	<	else{
1191	<	strcat( info[k].finalName, ".eor" );
1192	<	}
1193	<	}
1172	>	strcpy(info[k].finalName, inFileName);
1173	>	char* endTest;
1174	>	int nameLength = strlen(info[k].finalName);
1175	>	endTest = &(info[k].finalName[nameLength - 5]);
1176	>	if (!strcmp(endTest, ".bass")){
1177	>	strcpy(endTest, ".eor");
1178	>	}
1179	>	else if (!strcmp(endTest, ".BASS")){
1180	>	strcpy(endTest, ".eor");
1181	>	}
1182	>	else{
1183	>	endTest = &(info[k].finalName[nameLength - 4]);
1184	>	if (!strcmp(endTest, ".bss")){
1185	>	strcpy(endTest, ".eor");
1186	>	}
1187	>	else if (!strcmp(endTest, ".mdl")){
1188	>	strcpy(endTest, ".eor");
1189	>	}
1190	>	else{
1191	>	strcat(info[k].finalName, ".eor");
1192	>	}
1193	>	}
1194		}
1195	<
1195	>
1196		// make the sample and status out names
1197	<
1198	<	strcpy( info[k].sampleName, inFileName );
1197	>
1198	>	strcpy(info[k].sampleName, inFileName);
1199		char* endTest;
1200	<	int nameLength = strlen( info[k].sampleName );
1200	>	int nameLength = strlen(info[k].sampleName);
1201		endTest = &(info[k].sampleName[nameLength - 5]);
1202	<	if( !strcmp( endTest, ".bass" ) ){
1203	<	strcpy( endTest, ".dump" );
1202	>	if (!strcmp(endTest, ".bass")){
1203	>	strcpy(endTest, ".dump");
1204		}
1205	<	else if( !strcmp( endTest, ".BASS" ) ){
1206	<	strcpy( endTest, ".dump" );
1205	>	else if (!strcmp(endTest, ".BASS")){
1206	>	strcpy(endTest, ".dump");
1207		}
1208		else{
1209	<	endTest = &(info[k].sampleName[nameLength - 4]);
1210	<	if( !strcmp( endTest, ".bss" ) ){
1211	<	strcpy( endTest, ".dump" );
1212	<	}
1213	<	else if( !strcmp( endTest, ".mdl" ) ){
1214	<	strcpy( endTest, ".dump" );
1215	<	}
1216	<	else{
1217	<	strcat( info[k].sampleName, ".dump" );
1218	<	}
1209	>	endTest = &(info[k].sampleName[nameLength - 4]);
1210	>	if (!strcmp(endTest, ".bss")){
1211	>	strcpy(endTest, ".dump");
1212	>	}
1213	>	else if (!strcmp(endTest, ".mdl")){
1214	>	strcpy(endTest, ".dump");
1215	>	}
1216	>	else{
1217	>	strcat(info[k].sampleName, ".dump");
1218	>	}
1219		}
1220	<
1221	<	strcpy( info[k].statusName, inFileName );
1222	<	nameLength = strlen( info[k].statusName );
1220	>
1221	>	strcpy(info[k].statusName, inFileName);
1222	>	nameLength = strlen(info[k].statusName);
1223		endTest = &(info[k].statusName[nameLength - 5]);
1224	<	if( !strcmp( endTest, ".bass" ) ){
1225	<	strcpy( endTest, ".stat" );
1224	>	if (!strcmp(endTest, ".bass")){
1225	>	strcpy(endTest, ".stat");
1226		}
1227	<	else if( !strcmp( endTest, ".BASS" ) ){
1228	<	strcpy( endTest, ".stat" );
1227	>	else if (!strcmp(endTest, ".BASS")){
1228	>	strcpy(endTest, ".stat");
1229		}
1230		else{
1231	<	endTest = &(info[k].statusName[nameLength - 4]);
1232	<	if( !strcmp( endTest, ".bss" ) ){
1233	<	strcpy( endTest, ".stat" );
1234	<	}
1235	<	else if( !strcmp( endTest, ".mdl" ) ){
1236	<	strcpy( endTest, ".stat" );
1237	<	}
1238	<	else{
1239	<	strcat( info[k].statusName, ".stat" );
1240	<	}
1231	>	endTest = &(info[k].statusName[nameLength - 4]);
1232	>	if (!strcmp(endTest, ".bss")){
1233	>	strcpy(endTest, ".stat");
1234	>	}
1235	>	else if (!strcmp(endTest, ".mdl")){
1236	>	strcpy(endTest, ".stat");
1237	>	}
1238	>	else{
1239	>	strcat(info[k].statusName, ".stat");
1240	>	}
1241		}
1242	<
1242	>
1243		#ifdef IS_MPI
1244	+
1245		}
1246		#endif // is_mpi
1247		}
1248		}
1249
1250
1251	<	void SimSetup::sysObjectsCreation( void ){
1252	<
1253	<	int i,k;
1038	<
1251	>	void SimSetup::sysObjectsCreation(void){
1252	>	int i, k;
1253	>
1254		// create the forceField
1255
1256		createFF();
#	Line 1050 | Line 1265 | void SimSetup::sysObjectsCreation( void ){
1265
1266		#ifdef IS_MPI
1267		// divide the molecules among the processors
1268	<
1268	>
1269		mpiMolDivide();
1270		#endif //is_mpi
1271	<
1271	>
1272		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1273	<
1273	>
1274		makeSysArrays();
1275
1276		// make and initialize the molecules (all but atomic coordinates)
1277	<
1277	>
1278		makeMolecules();
1279	<
1280	<	for(k=0; k<nInfo; k++){
1279	>
1280	>	for (k = 0; k < nInfo; k++){
1281		info[k].identArray = new int[info[k].n_atoms];
1282	<	for(i=0; i<info[k].n_atoms; i++){
1282	>	for (i = 0; i < info[k].n_atoms; i++){
1283		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1284		}
1285		}
1286		}
1287
1288
1289	<	void SimSetup::createFF( void ){
1289	>	void SimSetup::createFF(void){
1290	>	switch (ffCase){
1291	>	case FF_DUFF:
1292	>	the_ff = new DUFF();
1293	>	break;
1294
1295	<	switch( ffCase ){
1295	>	case FF_LJ:
1296	>	the_ff = new LJFF();
1297	>	break;
1298
1299	<	case FF_DUFF:
1300	<	the_ff = new DUFF();
1301	<	break;
1299	>	case FF_EAM:
1300	>	the_ff = new EAM_FF();
1301	>	break;
1302
1303	<	case FF_LJ:
1304	<	the_ff = new LJFF();
1305	<	break;
1303	>	case FF_H2O:
1304	>	the_ff = new WATER();
1305	>	break;
1306
1307	<	case FF_EAM:
1308	<	the_ff = new EAM_FF();
1309	<	break;
1310	<
1311	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	simError();
1307	>	default:
1308	>	sprintf(painCave.errMsg,
1309	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1310	>	painCave.isFatal = 1;
1311	>	simError();
1312		}
1313
1314		#ifdef IS_MPI
1315	<	strcpy( checkPointMsg, "ForceField creation successful" );
1315	>	strcpy(checkPointMsg, "ForceField creation successful");
1316		MPIcheckPoint();
1317		#endif // is_mpi
1101	–
1318		}
1319
1320
1321	<	void SimSetup::compList( void ){
1106	<
1321	>	void SimSetup::compList(void){
1322		int i;
1323		char* id;
1324		LinkedMolStamp* headStamp = new LinkedMolStamp();
1325		LinkedMolStamp* currentStamp = NULL;
1326	<	comp_stamps = new MoleculeStamp*[n_components];
1326	>	comp_stamps = new MoleculeStamp * [n_components];
1327	>	bool haveCutoffGroups;
1328	>
1329	>	haveCutoffGroups = false;
1330
1331		// make an array of molecule stamps that match the components used.
1332		// also extract the used stamps out into a separate linked list
1333	<
1334	<	for(i=0; i<nInfo; i++){
1333	>
1334	>	for (i = 0; i < nInfo; i++){
1335		info[i].nComponents = n_components;
1336		info[i].componentsNmol = components_nmol;
1337		info[i].compStamps = comp_stamps;
1338		info[i].headStamp = headStamp;
1339		}
1122	–
1340
1124	–	for( i=0; i<n_components; i++ ){
1341
1342	+	for (i = 0; i < n_components; i++){
1343		id = the_components[i]->getType();
1344		comp_stamps[i] = NULL;
1345	<
1345	>
1346		// check to make sure the component isn't already in the list
1347
1348	<	comp_stamps[i] = headStamp->match( id );
1349	<	if( comp_stamps[i] == NULL ){
1133	<
1348	>	comp_stamps[i] = headStamp->match(id);
1349	>	if (comp_stamps[i] == NULL){
1350		// extract the component from the list;
1351	<
1352	<	currentStamp = stamps->extractMolStamp( id );
1353	<	if( currentStamp == NULL ){
1354	<	sprintf( painCave.errMsg,
1355	<	"SimSetup error: Component \"%s\" was not found in the "
1356	<	"list of declared molecules\n",
1357	<	id );
1358	<	painCave.isFatal = 1;
1359	<	simError();
1351	>
1352	>	currentStamp = stamps->extractMolStamp(id);
1353	>	if (currentStamp == NULL){
1354	>	sprintf(painCave.errMsg,
1355	>	"SimSetup error: Component \"%s\" was not found in the "
1356	>	"list of declared molecules\n",
1357	>	id);
1358	>	painCave.isFatal = 1;
1359	>	simError();
1360		}
1361	<
1362	<	headStamp->add( currentStamp );
1363	<	comp_stamps[i] = headStamp->match( id );
1361	>
1362	>	headStamp->add(currentStamp);
1363	>	comp_stamps[i] = headStamp->match(id);
1364		}
1365	+
1366	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1367	+	haveCutoffGroups = true;
1368		}
1369	+
1370	+	for (i = 0; i < nInfo; i++)
1371	+	info[i].haveCutoffGroups = haveCutoffGroups;
1372
1373		#ifdef IS_MPI
1374	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1374	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1375		MPIcheckPoint();
1376		#endif // is_mpi
1377	+	}
1378
1379	+	void SimSetup::calcSysValues(void){
1380	+	int i;
1381
1382	<	}
1382	>	int* molMembershipArray;
1383
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1384		tot_atoms = 0;
1385		tot_bonds = 0;
1386		tot_bends = 0;
1387		tot_torsions = 0;
1388	<	for( i=0; i<n_components; i++ ){
1389	<
1390	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1391	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1392	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1388	>	tot_rigid = 0;
1389	>	for (i = 0; i < n_components; i++){
1390	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1391	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1392	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1393		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1394	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1395		}
1396
1397		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1398		molMembershipArray = new int[tot_atoms];
1399	<
1400	<	for(i=0; i<nInfo; i++){
1399	>
1400	>	for (i = 0; i < nInfo; i++){
1401		info[i].n_atoms = tot_atoms;
1402		info[i].n_bonds = tot_bonds;
1403		info[i].n_bends = tot_bends;
1404		info[i].n_torsions = tot_torsions;
1405		info[i].n_SRI = tot_SRI;
1406		info[i].n_mol = tot_nmol;
1407	<
1407	>
1408		info[i].molMembershipArray = molMembershipArray;
1409	<	}
1409	>	}
1410		}
1411
1412		#ifdef IS_MPI
1413
1414	<	void SimSetup::mpiMolDivide( void ){
1194	<
1414	>	void SimSetup::mpiMolDivide(void){
1415		int i, j, k;
1416		int localMol, allMol;
1417		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1418	+	int local_rigid;
1419	+	vector<int> globalMolIndex;
1420
1421	<	mpiSim = new mpiSimulation( info );
1200	<
1201	<	globalIndex = mpiSim->divideLabor();
1421	>	mpiSim = new mpiSimulation(info);
1422
1423	+	mpiSim->divideLabor();
1424	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1425	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1426	+
1427		// set up the local variables
1428	<
1428	>
1429		mol2proc = mpiSim->getMolToProcMap();
1430		molCompType = mpiSim->getMolComponentType();
1431	<
1431	>
1432		allMol = 0;
1433		localMol = 0;
1434		local_atoms = 0;
1435		local_bonds = 0;
1436		local_bends = 0;
1437		local_torsions = 0;
1438	<	globalAtomIndex = 0;
1438	>	local_rigid = 0;
1439	>	globalAtomCounter = 0;
1440
1441	<
1442	<	for( i=0; i<n_components; i++ ){
1443	<
1444	<	for( j=0; j<components_nmol[i]; j++ ){
1445	<
1446	<	if( mol2proc[allMol] == worldRank ){
1447	<
1448	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1449	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1441	>	for (i = 0; i < n_components; i++){
1442	>	for (j = 0; j < components_nmol[i]; j++){
1443	>	if (mol2proc[allMol] == worldRank){
1444	>	local_atoms += comp_stamps[i]->getNAtoms();
1445	>	local_bonds += comp_stamps[i]->getNBonds();
1446	>	local_bends += comp_stamps[i]->getNBends();
1447	>	local_torsions += comp_stamps[i]->getNTorsions();
1448	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1449	>	localMol++;
1450		}
1451	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1452	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1453	<	globalAtomIndex++;
1451	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1452	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1453	>	globalAtomCounter++;
1454		}
1455
1456	<	allMol++;
1456	>	allMol++;
1457		}
1458		}
1459		local_SRI = local_bonds + local_bends + local_torsions;
1460	<
1460	>
1461		info[0].n_atoms = mpiSim->getMyNlocal();
1462
1463	<	if( local_atoms != info[0].n_atoms ){
1464	<	sprintf( painCave.errMsg,
1465	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1466	<	" localAtom (%d) are not equal.\n",
1467	<	info[0].n_atoms,
1468	<	local_atoms );
1463	>
1464	>	if (local_atoms != info[0].n_atoms){
1465	>	sprintf(painCave.errMsg,
1466	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1467	>	"\tlocalAtom (%d) are not equal.\n",
1468	>	info[0].n_atoms, local_atoms);
1469		painCave.isFatal = 1;
1470		simError();
1471		}
#	Line 1254 | Line 1476 | void SimSetup::mpiMolDivide( void ){
1476		info[0].n_SRI = local_SRI;
1477		info[0].n_mol = localMol;
1478
1479	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1479	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1480		MPIcheckPoint();
1481		}
1482	<
1482	>
1483		#endif // is_mpi
1484
1485
1486	<	void SimSetup::makeSysArrays( void ){
1487	<	int i, j, k, l;
1486	>	void SimSetup::makeSysArrays(void){
1487	>
1488	>	#ifndef IS_MPI
1489	>	int k, j;
1490	>	#endif // is_mpi
1491	>	int i, l;
1492
1493		Atom** the_atoms;
1494		Molecule* the_molecules;
1269	–	Exclude** the_excludes;
1495
1496	<
1272	<	for(l=0; l<nInfo; l++){
1273	<
1496	>	for (l = 0; l < nInfo; l++){
1497		// create the atom and short range interaction arrays
1498	<
1499	<	the_atoms = new Atom*[info[l].n_atoms];
1498	>
1499	>	the_atoms = new Atom * [info[l].n_atoms];
1500		the_molecules = new Molecule[info[l].n_mol];
1501		int molIndex;
1502
1503		// initialize the molecule's stampID's
1504	<
1504	>
1505		#ifdef IS_MPI
1506	<
1507	<
1506	>
1507	>
1508		molIndex = 0;
1509	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1510	<
1511	<	if(mol2proc[i] == worldRank ){
1512	<	the_molecules[molIndex].setStampID( molCompType[i] );
1513	<	the_molecules[molIndex].setMyIndex( molIndex );
1514	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
1509	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1510	>	if (mol2proc[i] == worldRank){
1511	>	the_molecules[molIndex].setStampID(molCompType[i]);
1512	>	the_molecules[molIndex].setMyIndex(molIndex);
1513	>	the_molecules[molIndex].setGlobalIndex(i);
1514	>	molIndex++;
1515		}
1516		}
1517	<
1517	>
1518		#else // is_mpi
1519	<
1519	>
1520		molIndex = 0;
1521	<	globalAtomIndex = 0;
1522	<	for(i=0; i<n_components; i++){
1523	<	for(j=0; j<components_nmol[i]; j++ ){
1524	<	the_molecules[molIndex].setStampID( i );
1525	<	the_molecules[molIndex].setMyIndex( molIndex );
1526	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1527	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1528	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1529	<	globalAtomIndex++;
1530	<	}
1531	<	molIndex++;
1521	>	globalAtomCounter = 0;
1522	>	for (i = 0; i < n_components; i++){
1523	>	for (j = 0; j < components_nmol[i]; j++){
1524	>	the_molecules[molIndex].setStampID(i);
1525	>	the_molecules[molIndex].setMyIndex(molIndex);
1526	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1527	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1528	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1529	>	globalAtomCounter++;
1530	>	}
1531	>	molIndex++;
1532		}
1533		}
1312	–
1313	–
1314	–	#endif // is_mpi
1534
1535
1536	<	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	<	}
1536	>	#endif // is_mpi
1537
1538	+	info[l].globalExcludes = new int;
1539	+	info[l].globalExcludes[0] = 0;
1540	+
1541		// set the arrays into the SimInfo object
1542
1543		info[l].atoms = the_atoms;
1544		info[l].molecules = the_molecules;
1545		info[l].nGlobalExcludes = 0;
1343	–	info[l].excludes = the_excludes;
1344	–
1345	–	the_ff->setSimInfo( info );
1546
1547	+	the_ff->setSimInfo(info);
1548		}
1549		}
1550
1551	<	void SimSetup::makeIntegrator( void ){
1351	<
1551	>	void SimSetup::makeIntegrator(void){
1552		int k;
1553
1554	<	NVT<RealIntegrator>*  myNVT = NULL;
1555	<	NPTi<RealIntegrator>* myNPTi = NULL;
1556	<	NPTf<RealIntegrator>* myNPTf = NULL;
1557	<	NPTim<RealIntegrator>* myNPTim = NULL;
1558	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1559	<
1560	<	for(k=0; k<nInfo; k++){
1561	<
1562	<	switch( ensembleCase ){
1563	<
1564	<	case NVE_ENS:
1565	<	if (globals->haveZconstraints()){
1566	<	setupZConstraint(info[k]);
1567	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1554	>	NVE<RealIntegrator>* myNVE = NULL;
1555	>	NVT<RealIntegrator>* myNVT = NULL;
1556	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1557	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1558	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1559	>
1560	>	for (k = 0; k < nInfo; k++){
1561	>	switch (ensembleCase){
1562	>	case NVE_ENS:
1563	>	if (globals->haveZconstraints()){
1564	>	setupZConstraint(info[k]);
1565	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1566	>	}
1567	>	else{
1568	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1569		}
1570	+
1571	+	info->the_integrator = myNVE;
1572	+	break;
1573
1574	<	else
1575	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1576	<	break;
1577	<
1578	<	case NVT_ENS:
1579	<	if (globals->haveZconstraints()){
1580	<	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 );
1574	>	case NVT_ENS:
1575	>	if (globals->haveZconstraints()){
1576	>	setupZConstraint(info[k]);
1577	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1578	>	}
1579	>	else
1580	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1581
1582	<	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 );
1582	>	myNVT->setTargetTemp(globals->getTargetTemp());
1583
1584	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1585	<
1586	<	if (globals->haveTargetPressure())
1587	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1588	<	else {
1589	<	sprintf( painCave.errMsg,
1590	<	"SimSetup error: If you use a constant pressure\n"
1591	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1592	<	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 );
1584	>	if (globals->haveTauThermostat())
1585	>	myNVT->setTauThermostat(globals->getTauThermostat());
1586	>	else{
1587	>	sprintf(painCave.errMsg,
1588	>	"SimSetup error: If you use the NVT\n"
1589	>	"\tensemble, you must set tauThermostat.\n");
1590	>	painCave.isFatal = 1;
1591	>	simError();
1592	>	}
1593
1594	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1595	<
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 );
1594	>	info->the_integrator = myNVT;
1595	>	break;
1596
1597	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1598	<
1599	<	if (globals->haveTargetPressure())
1600	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1601	<	else {
1602	<	sprintf( painCave.errMsg,
1603	<	"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 );
1597	>	case NPTi_ENS:
1598	>	if (globals->haveZconstraints()){
1599	>	setupZConstraint(info[k]);
1600	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1601	>	}
1602	>	else
1603	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1604
1605	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1606	<
1607	<	if (globals->haveTargetPressure())
1608	<	myNPTfm->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;
1614	<	simError();
1615	<	}
1616	<
1617	<	if( globals->haveTauThermostat() )
1618	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1619	<	else{
1620	<	sprintf( painCave.errMsg,
1621	<	"SimSetup error: If you use an NPT\n"
1622	<	"    ensemble, you must set tauThermostat.\n");
1623	<	painCave.isFatal = 1;
1624	<	simError();
1625	<	}
1626	<
1627	<	if( globals->haveTauBarostat() )
1628	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1629	<	else{
1630	<	sprintf( painCave.errMsg,
1631	<	"SimSetup error: If you use an NPT\n"
1632	<	"    ensemble, you must set tauBarostat.\n");
1633	<	painCave.isFatal = 1;
1634	<	simError();
1635	<	}
1636	<	break;
1637	<
1638	<	default:
1639	<	sprintf( painCave.errMsg,
1640	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1641	<	painCave.isFatal = 1;
1642	<	simError();
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	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1613	>	painCave.isFatal = 1;
1614	>	simError();
1615	>	}
1616	>
1617	>	if (globals->haveTauThermostat())
1618	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1619	>	else{
1620	>	sprintf(painCave.errMsg,
1621	>	"SimSetup error: If you use an NPT\n"
1622	>	"\tensemble, you must set tauThermostat.\n");
1623	>	painCave.isFatal = 1;
1624	>	simError();
1625	>	}
1626	>
1627	>	if (globals->haveTauBarostat())
1628	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1629	>	else{
1630	>	sprintf(painCave.errMsg,
1631	>	"SimSetup error: If you use an NPT\n"
1632	>	"\tensemble, you must set tauBarostat.\n");
1633	>	painCave.isFatal = 1;
1634	>	simError();
1635	>	}
1636	>
1637	>	info->the_integrator = myNPTi;
1638	>	break;
1639	>
1640	>	case NPTf_ENS:
1641	>	if (globals->haveZconstraints()){
1642	>	setupZConstraint(info[k]);
1643	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1644	>	}
1645	>	else
1646	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1647	>
1648	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1649	>
1650	>	if (globals->haveTargetPressure())
1651	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1652	>	else{
1653	>	sprintf(painCave.errMsg,
1654	>	"SimSetup error: If you use a constant pressure\n"
1655	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1656	>	painCave.isFatal = 1;
1657	>	simError();
1658	>	}
1659	>
1660	>	if (globals->haveTauThermostat())
1661	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1662	>
1663	>	else{
1664	>	sprintf(painCave.errMsg,
1665	>	"SimSetup error: If you use an NPT\n"
1666	>	"\tensemble, you must set tauThermostat.\n");
1667	>	painCave.isFatal = 1;
1668	>	simError();
1669	>	}
1670	>
1671	>	if (globals->haveTauBarostat())
1672	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1673	>
1674	>	else{
1675	>	sprintf(painCave.errMsg,
1676	>	"SimSetup error: If you use an NPT\n"
1677	>	"\tensemble, you must set tauBarostat.\n");
1678	>	painCave.isFatal = 1;
1679	>	simError();
1680	>	}
1681	>
1682	>	info->the_integrator = myNPTf;
1683	>	break;
1684	>
1685	>	case NPTxyz_ENS:
1686	>	if (globals->haveZconstraints()){
1687	>	setupZConstraint(info[k]);
1688	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1689	>	}
1690	>	else
1691	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1692	>
1693	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1694	>
1695	>	if (globals->haveTargetPressure())
1696	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1697	>	else{
1698	>	sprintf(painCave.errMsg,
1699	>	"SimSetup error: If you use a constant pressure\n"
1700	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1701	>	painCave.isFatal = 1;
1702	>	simError();
1703	>	}
1704	>
1705	>	if (globals->haveTauThermostat())
1706	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1707	>	else{
1708	>	sprintf(painCave.errMsg,
1709	>	"SimSetup error: If you use an NPT\n"
1710	>	"\tensemble, you must set tauThermostat.\n");
1711	>	painCave.isFatal = 1;
1712	>	simError();
1713	>	}
1714	>
1715	>	if (globals->haveTauBarostat())
1716	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1717	>	else{
1718	>	sprintf(painCave.errMsg,
1719	>	"SimSetup error: If you use an NPT\n"
1720	>	"\tensemble, you must set tauBarostat.\n");
1721	>	painCave.isFatal = 1;
1722	>	simError();
1723	>	}
1724	>
1725	>	info->the_integrator = myNPTxyz;
1726	>	break;
1727	>
1728	>	default:
1729	>	sprintf(painCave.errMsg,
1730	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1731	>	painCave.isFatal = 1;
1732	>	simError();
1733		}
1734		}
1735		}
1736
1737	<	void SimSetup::initFortran( void ){
1570	<
1737	>	void SimSetup::initFortran(void){
1738		info[0].refreshSim();
1739	<
1740	<	if( !strcmp( info[0].mixingRule, "standard") ){
1741	<	the_ff->initForceField( LB_MIXING_RULE );
1739	>
1740	>	if (!strcmp(info[0].mixingRule, "standard")){
1741	>	the_ff->initForceField(LB_MIXING_RULE);
1742		}
1743	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1744	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1743	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1744	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1745		}
1746		else{
1747	<	sprintf( painCave.errMsg,
1748	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1747	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1748	>	info[0].mixingRule);
1749		painCave.isFatal = 1;
1750		simError();
1751		}
1752
1753
1754		#ifdef IS_MPI
1755	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1755	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1756		MPIcheckPoint();
1757		#endif // is_mpi
1758	+	}
1759
1760	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1761	+	int nZConstraints;
1762	+	ZconStamp** zconStamp;
1763	+
1764	+	if (globals->haveZconstraintTime()){
1765	+	//add sample time of z-constraint  into SimInfo's property list
1766	+	DoubleData* zconsTimeProp = new DoubleData();
1767	+	zconsTimeProp->setID(ZCONSTIME_ID);
1768	+	zconsTimeProp->setData(globals->getZconsTime());
1769	+	theInfo.addProperty(zconsTimeProp);
1770	+	}
1771	+	else{
1772	+	sprintf(painCave.errMsg,
1773	+	"ZConstraint error: If you use a ZConstraint,\n"
1774	+	"\tyou must set zconsTime.\n");
1775	+	painCave.isFatal = 1;
1776	+	simError();
1777	+	}
1778	+
1779	+	//push zconsTol into siminfo, if user does not specify
1780	+	//value for zconsTol, a default value will be used
1781	+	DoubleData* zconsTol = new DoubleData();
1782	+	zconsTol->setID(ZCONSTOL_ID);
1783	+	if (globals->haveZconsTol()){
1784	+	zconsTol->setData(globals->getZconsTol());
1785	+	}
1786	+	else{
1787	+	double defaultZConsTol = 0.01;
1788	+	sprintf(painCave.errMsg,
1789	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1790	+	"\tOOPSE will use a default value of %f.\n"
1791	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1792	+	defaultZConsTol);
1793	+	painCave.isFatal = 0;
1794	+	simError();
1795	+
1796	+	zconsTol->setData(defaultZConsTol);
1797	+	}
1798	+	theInfo.addProperty(zconsTol);
1799	+
1800	+	//set Force Subtraction Policy
1801	+	StringData* zconsForcePolicy = new StringData();
1802	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1803	+
1804	+	if (globals->haveZconsForcePolicy()){
1805	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1806	+	}
1807	+	else{
1808	+	sprintf(painCave.errMsg,
1809	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1810	+	"\tOOPSE will use PolicyByMass.\n"
1811	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1812	+	painCave.isFatal = 0;
1813	+	simError();
1814	+	zconsForcePolicy->setData("BYMASS");
1815	+	}
1816	+
1817	+	theInfo.addProperty(zconsForcePolicy);
1818	+
1819	+	//set zcons gap
1820	+	DoubleData* zconsGap = new DoubleData();
1821	+	zconsGap->setID(ZCONSGAP_ID);
1822	+
1823	+	if (globals->haveZConsGap()){
1824	+	zconsGap->setData(globals->getZconsGap());
1825	+	theInfo.addProperty(zconsGap);
1826	+	}
1827	+
1828	+	//set zcons fixtime
1829	+	DoubleData* zconsFixtime = new DoubleData();
1830	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1831	+
1832	+	if (globals->haveZConsFixTime()){
1833	+	zconsFixtime->setData(globals->getZconsFixtime());
1834	+	theInfo.addProperty(zconsFixtime);
1835	+	}
1836	+
1837	+	//set zconsUsingSMD
1838	+	IntData* zconsUsingSMD = new IntData();
1839	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1840	+
1841	+	if (globals->haveZConsUsingSMD()){
1842	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1843	+	theInfo.addProperty(zconsUsingSMD);
1844	+	}
1845	+
1846	+	//Determine the name of ouput file and add it into SimInfo's property list
1847	+	//Be careful, do not use inFileName, since it is a pointer which
1848	+	//point to a string at master node, and slave nodes do not contain that string
1849	+
1850	+	string zconsOutput(theInfo.finalName);
1851	+
1852	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1853	+
1854	+	StringData* zconsFilename = new StringData();
1855	+	zconsFilename->setID(ZCONSFILENAME_ID);
1856	+	zconsFilename->setData(zconsOutput);
1857	+
1858	+	theInfo.addProperty(zconsFilename);
1859	+
1860	+	//setup index, pos and other parameters of z-constraint molecules
1861	+	nZConstraints = globals->getNzConstraints();
1862	+	theInfo.nZconstraints = nZConstraints;
1863	+
1864	+	zconStamp = globals->getZconStamp();
1865	+	ZConsParaItem tempParaItem;
1866	+
1867	+	ZConsParaData* zconsParaData = new ZConsParaData();
1868	+	zconsParaData->setID(ZCONSPARADATA_ID);
1869	+
1870	+	for (int i = 0; i < nZConstraints; i++){
1871	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1872	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1873	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1874	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1875	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1876	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1877	+	zconsParaData->addItem(tempParaItem);
1878	+	}
1879	+
1880	+	//check the uniqueness of index
1881	+	if(!zconsParaData->isIndexUnique()){
1882	+	sprintf(painCave.errMsg,
1883	+	"ZConstraint Error: molIndex is not unique!\n");
1884	+	painCave.isFatal = 1;
1885	+	simError();
1886	+	}
1887	+
1888	+	//sort the parameters by index of molecules
1889	+	zconsParaData->sortByIndex();
1890	+
1891	+	//push data into siminfo, therefore, we can retrieve later
1892	+	theInfo.addProperty(zconsParaData);
1893		}
1894
1895	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1896	<	{
1897	<	int nZConstraints;
1898	<	ZconStamp** zconStamp;
1899	<
1900	<	if(globals->haveZconstraintTime()){
1901	<
1902	<	//add sample time of z-constraint  into SimInfo's property list
1903	<	DoubleData* zconsTimeProp = new DoubleData();
1904	<	zconsTimeProp->setID(ZCONSTIME_ID);
1905	<	zconsTimeProp->setData(globals->getZconsTime());
1906	<	theInfo.addProperty(zconsTimeProp);
1895	>	void SimSetup::makeMinimizer(){
1896	>
1897	>	OOPSEMinimizer* myOOPSEMinimizer;
1898	>	MinimizerParameterSet* param;
1899	>	char minimizerName[100];
1900	>
1901	>	for (int i = 0; i < nInfo; i++){
1902	>
1903	>	//prepare parameter set for minimizer
1904	>	param = new MinimizerParameterSet();
1905	>	param->setDefaultParameter();
1906	>
1907	>	if (globals->haveMinimizer()){
1908	>	param->setFTol(globals->getMinFTol());
1909		}
1910	<	else{
1911	<	sprintf( painCave.errMsg,
1912	<	"ZConstraint error: If you use an ZConstraint\n"
1612	<	" , you must set sample time.\n");
1613	<	painCave.isFatal = 1;
1614	<	simError();
1910	>
1911	>	if (globals->haveMinGTol()){
1912	>	param->setGTol(globals->getMinGTol());
1913		}
1914
1915	<	//push zconsTol into siminfo, if user does not specify
1916	<	//value for zconsTol, a default value will be used
1619	<	DoubleData* zconsTol = new DoubleData();
1620	<	zconsTol->setID(ZCONSTOL_ID);
1621	<	if(globals->haveZconsTol()){
1622	<	zconsTol->setData(globals->getZconsTol());
1915	>	if (globals->haveMinMaxIter()){
1916	>	param->setMaxIteration(globals->getMinMaxIter());
1917		}
1624	–	else{
1625	–	double defaultZConsTol = 0.01;
1626	–	sprintf( painCave.errMsg,
1627	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	–	" , default value %f is used.\n", defaultZConsTol);
1629	–	painCave.isFatal = 0;
1630	–	simError();
1918
1919	<	zconsTol->setData(defaultZConsTol);
1920	<	}
1921	<	theInfo.addProperty(zconsTol);
1919	>	if (globals->haveMinWriteFrq()){
1920	>	param->setMaxIteration(globals->getMinMaxIter());
1921	>	}
1922
1923	<	//set Force Substraction Policy
1924	<	StringData* zconsForcePolicy =  new StringData();
1925	<	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	<
1640	<	if(globals->haveZconsForcePolicy()){
1641	<	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	<	}
1643	<	else{
1644	<	sprintf( painCave.errMsg,
1645	<	"ZConstraint Warning: User does not set force substraction policy, "
1646	<	"average force substraction policy is used\n");
1647	<	painCave.isFatal = 0;
1648	<	simError();
1649	<	zconsForcePolicy->setData("BYNUMBER");
1650	<	}
1651	<
1652	<	theInfo.addProperty(zconsForcePolicy);
1653	<
1654	<	//Determine the name of ouput file and add it into SimInfo's property list
1655	<	//Be careful, do not use inFileName, since it is a pointer which
1656	<	//point to a string at master node, and slave nodes do not contain that string
1923	>	if (globals->haveMinWriteFrq()){
1924	>	param->setWriteFrq(globals->getMinWriteFrq());
1925	>	}
1926
1927	<	string zconsOutput(theInfo.finalName);
1928	<
1929	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	<
1662	<	StringData* zconsFilename = new StringData();
1663	<	zconsFilename->setID(ZCONSFILENAME_ID);
1664	<	zconsFilename->setData(zconsOutput);
1665	<
1666	<	theInfo.addProperty(zconsFilename);
1667	<
1668	<	//setup index, pos and other parameters of z-constraint molecules
1669	<	nZConstraints = globals->getNzConstraints();
1670	<	theInfo.nZconstraints = nZConstraints;
1671	<
1672	<	zconStamp = globals->getZconStamp();
1673	<	ZConsParaItem tempParaItem;
1927	>	if (globals->haveMinStepSize()){
1928	>	param->setStepSize(globals->getMinStepSize());
1929	>	}
1930
1931	<	ZConsParaData* zconsParaData = new ZConsParaData();
1932	<	zconsParaData->setID(ZCONSPARADATA_ID);
1933	<
1678	<	for(int i = 0; i < nZConstraints; i++){
1679	<	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	<	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	<	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	<	tempParaItem.kRatio = zconStamp[i]->getKratio();
1931	>	if (globals->haveMinLSMaxIter()){
1932	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1933	>	}
1934
1935	<	zconsParaData->addItem(tempParaItem);
1935	>	if (globals->haveMinLSTol()){
1936	>	param->setLineSearchTol(globals->getMinLSTol());
1937	>	}
1938	>
1939	>	strcpy(minimizerName, globals->getMinimizer());
1940	>
1941	>	if (!strcasecmp(minimizerName, "CG")){
1942	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1943		}
1944	+	else if (!strcasecmp(minimizerName, "SD")){
1945	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1946	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1947	+	}
1948	+	else{
1949	+	sprintf(painCave.errMsg,
1950	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1951	+	painCave.isFatal = 0;
1952	+	simError();
1953
1954	<	//sort the parameters by index of molecules
1955	<	zconsParaData->sortByIndex();
1956	<
1957	<	//push data into siminfo, therefore, we can retrieve later
1958	<	theInfo.addProperty(zconsParaData);
1959	<
1954	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1955	>	}
1956	>	info[i].the_integrator = myOOPSEMinimizer;
1957	>
1958	>	//store the minimizer into simInfo
1959	>	info[i].the_minimizer = myOOPSEMinimizer;
1960	>	info[i].has_minimizer = true;
1961	>	}
1962	>
1963		}

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