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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 21 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 50 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87		}
88
89
90	<	void SimSetup::parseFile( char* fileName ){
61	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
97	–	int i, j, k, globalAtomIndex;
98	–
126		// gather all of the information from the Bass file
127
128		gatherInfo();
#	Line 110 | Line 137 | void SimSetup::createSim(void){
137
138		// initialize the system coordinates
139
140	<	if( !isInfoArray ) initSystemCoords();
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
118	–
119	–	// make the integrator
150
121	–	makeIntegrator();
122	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 128 | Line 156 | void SimSetup::createSim(void){
156
157		initFortran();
158
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165
132	–
166		}
167
168
169	<	void SimSetup::makeMolecules( void ){
170	<
171	<	int k,l;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186
187		bond_pair* theBonds;
188		bend_set* theBends;
189		torsion_set* theTorsions;
190
191	<
191	>	set<int> skipList;
192	>
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196	>
197		//init the forceField paramters
198
199		the_ff->readParams();
200
158	–
201		// init the atoms
202
203	<	double ux, uy, uz, u, uSqr;
162	<
163	<	for(k=0; k<nInfo; k++){
164	<
165	<	the_ff->setSimInfo( &(info[k]) );
203	>	int nMembers, nNew, rb1, rb2;
204
205	+	for (k = 0; k < nInfo; k++){
206	+	the_ff->setSimInfo(&(info[k]));
207	+
208		atomOffset = 0;
209	<	excludeOffset = 0;
210	<	for(i=0; i<info[k].n_mol; i++){
170	<
209	>
210	>	for (i = 0; i < info[k].n_mol; i++){
211		stampID = info[k].molecules[i].getStampID();
212	+	molName = comp_stamps[stampID]->getID();
213
214	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
215	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
216	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219
220		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];
221
222	+	if (molInfo.nBonds > 0)
223	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	+	else
225	+	molInfo.myBonds = NULL;
226	+
227	+	if (molInfo.nBends > 0)
228	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	+	else
230	+	molInfo.myBends = NULL;
231	+
232	+	if (molInfo.nTorsions > 0)
233	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	+	else
235	+	molInfo.myTorsions = NULL;
236	+
237		theBonds = new bond_pair[molInfo.nBonds];
238		theBends = new bend_set[molInfo.nBends];
239		theTorsions = new torsion_set[molInfo.nTorsions];
240	<
240	>
241		// make the Atoms
242	<
243	<	for(j=0; j<molInfo.nAtoms; j++){
244	<
245	<	currentAtom = comp_stamps[stampID]->getAtom( j );
246	<	if( currentAtom->haveOrientation() ){
247	<
248	<	dAtom = new DirectionalAtom( (j + atomOffset),
249	<	info[k].getConfiguration() );
250	<	info[k].n_oriented++;
251	<	molInfo.myAtoms[j] = dAtom;
252	<
253	<	ux = currentAtom->getOrntX();
254	<	uy = currentAtom->getOrntY();
255	<	uz = currentAtom->getOrntZ();
256	<
257	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258	<
259	<	u = sqrt( uSqr );
260	<	ux = ux / u;
261	<	uy = uy / u;
262	<	uz = uz / u;
263	<
264	<	dAtom->setSUx( ux );
265	<	dAtom->setSUy( uy );
266	<	dAtom->setSUz( uz );
267	<	}
268	<	else{
269	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	<	info[k].getConfiguration() );
219	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
242	>
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245	>
246	>	if (currentAtom->haveOrientation()){
247	>	dAtom = new DirectionalAtom((j + atomOffset),
248	>	info[k].getConfiguration());
249	>	info[k].n_oriented++;
250	>	molInfo.myAtoms[j] = dAtom;
251	>
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255	>
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259	>
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264	>
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266	>
267	>	}
268	>
269	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271	<
272	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
273	<
271	>
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273	>
274		#endif // is_mpi
275		}
276	<
277	<	// make the bonds
278	<	for(j=0; j<molInfo.nBonds; j++){
279	<
280	<	currentBond = comp_stamps[stampID]->getBond( j );
281	<	theBonds[j].a = currentBond->getA() + atomOffset;
282	<	theBonds[j].b = currentBond->getB() + atomOffset;
283	<
284	<	exI = theBonds[j].a;
285	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
276	>
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282	>
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285	>
286		#ifdef IS_MPI
287	<	tempEx = exI;
288	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
289	<	tempEx = exJ;
290	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
291	<
292	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
293	<	#else  // isn't MPI
294	<
295	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
296	<	#endif  //is_mpi
256	<	}
257	<	excludeOffset += molInfo.nBonds;
258	<
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293	>
294	>	info[k].excludes->addPair(exI, exJ);
295	>	}
296	>
297		//make the bends
298	<	for(j=0; j<molInfo.nBends; j++){
299	<
300	<	currentBend = comp_stamps[stampID]->getBend( j );
301	<	theBends[j].a = currentBend->getA() + atomOffset;
302	<	theBends[j].b = currentBend->getB() + atomOffset;
303	<	theBends[j].c = currentBend->getC() + atomOffset;
304	<
305	<	if( currentBend->haveExtras() ){
306	<
307	<	extras = currentBend->getExtras();
308	<	current_extra = extras;
309	<
310	<	while( current_extra != NULL ){
311	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
312	<
313	<	switch( current_extra->getType() ){
314	<
315	<	case 0:
316	<	theBends[j].ghost =
317	<	current_extra->getInt() + atomOffset;
318	<	theBends[j].isGhost = 1;
319	<	break;
320	<
321	<	case 1:
322	<	theBends[j].ghost =
323	<	(int)current_extra->getDouble() + atomOffset;
324	<	theBends[j].isGhost = 1;
325	<	break;
326	<
327	<	default:
328	<	sprintf( painCave.errMsg,
329	<	"SimSetup Error: ghostVectorSource was neither a "
330	<	"double nor an int.\n"
331	<	"-->Bend[%d] in %s\n",
332	<	j, comp_stamps[stampID]->getID() );
333	<	painCave.isFatal = 1;
334	<	simError();
335	<	}
336	<	}
337	<
338	<	else{
339	<
340	<	sprintf( painCave.errMsg,
341	<	"SimSetup Error: unhandled bend assignment:\n"
342	<	"    -->%s in Bend[%d] in %s\n",
343	<	current_extra->getlhs(),
344	<	j, comp_stamps[stampID]->getID() );
345	<	painCave.isFatal = 1;
346	<	simError();
347	<	}
348	<
349	<	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	<	}
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303	>
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307	>
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315	>
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321	>
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>
341	>	current_extra = current_extra->getNext();
342	>	}
343	>	}
344	>
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350		#ifdef IS_MPI
351	<	tempEx = exI;
352	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
353	<	tempEx = exJ;
354	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
355	<
356	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
357	<	#else  // isn't MPI
358	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
359	<	#endif  //is_mpi
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358	>
359	>	} else {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
380	<	excludeOffset += molInfo.nBends;
381	<
382	<	for(j=0; j<molInfo.nTorsions; j++){
383	<
384	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
385	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
386	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
387	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
388	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
389	<
390	<	exI = theTorsions[j].a;
391	<	exJ = theTorsions[j].d;
392	<
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	<	}
380	>
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387	>
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392	>
393		#ifdef IS_MPI
394	<	tempEx = exI;
395	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
396	<	tempEx = exJ;
397	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
398	<
399	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
400	<	#else  // isn't MPI
401	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
402	<	#endif  //is_mpi
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404	>
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411		}
412	<	excludeOffset += molInfo.nTorsions;
412	>
413
414	+	molInfo.myRigidBodies.clear();
415
416	<	// send the arrays off to the forceField for init.
417	<
418	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
419	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
420	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
421	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417	>
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420	>
421	>	// Create the Rigid Body:
422	>
423	>	myRB = new RigidBody();
424	>
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	>
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432	>
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435	>
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	>
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478	>
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481	>	}
482
483	+
484	+	// After this is all set up, scan through the atoms to
485	+	// see if they can be added to the integrableObjects:
486	+
487	+	molInfo.myIntegrableObjects.clear();
488
384	–	info[k].molecules[i].initialize( molInfo );
489
490	+	for (j = 0; j < molInfo.nAtoms; j++){
491	+
492	+	#ifdef IS_MPI
493	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	+	#else
495	+	slJ = j+atomOffset;
496	+	#endif
497	+
498	+	// if they aren't on the skip list, then they can be integrated
499	+
500	+	if (skipList.find(slJ) == skipList.end()) {
501	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	+	info[k].integrableObjects.push_back(mySD);
503	+	molInfo.myIntegrableObjects.push_back(mySD);
504	+	}
505	+	}
506	+
507	+	// all rigid bodies are integrated:
508	+
509	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	+	info[k].integrableObjects.push_back(mySD);
512	+	molInfo.myIntegrableObjects.push_back(mySD);
513	+	}
514	+
515
516	+	// send the arrays off to the forceField for init.
517	+
518	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	+	theTorsions);
523	+
524	+	info[k].molecules[i].initialize(molInfo);
525	+
526	+
527		atomOffset += molInfo.nAtoms;
528		delete[] theBonds;
529		delete[] theBends;
530		delete[] theTorsions;
531	<	}
531	>	}
532		}
533	<
533	>
534		#ifdef IS_MPI
535	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
538	<
538	>
539		// clean up the forcefield
540
541	<	the_ff->calcRcut();
541	>	if (!globals->haveRcut()){
542	>
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getRcut() );
548	>	}
549	>
550		the_ff->cleanMe();
403	–
551		}
552
553	<	void SimSetup::initFromBass( void ){
407	<
553	>	void SimSetup::initFromBass(void){
554		int i, j, k;
555		int n_cells;
556		double cellx, celly, cellz;
#	Line 418 | Line 564 | void SimSetup::initFromBass( void ){
564		vel[1] = 0.0;
565		vel[2] = 0.0;
566
567	<	temp1 = (double)tot_nmol / 4.0;
568	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
569	<	temp3 = ceil( temp2 );
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	<	have_extra =0;
572	<	if( temp2 < temp3 ){ // we have a non-complete lattice
573	<	have_extra =1;
571	>	have_extra = 0;
572	>	if (temp2 < temp3){
573	>	// we have a non-complete lattice
574	>	have_extra = 1;
575
576	<	n_cells = (int)temp3 - 1;
576	>	n_cells = (int) temp3 - 1;
577		cellx = info[0].boxL[0] / temp3;
578		celly = info[0].boxL[1] / temp3;
579		cellz = info[0].boxL[2] / temp3;
580	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
581	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
582	<	n_per_extra = (int)ceil( temp1 );
580	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	>	n_per_extra = (int) ceil(temp1);
583
584	<	if( n_per_extra > 4){
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup error. There has been an error in constructing"
587	<	" the non-complete lattice.\n" );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588		painCave.isFatal = 1;
589		simError();
590		}
591		}
592		else{
593	<	n_cells = (int)temp3;
593	>	n_cells = (int) temp3;
594		cellx = info[0].boxL[0] / temp3;
595		celly = info[0].boxL[1] / temp3;
596		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 601 | void SimSetup::initFromBass( void ){
601		current_comp = 0;
602		current_atom_ndx = 0;
603
604	<	for( i=0; i < n_cells ; i++ ){
605	<	for( j=0; j < n_cells; j++ ){
606	<	for( k=0; k < n_cells; k++ ){
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	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 );
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
615		}
616		}
617
618	<	if( have_extra ){
618	>	if (have_extra){
619		done = 0;
620
621		int start_ndx;
622	<	for( i=0; i < (n_cells+1) && !done; i++ ){
623	<	for( j=0; j < (n_cells+1) && !done; j++ ){
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	if( i < n_cells ){
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( j < n_cells ){
639	<	start_ndx = n_cells;
640	<	}
641	<	else start_ndx = 0;
642	<	}
494	<	else start_ndx = 0;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	makeElement( i * cellx,
651	<	j * celly,
652	<	k * cellz );
653	<	done = ( current_mol >= tot_nmol );
654	<
655	<	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	<	}
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657		}
658		}
659
660	<	for( i=0; i<info[0].n_atoms; i++ ){
661	<	info[0].atoms[i]->setVel( vel );
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662		}
663		}
664
665	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
665	>	void SimSetup::makeElement(double x, double y, double z){
666		int k;
667		AtomStamp* current_atom;
668		DirectionalAtom* dAtom;
669		double rotMat[3][3];
670		double pos[3];
671
672	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
673	<
674	<	current_atom = comp_stamps[current_comp]->getAtom( k );
675	<	if( !current_atom->havePosition() ){
676	<	sprintf( painCave.errMsg,
677	<	"SimSetup:initFromBass error.\n"
678	<	"\tComponent %s, atom %s does not have a position specified.\n"
679	<	"\tThe initialization routine is unable to give a start"
680	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
684	<
684	>
685		pos[0] = x + current_atom->getPosX();
686		pos[1] = y + current_atom->getPosY();
687		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
688
689	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694		rotMat[0][0] = 1.0;
695		rotMat[0][1] = 0.0;
#	Line 575 | Line 703 | void SimSetup::makeElement( double x, double y, double
703		rotMat[2][1] = 0.0;
704		rotMat[2][2] = 1.0;
705
706	<	dAtom->setA( rotMat );
706	>	dAtom->setA(rotMat);
707		}
708
709		current_atom_ndx++;
#	Line 584 | Line 712 | void SimSetup::makeElement( double x, double y, double
712		current_mol++;
713		current_comp_mol++;
714
715	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716		current_comp_mol = 0;
717		current_comp++;
718		}
719		}
720
721
722	<	void SimSetup::gatherInfo( void ){
723	<	int i,j,k;
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725		ensembleCase = -1;
726		ffCase = -1;
727
728		// set the easy ones first
729
730	<	for( i=0; i<nInfo; i++){
730	>	for (i = 0; i < nInfo; i++){
731		info[i].target_temp = globals->getTargetTemp();
732		info[i].dt = globals->getDt();
733		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 737 | void SimSetup::gatherInfo( void ){
737
738		// get the forceField
739
740	<	strcpy( force_field, globals->getForceField() );
740	>	strcpy(force_field, globals->getForceField());
741
742	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
743	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
744	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
742	>	if (!strcasecmp(force_field, "DUFF")){
743	>	ffCase = FF_DUFF;
744	>	}
745	>	else if (!strcasecmp(force_field, "LJ")){
746	>	ffCase = FF_LJ;
747	>	}
748	>	else if (!strcasecmp(force_field, "EAM")){
749	>	ffCase = FF_EAM;
750	>	}
751	>	else if (!strcasecmp(force_field, "WATER")){
752	>	ffCase = FF_H2O;
753	>	}
754		else{
755	<	sprintf( painCave.errMsg,
756	<	"SimSetup Error. Unrecognized force field -> %s\n",
757	<	force_field );
758	<	painCave.isFatal = 1;
623	<	simError();
755	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	>	force_field);
757	>	painCave.isFatal = 1;
758	>	simError();
759		}
760
761	<	// get the ensemble
761	>	// get the ensemble
762
763	<	strcpy( ensemble, globals->getEnsemble() );
763	>	strcpy(ensemble, globals->getEnsemble());
764
765	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
766	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
767	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
765	>	if (!strcasecmp(ensemble, "NVE")){
766	>	ensembleCase = NVE_ENS;
767	>	}
768	>	else if (!strcasecmp(ensemble, "NVT")){
769	>	ensembleCase = NVT_ENS;
770	>	}
771	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772		ensembleCase = NPTi_ENS;
773	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
774	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
775	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
773	>	}
774	>	else if (!strcasecmp(ensemble, "NPTf")){
775	>	ensembleCase = NPTf_ENS;
776	>	}
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779	>	}
780		else{
781	<	sprintf( painCave.errMsg,
782	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
783	<	"reverting to NVE for this simulation.\n",
784	<	ensemble );
785	<	painCave.isFatal = 0;
786	<	simError();
787	<	strcpy( ensemble, "NVE" );
788	<	ensembleCase = NVE_ENS;
781	>	sprintf(painCave.errMsg,
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784	>	ensemble);
785	>	painCave.isFatal = 0;
786	>	simError();
787	>	strcpy(ensemble, "NVE");
788	>	ensembleCase = NVE_ENS;
789		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
790
791	+	for (i = 0; i < nInfo; i++){
792	+	strcpy(info[i].ensemble, ensemble);
793	+
794		// get the mixing rule
795
796	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797		info[i].usePBC = globals->getPBC();
798		}
799	<
799	>
800		// get the components and calculate the tot_nMol and indvidual n_mol
801	<
801	>
802		the_components = globals->getComponents();
803		components_nmol = new int[n_components];
804
805
806	<	if( !globals->haveNMol() ){
806	>	if (!globals->haveNMol()){
807		// we don't have the total number of molecules, so we assume it is
808		// given in each component
809
810		tot_nmol = 0;
811	<	for( i=0; i<n_components; i++ ){
812	<
813	<	if( !the_components[i]->haveNMol() ){
814	<	// we have a problem
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup Error. No global NMol or component NMol"
817	<	" given. Cannot calculate the number of atoms.\n" );
818	<	painCave.isFatal = 1;
677	<	simError();
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819		}
820
821		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 823 | void SimSetup::gatherInfo( void ){
823		}
824		}
825		else{
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup error.\n"
828	<	"\tSorry, the ability to specify total"
829	<	" nMols and then give molfractions in the components\n"
830	<	"\tis not currently supported."
831	<	" Please give nMol in the components.\n" );
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup error.\n"
828	>	"\tSorry, the ability to specify total"
829	>	" nMols and then give molfractions in the components\n"
830	>	"\tis not currently supported."
831	>	" Please give nMol in the components.\n");
832		painCave.isFatal = 1;
833		simError();
834		}
835
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time.  If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time.  If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time.  If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time.  If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876	+
877		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
878
879	<	if( globals->haveSampleTime() ){
879	>	for (i = 0; i < nInfo; i++){
880	>	if (globals->haveSampleTime()){
881		info[i].sampleTime = globals->getSampleTime();
882		info[i].statusTime = info[i].sampleTime;
702	–	info[i].thermalTime = info[i].sampleTime;
883		}
884		else{
885		info[i].sampleTime = globals->getRunTime();
886		info[i].statusTime = info[i].sampleTime;
707	–	info[i].thermalTime = info[i].sampleTime;
887		}
888	<
889	<	if( globals->haveStatusTime() ){
888	>
889	>	if (globals->haveStatusTime()){
890		info[i].statusTime = globals->getStatusTime();
891		}
892	<
893	<	if( globals->haveThermalTime() ){
892	>
893	>	if (globals->haveThermalTime()){
894		info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897		}
898
899	+	info[i].resetIntegrator = 0;
900	+	if( globals->haveResetTime() ){
901	+	info[i].resetTime = globals->getResetTime();
902	+	info[i].resetIntegrator = 1;
903	+	}
904	+
905		// check for the temperature set flag
906	+
907	+	if (globals->haveTempSet())
908	+	info[i].setTemp = globals->getTempSet();
909
910	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
910	>	// check for the extended State init
911	>
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914
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 );
915		}
916	<	else{
917	<	if( !globals->haveBoxX() ){
918	<	sprintf( painCave.errMsg,
919	<	"SimSetup error, no periodic BoxX size given.\n" );
920	<	painCave.isFatal = 1;
921	<	simError();
922	<	}
923	<	boxVector[0] = globals->getBoxX();
924	<
925	<	if( !globals->haveBoxY() ){
926	<	sprintf( painCave.errMsg,
927	<	"SimSetup error, no periodic BoxY size given.\n" );
928	<	painCave.isFatal = 1;
929	<	simError();
916	>
917	>	//setup seed for random number generator
918	>	int seedValue;
919	>
920	>	if (globals->haveSeed()){
921	>	seedValue = globals->getSeed();
922	>
923	>	if(seedValue / 1E9 == 0){
924	>	sprintf(painCave.errMsg,
925	>	"Seed for sprng library should contain at least 9 digits\n"
926	>	"OOPSE will generate a seed for user\n");
927	>	painCave.isFatal = 0;
928	>	simError();
929	>
930	>	//using seed generated by system instead of invalid seed set by user
931	>	#ifndef IS_MPI
932	>	seedValue = make_sprng_seed();
933	>	#else
934	>	if (worldRank == 0){
935	>	seedValue = make_sprng_seed();
936		}
937	<	boxVector[1] = globals->getBoxY();
938	<
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 );
937	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
938	>	#endif
939		}
940	+	}//end of if branch of globals->haveSeed()
941	+	else{
942	+
943	+	#ifndef IS_MPI
944	+	seedValue = make_sprng_seed();
945	+	#else
946	+	if (worldRank == 0){
947	+	seedValue = make_sprng_seed();
948	+	}
949	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
950	+	#endif
951	+	}//end of globals->haveSeed()
952
953	+	for (int i = 0; i < nInfo; i++){
954	+	info[i].setSeed(seedValue);
955		}
956	<
956	>
957		#ifdef IS_MPI
958	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
958	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959		MPIcheckPoint();
960		#endif // is_mpi
776	–
961		}
962
963
964	<	void SimSetup::finalInfoCheck( void ){
964	>	void SimSetup::finalInfoCheck(void){
965		int index;
966		int usesDipoles;
967	+	int usesCharges;
968		int i;
969
970	<	for(i=0; i<nInfo; i++){
970	>	for (i = 0; i < nInfo; i++){
971		// check electrostatic parameters
972	<
972	>
973		index = 0;
974		usesDipoles = 0;
975	<	while( (index < info[i].n_atoms) && !usesDipoles ){
975	>	while ((index < info[i].n_atoms) && !usesDipoles){
976		usesDipoles = (info[i].atoms[index])->hasDipole();
977		index++;
978		}
979	<
979	>	index = 0;
980	>	usesCharges = 0;
981	>	while ((index < info[i].n_atoms) && !usesCharges){
982	>	usesCharges= (info[i].atoms[index])->hasCharge();
983	>	index++;
984	>	}
985		#ifdef IS_MPI
986		int myUse = usesDipoles;
987	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
987	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988		#endif //is_mpi
989	<
990	<	double theEcr, theEst;
991	<
992	<	if (globals->getUseRF() ) {
989	>
990	>	double theRcut, theRsw;
991	>
992	>	if (globals->getUseRF()){
993		info[i].useReactionField = 1;
994	<
995	<	if( !globals->haveECR() ){
996	<	sprintf( painCave.errMsg,
997	<	"SimSetup Warning: using default value of 1/2 the smallest "
998	<	"box length for the electrostaticCutoffRadius.\n"
999	<	"I hope you have a very fast processor!\n");
1000	<	painCave.isFatal = 0;
1001	<	simError();
1002	<	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();
994	>
995	>	if (!globals->haveRcut()){
996	>	sprintf(painCave.errMsg,
997	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
998	>	"\tOOPSE will use a default value of 15.0 angstroms"
999	>	"\tfor the cutoffRadius.\n");
1000	>	painCave.isFatal = 0;
1001	>	simError();
1002	>	theRcut = 15.0;
1003		}
1004	<
1005	<	if( !globals->haveEST() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	<	);
826	<	painCave.isFatal = 0;
827	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
1004	>	else{
1005	>	theRcut = globals->getRcut();
1006		}
1007	<
1008	<	info[i].setEcr( theEcr, theEst );
1009	<
1010	<	if(!globals->haveDielectric() ){
1011	<	sprintf( painCave.errMsg,
1012	<	"SimSetup Error: You are trying to use Reaction Field without"
1013	<	"setting a dielectric constant!\n"
1014	<	);
1015	<	painCave.isFatal = 1;
841	<	simError();
1007	>
1008	>	if (!globals->haveRsw()){
1009	>	sprintf(painCave.errMsg,
1010	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	theRsw = 0.95 * theRcut;
1016		}
1017	<	info[i].dielectric = globals->getDielectric();
1018	<	}
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 );
1017	>	else{
1018	>	theRsw = globals->getRsw();
1019		}
879	–	}
880	–	}
1020
1021	+	info[i].setDefaultRcut(theRcut, theRsw);
1022	+
1023	+	if (!globals->haveDielectric()){
1024	+	sprintf(painCave.errMsg,
1025	+	"SimSetup Error: No Dielectric constant was set.\n"
1026	+	"\tYou are trying to use Reaction Field without"
1027	+	"\tsetting a dielectric constant!\n");
1028	+	painCave.isFatal = 1;
1029	+	simError();
1030	+	}
1031	+	info[i].dielectric = globals->getDielectric();
1032	+	}
1033	+	else{
1034	+	if (usesDipoles || usesCharges){
1035	+
1036	+	if (!globals->haveRcut()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1039	+	"\tOOPSE will use a default value of 15.0 angstroms"
1040	+	"\tfor the cutoffRadius.\n");
1041	+	painCave.isFatal = 0;
1042	+	simError();
1043	+	theRcut = 15.0;
1044	+	}
1045	+	else{
1046	+	theRcut = globals->getRcut();
1047	+	}
1048	+
1049	+	if (!globals->haveRsw()){
1050	+	sprintf(painCave.errMsg,
1051	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1052	+	"\tOOPSE will use a default value of\n"
1053	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1054	+	painCave.isFatal = 0;
1055	+	simError();
1056	+	theRsw = 0.95 * theRcut;
1057	+	}
1058	+	else{
1059	+	theRsw = globals->getRsw();
1060	+	}
1061	+
1062	+	info[i].setDefaultRcut(theRcut, theRsw);
1063	+
1064	+	}
1065	+	}
1066	+	}
1067		#ifdef IS_MPI
1068	<	strcpy( checkPointMsg, "post processing checks out" );
1068	>	strcpy(checkPointMsg, "post processing checks out");
1069		MPIcheckPoint();
1070		#endif // is_mpi
886	–
1071		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
1072
1073	+	void SimSetup::initSystemCoords(void){
1074	+	int i;
1075	+
1076		char* inName;
1077
1078	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079
1080	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1081	<
1082	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1083	<
899	<	if( globals->haveInitialConfig() ){
900	<
1080	>	for (i = 0; i < info[0].n_atoms; i++)
1081	>	info[0].atoms[i]->setCoords();
1082	>
1083	>	if (globals->haveInitialConfig()){
1084		InitializeFromFile* fileInit;
1085		#ifdef IS_MPI // is_mpi
1086	<	if( worldRank == 0 ){
1086	>	if (worldRank == 0){
1087		#endif //is_mpi
1088		inName = globals->getInitialConfig();
1089	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
1089	>	fileInit = new InitializeFromFile(inName);
1090		#ifdef IS_MPI
1091	<	}else fileInit = new InitializeFromFile( NULL );
1091	>	}
1092	>	else
1093	>	fileInit = new InitializeFromFile(NULL);
1094		#endif
1095	<	fileInit->readInit( info ); // default velocities on
1096	<
1095	>	fileInit->readInit(info); // default velocities on
1096	>
1097		delete fileInit;
1098		}
1099		else{
1100
917	–	#ifdef IS_MPI
918	–
1101		// no init from bass
1102
1103	<	sprintf( painCave.errMsg,
1104	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1105	<	painCave.isFatal;
1103	>	sprintf(painCave.errMsg,
1104	>	"Cannot intialize a simulation without an initial configuration file.\n");
1105	>	painCave.isFatal = 1;;
1106		simError();
1107
926	–	#else
927	–
928	–	initFromBass();
929	–
930	–
931	–	#endif
1108		}
1109	<
1109	>
1110		#ifdef IS_MPI
1111	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1111	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112		MPIcheckPoint();
1113		#endif // is_mpi
938	–
1114		}
1115
1116
1117	<	void SimSetup::makeOutNames( void ){
943	<
1117	>	void SimSetup::makeOutNames(void){
1118		int k;
1119
946	–
947	–	for(k=0; k<nInfo; k++){
1120
1121	+	for (k = 0; k < nInfo; k++){
1122		#ifdef IS_MPI
1123	<	if( worldRank == 0 ){
1123	>	if (worldRank == 0){
1124		#endif // is_mpi
1125	<
1126	<	if( globals->haveFinalConfig() ){
1127	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1125	>
1126	>	if (globals->haveFinalConfig()){
1127	>	strcpy(info[k].finalName, globals->getFinalConfig());
1128		}
1129		else{
1130	<	strcpy( info[k].finalName, inFileName );
1131	<	char* endTest;
1132	<	int nameLength = strlen( info[k].finalName );
1133	<	endTest = &(info[k].finalName[nameLength - 5]);
1134	<	if( !strcmp( endTest, ".bass" ) ){
1135	<	strcpy( endTest, ".eor" );
1136	<	}
1137	<	else if( !strcmp( endTest, ".BASS" ) ){
1138	<	strcpy( endTest, ".eor" );
1139	<	}
1140	<	else{
1141	<	endTest = &(info[k].finalName[nameLength - 4]);
1142	<	if( !strcmp( endTest, ".bss" ) ){
1143	<	strcpy( endTest, ".eor" );
1144	<	}
1145	<	else if( !strcmp( endTest, ".mdl" ) ){
1146	<	strcpy( endTest, ".eor" );
1147	<	}
1148	<	else{
1149	<	strcat( info[k].finalName, ".eor" );
1150	<	}
1151	<	}
1130	>	strcpy(info[k].finalName, inFileName);
1131	>	char* endTest;
1132	>	int nameLength = strlen(info[k].finalName);
1133	>	endTest = &(info[k].finalName[nameLength - 5]);
1134	>	if (!strcmp(endTest, ".bass")){
1135	>	strcpy(endTest, ".eor");
1136	>	}
1137	>	else if (!strcmp(endTest, ".BASS")){
1138	>	strcpy(endTest, ".eor");
1139	>	}
1140	>	else{
1141	>	endTest = &(info[k].finalName[nameLength - 4]);
1142	>	if (!strcmp(endTest, ".bss")){
1143	>	strcpy(endTest, ".eor");
1144	>	}
1145	>	else if (!strcmp(endTest, ".mdl")){
1146	>	strcpy(endTest, ".eor");
1147	>	}
1148	>	else{
1149	>	strcat(info[k].finalName, ".eor");
1150	>	}
1151	>	}
1152		}
1153	<
1153	>
1154		// make the sample and status out names
1155	<
1156	<	strcpy( info[k].sampleName, inFileName );
1155	>
1156	>	strcpy(info[k].sampleName, inFileName);
1157		char* endTest;
1158	<	int nameLength = strlen( info[k].sampleName );
1158	>	int nameLength = strlen(info[k].sampleName);
1159		endTest = &(info[k].sampleName[nameLength - 5]);
1160	<	if( !strcmp( endTest, ".bass" ) ){
1161	<	strcpy( endTest, ".dump" );
1160	>	if (!strcmp(endTest, ".bass")){
1161	>	strcpy(endTest, ".dump");
1162		}
1163	<	else if( !strcmp( endTest, ".BASS" ) ){
1164	<	strcpy( endTest, ".dump" );
1163	>	else if (!strcmp(endTest, ".BASS")){
1164	>	strcpy(endTest, ".dump");
1165		}
1166		else{
1167	<	endTest = &(info[k].sampleName[nameLength - 4]);
1168	<	if( !strcmp( endTest, ".bss" ) ){
1169	<	strcpy( endTest, ".dump" );
1170	<	}
1171	<	else if( !strcmp( endTest, ".mdl" ) ){
1172	<	strcpy( endTest, ".dump" );
1173	<	}
1174	<	else{
1175	<	strcat( info[k].sampleName, ".dump" );
1176	<	}
1004	<	}
1005	<
1006	<	strcpy( info[k].statusName, inFileName );
1007	<	nameLength = strlen( info[k].statusName );
1008	<	endTest = &(info[k].statusName[nameLength - 5]);
1009	<	if( !strcmp( endTest, ".bass" ) ){
1010	<	strcpy( endTest, ".stat" );
1011	<	}
1012	<	else if( !strcmp( endTest, ".BASS" ) ){
1013	<	strcpy( endTest, ".stat" );
1167	>	endTest = &(info[k].sampleName[nameLength - 4]);
1168	>	if (!strcmp(endTest, ".bss")){
1169	>	strcpy(endTest, ".dump");
1170	>	}
1171	>	else if (!strcmp(endTest, ".mdl")){
1172	>	strcpy(endTest, ".dump");
1173	>	}
1174	>	else{
1175	>	strcat(info[k].sampleName, ".dump");
1176	>	}
1177		}
1178	+
1179	+	strcpy(info[k].statusName, inFileName);
1180	+	nameLength = strlen(info[k].statusName);
1181	+	endTest = &(info[k].statusName[nameLength - 5]);
1182	+	if (!strcmp(endTest, ".bass")){
1183	+	strcpy(endTest, ".stat");
1184	+	}
1185	+	else if (!strcmp(endTest, ".BASS")){
1186	+	strcpy(endTest, ".stat");
1187	+	}
1188		else{
1189	<	endTest = &(info[k].statusName[nameLength - 4]);
1190	<	if( !strcmp( endTest, ".bss" ) ){
1191	<	strcpy( endTest, ".stat" );
1192	<	}
1193	<	else if( !strcmp( endTest, ".mdl" ) ){
1194	<	strcpy( endTest, ".stat" );
1195	<	}
1196	<	else{
1197	<	strcat( info[k].statusName, ".stat" );
1198	<	}
1189	>	endTest = &(info[k].statusName[nameLength - 4]);
1190	>	if (!strcmp(endTest, ".bss")){
1191	>	strcpy(endTest, ".stat");
1192	>	}
1193	>	else if (!strcmp(endTest, ".mdl")){
1194	>	strcpy(endTest, ".stat");
1195	>	}
1196	>	else{
1197	>	strcat(info[k].statusName, ".stat");
1198	>	}
1199		}
1200	<
1200	>
1201		#ifdef IS_MPI
1202	+
1203		}
1204		#endif // is_mpi
1205		}
1206		}
1207
1208
1209	<	void SimSetup::sysObjectsCreation( void ){
1210	<
1211	<	int i,k;
1038	<
1209	>	void SimSetup::sysObjectsCreation(void){
1210	>	int i, k;
1211	>
1212		// create the forceField
1213
1214		createFF();
#	Line 1050 | Line 1223 | void SimSetup::sysObjectsCreation( void ){
1223
1224		#ifdef IS_MPI
1225		// divide the molecules among the processors
1226	<
1226	>
1227		mpiMolDivide();
1228		#endif //is_mpi
1229	<
1229	>
1230		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231	<
1231	>
1232		makeSysArrays();
1233
1234		// make and initialize the molecules (all but atomic coordinates)
1235	<
1235	>
1236		makeMolecules();
1237	<
1238	<	for(k=0; k<nInfo; k++){
1237	>
1238	>	for (k = 0; k < nInfo; k++){
1239		info[k].identArray = new int[info[k].n_atoms];
1240	<	for(i=0; i<info[k].n_atoms; i++){
1240	>	for (i = 0; i < info[k].n_atoms; i++){
1241		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1242		}
1243		}
1244		}
1245
1246
1247	<	void SimSetup::createFF( void ){
1247	>	void SimSetup::createFF(void){
1248	>	switch (ffCase){
1249	>	case FF_DUFF:
1250	>	the_ff = new DUFF();
1251	>	break;
1252
1253	<	switch( ffCase ){
1253	>	case FF_LJ:
1254	>	the_ff = new LJFF();
1255	>	break;
1256
1257	<	case FF_DUFF:
1258	<	the_ff = new DUFF();
1259	<	break;
1257	>	case FF_EAM:
1258	>	the_ff = new EAM_FF();
1259	>	break;
1260
1261	<	case FF_LJ:
1262	<	the_ff = new LJFF();
1263	<	break;
1261	>	case FF_H2O:
1262	>	the_ff = new WATER();
1263	>	break;
1264
1265	<	case FF_EAM:
1266	<	the_ff = new EAM_FF();
1267	<	break;
1268	<
1269	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	simError();
1265	>	default:
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1268	>	painCave.isFatal = 1;
1269	>	simError();
1270		}
1271
1272		#ifdef IS_MPI
1273	<	strcpy( checkPointMsg, "ForceField creation successful" );
1273	>	strcpy(checkPointMsg, "ForceField creation successful");
1274		MPIcheckPoint();
1275		#endif // is_mpi
1101	–
1276		}
1277
1278
1279	<	void SimSetup::compList( void ){
1106	<
1279	>	void SimSetup::compList(void){
1280		int i;
1281		char* id;
1282		LinkedMolStamp* headStamp = new LinkedMolStamp();
1283		LinkedMolStamp* currentStamp = NULL;
1284	<	comp_stamps = new MoleculeStamp*[n_components];
1285	<
1284	>	comp_stamps = new MoleculeStamp * [n_components];
1285	>
1286		// make an array of molecule stamps that match the components used.
1287		// also extract the used stamps out into a separate linked list
1288	<
1289	<	for(i=0; i<nInfo; i++){
1288	>
1289	>	for (i = 0; i < nInfo; i++){
1290		info[i].nComponents = n_components;
1291		info[i].componentsNmol = components_nmol;
1292		info[i].compStamps = comp_stamps;
1293		info[i].headStamp = headStamp;
1294		}
1122	–
1295
1124	–	for( i=0; i<n_components; i++ ){
1296
1297	+	for (i = 0; i < n_components; i++){
1298		id = the_components[i]->getType();
1299		comp_stamps[i] = NULL;
1300	<
1300	>
1301		// check to make sure the component isn't already in the list
1302
1303	<	comp_stamps[i] = headStamp->match( id );
1304	<	if( comp_stamps[i] == NULL ){
1133	<
1303	>	comp_stamps[i] = headStamp->match(id);
1304	>	if (comp_stamps[i] == NULL){
1305		// extract the component from the list;
1306	<
1307	<	currentStamp = stamps->extractMolStamp( id );
1308	<	if( currentStamp == NULL ){
1309	<	sprintf( painCave.errMsg,
1310	<	"SimSetup error: Component \"%s\" was not found in the "
1311	<	"list of declared molecules\n",
1312	<	id );
1313	<	painCave.isFatal = 1;
1314	<	simError();
1306	>
1307	>	currentStamp = stamps->extractMolStamp(id);
1308	>	if (currentStamp == NULL){
1309	>	sprintf(painCave.errMsg,
1310	>	"SimSetup error: Component \"%s\" was not found in the "
1311	>	"list of declared molecules\n",
1312	>	id);
1313	>	painCave.isFatal = 1;
1314	>	simError();
1315		}
1316	<
1317	<	headStamp->add( currentStamp );
1318	<	comp_stamps[i] = headStamp->match( id );
1316	>
1317	>	headStamp->add(currentStamp);
1318	>	comp_stamps[i] = headStamp->match(id);
1319		}
1320		}
1321
1322		#ifdef IS_MPI
1323	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1323	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1324		MPIcheckPoint();
1325		#endif // is_mpi
1326	+	}
1327
1328	+	void SimSetup::calcSysValues(void){
1329	+	int i;
1330
1331	<	}
1331	>	int* molMembershipArray;
1332
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1333		tot_atoms = 0;
1334		tot_bonds = 0;
1335		tot_bends = 0;
1336		tot_torsions = 0;
1337	<	for( i=0; i<n_components; i++ ){
1338	<
1339	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1341	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1337	>	tot_rigid = 0;
1338	>	for (i = 0; i < n_components; i++){
1339	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344		}
1345
1346		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347		molMembershipArray = new int[tot_atoms];
1348	<
1349	<	for(i=0; i<nInfo; i++){
1348	>
1349	>	for (i = 0; i < nInfo; i++){
1350		info[i].n_atoms = tot_atoms;
1351		info[i].n_bonds = tot_bonds;
1352		info[i].n_bends = tot_bends;
1353		info[i].n_torsions = tot_torsions;
1354		info[i].n_SRI = tot_SRI;
1355		info[i].n_mol = tot_nmol;
1356	<
1356	>
1357		info[i].molMembershipArray = molMembershipArray;
1358	<	}
1358	>	}
1359		}
1360
1361		#ifdef IS_MPI
1362
1363	<	void SimSetup::mpiMolDivide( void ){
1194	<
1363	>	void SimSetup::mpiMolDivide(void){
1364		int i, j, k;
1365		int localMol, allMol;
1366		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	+	int local_rigid;
1368	+	vector<int> globalMolIndex;
1369
1370	<	mpiSim = new mpiSimulation( info );
1200	<
1201	<	globalIndex = mpiSim->divideLabor();
1370	>	mpiSim = new mpiSimulation(info);
1371
1372	+	mpiSim->divideLabor();
1373	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1374	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1375	+
1376		// set up the local variables
1377	<
1377	>
1378		mol2proc = mpiSim->getMolToProcMap();
1379		molCompType = mpiSim->getMolComponentType();
1380	<
1380	>
1381		allMol = 0;
1382		localMol = 0;
1383		local_atoms = 0;
1384		local_bonds = 0;
1385		local_bends = 0;
1386		local_torsions = 0;
1387	<	globalAtomIndex = 0;
1387	>	local_rigid = 0;
1388	>	globalAtomCounter = 0;
1389
1390	<
1391	<	for( i=0; i<n_components; i++ ){
1392	<
1393	<	for( j=0; j<components_nmol[i]; j++ ){
1394	<
1395	<	if( mol2proc[allMol] == worldRank ){
1396	<
1397	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1398	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1390	>	for (i = 0; i < n_components; i++){
1391	>	for (j = 0; j < components_nmol[i]; j++){
1392	>	if (mol2proc[allMol] == worldRank){
1393	>	local_atoms += comp_stamps[i]->getNAtoms();
1394	>	local_bonds += comp_stamps[i]->getNBonds();
1395	>	local_bends += comp_stamps[i]->getNBends();
1396	>	local_torsions += comp_stamps[i]->getNTorsions();
1397	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1398	>	localMol++;
1399		}
1400	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1401	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1402	<	globalAtomIndex++;
1400	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1401	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1402	>	globalAtomCounter++;
1403		}
1404
1405	<	allMol++;
1405	>	allMol++;
1406		}
1407		}
1408		local_SRI = local_bonds + local_bends + local_torsions;
1409	<
1409	>
1410		info[0].n_atoms = mpiSim->getMyNlocal();
1411
1412	<	if( local_atoms != info[0].n_atoms ){
1413	<	sprintf( painCave.errMsg,
1414	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1415	<	" localAtom (%d) are not equal.\n",
1416	<	info[0].n_atoms,
1417	<	local_atoms );
1412	>
1413	>	if (local_atoms != info[0].n_atoms){
1414	>	sprintf(painCave.errMsg,
1415	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1416	>	"\tlocalAtom (%d) are not equal.\n",
1417	>	info[0].n_atoms, local_atoms);
1418		painCave.isFatal = 1;
1419		simError();
1420		}
#	Line 1254 | Line 1425 | void SimSetup::mpiMolDivide( void ){
1425		info[0].n_SRI = local_SRI;
1426		info[0].n_mol = localMol;
1427
1428	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1428	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1429		MPIcheckPoint();
1430		}
1431	<
1431	>
1432		#endif // is_mpi
1433
1434
1435	<	void SimSetup::makeSysArrays( void ){
1436	<	int i, j, k, l;
1435	>	void SimSetup::makeSysArrays(void){
1436	>
1437	>	#ifndef IS_MPI
1438	>	int k, j;
1439	>	#endif // is_mpi
1440	>	int i, l;
1441
1442		Atom** the_atoms;
1443		Molecule* the_molecules;
1269	–	Exclude** the_excludes;
1444
1445	<
1272	<	for(l=0; l<nInfo; l++){
1273	<
1445	>	for (l = 0; l < nInfo; l++){
1446		// create the atom and short range interaction arrays
1447	<
1448	<	the_atoms = new Atom*[info[l].n_atoms];
1447	>
1448	>	the_atoms = new Atom * [info[l].n_atoms];
1449		the_molecules = new Molecule[info[l].n_mol];
1450		int molIndex;
1451
1452		// initialize the molecule's stampID's
1453	<
1453	>
1454		#ifdef IS_MPI
1455	<
1456	<
1455	>
1456	>
1457		molIndex = 0;
1458	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1459	<
1460	<	if(mol2proc[i] == worldRank ){
1461	<	the_molecules[molIndex].setStampID( molCompType[i] );
1462	<	the_molecules[molIndex].setMyIndex( molIndex );
1463	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
1458	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1459	>	if (mol2proc[i] == worldRank){
1460	>	the_molecules[molIndex].setStampID(molCompType[i]);
1461	>	the_molecules[molIndex].setMyIndex(molIndex);
1462	>	the_molecules[molIndex].setGlobalIndex(i);
1463	>	molIndex++;
1464		}
1465		}
1466	<
1466	>
1467		#else // is_mpi
1468	<
1468	>
1469		molIndex = 0;
1470	<	globalAtomIndex = 0;
1471	<	for(i=0; i<n_components; i++){
1472	<	for(j=0; j<components_nmol[i]; j++ ){
1473	<	the_molecules[molIndex].setStampID( i );
1474	<	the_molecules[molIndex].setMyIndex( molIndex );
1475	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1476	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1477	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1478	<	globalAtomIndex++;
1479	<	}
1480	<	molIndex++;
1470	>	globalAtomCounter = 0;
1471	>	for (i = 0; i < n_components; i++){
1472	>	for (j = 0; j < components_nmol[i]; j++){
1473	>	the_molecules[molIndex].setStampID(i);
1474	>	the_molecules[molIndex].setMyIndex(molIndex);
1475	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1476	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1477	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1478	>	globalAtomCounter++;
1479	>	}
1480	>	molIndex++;
1481		}
1482		}
1312	–
1313	–
1314	–	#endif // is_mpi
1483
1484
1485	<	if( info[l].n_SRI ){
1485	>	#endif // is_mpi
1486	>
1487	>	info[l].globalExcludes = new int;
1488	>	info[l].globalExcludes[0] = 0;
1489
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	–	}
1337	–
1490		// set the arrays into the SimInfo object
1491
1492		info[l].atoms = the_atoms;
1493		info[l].molecules = the_molecules;
1494		info[l].nGlobalExcludes = 0;
1343	–	info[l].excludes = the_excludes;
1495
1496	<	the_ff->setSimInfo( info );
1346	<
1496	>	the_ff->setSimInfo(info);
1497		}
1498		}
1499
1500	<	void SimSetup::makeIntegrator( void ){
1351	<
1500	>	void SimSetup::makeIntegrator(void){
1501		int k;
1502
1503	<	NVT<RealIntegrator>*  myNVT = NULL;
1504	<	NPTi<RealIntegrator>* myNPTi = NULL;
1505	<	NPTf<RealIntegrator>* myNPTf = NULL;
1506	<	NPTim<RealIntegrator>* myNPTim = NULL;
1507	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1508	<
1509	<	for(k=0; k<nInfo; k++){
1510	<
1511	<	switch( ensembleCase ){
1512	<
1513	<	case NVE_ENS:
1514	<	if (globals->haveZconstraints()){
1515	<	setupZConstraint(info[k]);
1516	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1503	>	NVE<RealIntegrator>* myNVE = NULL;
1504	>	NVT<RealIntegrator>* myNVT = NULL;
1505	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1506	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1507	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1508	>
1509	>	for (k = 0; k < nInfo; k++){
1510	>	switch (ensembleCase){
1511	>	case NVE_ENS:
1512	>	if (globals->haveZconstraints()){
1513	>	setupZConstraint(info[k]);
1514	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1515	>	}
1516	>	else{
1517	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1518		}
1519	+
1520	+	info->the_integrator = myNVE;
1521	+	break;
1522
1523	<	else
1524	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1525	<	break;
1526	<
1527	<	case NVT_ENS:
1528	<	if (globals->haveZconstraints()){
1529	<	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 );
1523	>	case NVT_ENS:
1524	>	if (globals->haveZconstraints()){
1525	>	setupZConstraint(info[k]);
1526	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1527	>	}
1528	>	else
1529	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1530
1531	<	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 );
1531	>	myNVT->setTargetTemp(globals->getTargetTemp());
1532
1533	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1534	<
1535	<	if (globals->haveTargetPressure())
1536	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1537	<	else {
1538	<	sprintf( painCave.errMsg,
1539	<	"SimSetup error: If you use a constant pressure\n"
1540	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1541	<	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 );
1533	>	if (globals->haveTauThermostat())
1534	>	myNVT->setTauThermostat(globals->getTauThermostat());
1535	>	else{
1536	>	sprintf(painCave.errMsg,
1537	>	"SimSetup error: If you use the NVT\n"
1538	>	"\tensemble, you must set tauThermostat.\n");
1539	>	painCave.isFatal = 1;
1540	>	simError();
1541	>	}
1542
1543	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1544	<
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 );
1543	>	info->the_integrator = myNVT;
1544	>	break;
1545
1546	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1547	<
1548	<	if (globals->haveTargetPressure())
1549	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1550	<	else {
1551	<	sprintf( painCave.errMsg,
1552	<	"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 );
1546	>	case NPTi_ENS:
1547	>	if (globals->haveZconstraints()){
1548	>	setupZConstraint(info[k]);
1549	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1550	>	}
1551	>	else
1552	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1553
1554	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1555	<
1556	<	if (globals->haveTargetPressure())
1557	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1558	<	else {
1559	<	sprintf( painCave.errMsg,
1560	<	"SimSetup error: If you use a constant pressure\n"
1561	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1562	<	painCave.isFatal = 1;
1563	<	simError();
1564	<	}
1565	<
1566	<	if( globals->haveTauThermostat() )
1567	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1568	<	else{
1569	<	sprintf( painCave.errMsg,
1570	<	"SimSetup error: If you use an NPT\n"
1571	<	"    ensemble, you must set tauThermostat.\n");
1572	<	painCave.isFatal = 1;
1573	<	simError();
1574	<	}
1575	<
1576	<	if( globals->haveTauBarostat() )
1577	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1578	<	else{
1579	<	sprintf( painCave.errMsg,
1580	<	"SimSetup error: If you use an NPT\n"
1581	<	"    ensemble, you must set tauBarostat.\n");
1582	<	painCave.isFatal = 1;
1583	<	simError();
1584	<	}
1585	<	break;
1586	<
1587	<	default:
1588	<	sprintf( painCave.errMsg,
1589	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1590	<	painCave.isFatal = 1;
1591	<	simError();
1554	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1555	>
1556	>	if (globals->haveTargetPressure())
1557	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1558	>	else{
1559	>	sprintf(painCave.errMsg,
1560	>	"SimSetup error: If you use a constant pressure\n"
1561	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1562	>	painCave.isFatal = 1;
1563	>	simError();
1564	>	}
1565	>
1566	>	if (globals->haveTauThermostat())
1567	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1568	>	else{
1569	>	sprintf(painCave.errMsg,
1570	>	"SimSetup error: If you use an NPT\n"
1571	>	"\tensemble, you must set tauThermostat.\n");
1572	>	painCave.isFatal = 1;
1573	>	simError();
1574	>	}
1575	>
1576	>	if (globals->haveTauBarostat())
1577	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1578	>	else{
1579	>	sprintf(painCave.errMsg,
1580	>	"SimSetup error: If you use an NPT\n"
1581	>	"\tensemble, you must set tauBarostat.\n");
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585	>
1586	>	info->the_integrator = myNPTi;
1587	>	break;
1588	>
1589	>	case NPTf_ENS:
1590	>	if (globals->haveZconstraints()){
1591	>	setupZConstraint(info[k]);
1592	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1593	>	}
1594	>	else
1595	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1596	>
1597	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1598	>
1599	>	if (globals->haveTargetPressure())
1600	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1601	>	else{
1602	>	sprintf(painCave.errMsg,
1603	>	"SimSetup error: If you use a constant pressure\n"
1604	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1605	>	painCave.isFatal = 1;
1606	>	simError();
1607	>	}
1608	>
1609	>	if (globals->haveTauThermostat())
1610	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1611	>
1612	>	else{
1613	>	sprintf(painCave.errMsg,
1614	>	"SimSetup error: If you use an NPT\n"
1615	>	"\tensemble, you must set tauThermostat.\n");
1616	>	painCave.isFatal = 1;
1617	>	simError();
1618	>	}
1619	>
1620	>	if (globals->haveTauBarostat())
1621	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1622	>
1623	>	else{
1624	>	sprintf(painCave.errMsg,
1625	>	"SimSetup error: If you use an NPT\n"
1626	>	"\tensemble, you must set tauBarostat.\n");
1627	>	painCave.isFatal = 1;
1628	>	simError();
1629	>	}
1630	>
1631	>	info->the_integrator = myNPTf;
1632	>	break;
1633	>
1634	>	case NPTxyz_ENS:
1635	>	if (globals->haveZconstraints()){
1636	>	setupZConstraint(info[k]);
1637	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1638	>	}
1639	>	else
1640	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1641	>
1642	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1643	>
1644	>	if (globals->haveTargetPressure())
1645	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1646	>	else{
1647	>	sprintf(painCave.errMsg,
1648	>	"SimSetup error: If you use a constant pressure\n"
1649	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1650	>	painCave.isFatal = 1;
1651	>	simError();
1652	>	}
1653	>
1654	>	if (globals->haveTauThermostat())
1655	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1656	>	else{
1657	>	sprintf(painCave.errMsg,
1658	>	"SimSetup error: If you use an NPT\n"
1659	>	"\tensemble, you must set tauThermostat.\n");
1660	>	painCave.isFatal = 1;
1661	>	simError();
1662	>	}
1663	>
1664	>	if (globals->haveTauBarostat())
1665	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1666	>	else{
1667	>	sprintf(painCave.errMsg,
1668	>	"SimSetup error: If you use an NPT\n"
1669	>	"\tensemble, you must set tauBarostat.\n");
1670	>	painCave.isFatal = 1;
1671	>	simError();
1672	>	}
1673	>
1674	>	info->the_integrator = myNPTxyz;
1675	>	break;
1676	>
1677	>	default:
1678	>	sprintf(painCave.errMsg,
1679	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1680	>	painCave.isFatal = 1;
1681	>	simError();
1682		}
1683		}
1684		}
1685
1686	<	void SimSetup::initFortran( void ){
1570	<
1686	>	void SimSetup::initFortran(void){
1687		info[0].refreshSim();
1688	<
1689	<	if( !strcmp( info[0].mixingRule, "standard") ){
1690	<	the_ff->initForceField( LB_MIXING_RULE );
1688	>
1689	>	if (!strcmp(info[0].mixingRule, "standard")){
1690	>	the_ff->initForceField(LB_MIXING_RULE);
1691		}
1692	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1693	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1692	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1693	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1694		}
1695		else{
1696	<	sprintf( painCave.errMsg,
1697	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1696	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1697	>	info[0].mixingRule);
1698		painCave.isFatal = 1;
1699		simError();
1700		}
1701
1702
1703		#ifdef IS_MPI
1704	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1704	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1705		MPIcheckPoint();
1706		#endif // is_mpi
1593	–
1707		}
1708
1709	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1710	<	{
1711	<	int nZConstraints;
1599	<	ZconStamp** zconStamp;
1600	<
1601	<	if(globals->haveZconstraintTime()){
1602	<
1603	<	//add sample time of z-constraint  into SimInfo's property list
1604	<	DoubleData* zconsTimeProp = new DoubleData();
1605	<	zconsTimeProp->setID(ZCONSTIME_ID);
1606	<	zconsTimeProp->setData(globals->getZconsTime());
1607	<	theInfo.addProperty(zconsTimeProp);
1608	<	}
1609	<	else{
1610	<	sprintf( painCave.errMsg,
1611	<	"ZConstraint error: If you use an ZConstraint\n"
1612	<	" , you must set sample time.\n");
1613	<	painCave.isFatal = 1;
1614	<	simError();
1615	<	}
1709	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1710	>	int nZConstraints;
1711	>	ZconStamp** zconStamp;
1712
1713	<	//
1714	<	nZConstraints = globals->getNzConstraints();
1715	<	theInfo.nZconstraints = nZConstraints;
1716	<
1717	<	zconStamp = globals->getZconStamp();
1718	<	ZConsParaItem tempParaItem;
1713	>	if (globals->haveZconstraintTime()){
1714	>	//add sample time of z-constraint  into SimInfo's property list
1715	>	DoubleData* zconsTimeProp = new DoubleData();
1716	>	zconsTimeProp->setID(ZCONSTIME_ID);
1717	>	zconsTimeProp->setData(globals->getZconsTime());
1718	>	theInfo.addProperty(zconsTimeProp);
1719	>	}
1720	>	else{
1721	>	sprintf(painCave.errMsg,
1722	>	"ZConstraint error: If you use a ZConstraint,\n"
1723	>	"\tyou must set zconsTime.\n");
1724	>	painCave.isFatal = 1;
1725	>	simError();
1726	>	}
1727
1728	<	ZConsParaData* zconsParaData = new ZConsParaData();
1729	<	zconsParaData->setID(ZCONSPARADATA_ID);
1730	<
1731	<	for(int i = 0; i < nZConstraints; i++){
1728	>	//push zconsTol into siminfo, if user does not specify
1729	>	//value for zconsTol, a default value will be used
1730	>	DoubleData* zconsTol = new DoubleData();
1731	>	zconsTol->setID(ZCONSTOL_ID);
1732	>	if (globals->haveZconsTol()){
1733	>	zconsTol->setData(globals->getZconsTol());
1734	>	}
1735	>	else{
1736	>	double defaultZConsTol = 0.01;
1737	>	sprintf(painCave.errMsg,
1738	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1739	>	"\tOOPSE will use a default value of %f.\n"
1740	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1741	>	defaultZConsTol);
1742	>	painCave.isFatal = 0;
1743	>	simError();
1744	>
1745	>	zconsTol->setData(defaultZConsTol);
1746	>	}
1747	>	theInfo.addProperty(zconsTol);
1748	>
1749	>	//set Force Subtraction Policy
1750	>	StringData* zconsForcePolicy = new StringData();
1751	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1752	>
1753	>	if (globals->haveZconsForcePolicy()){
1754	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1755	>	}
1756	>	else{
1757	>	sprintf(painCave.errMsg,
1758	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1759	>	"\tOOPSE will use PolicyByMass.\n"
1760	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1761	>	painCave.isFatal = 0;
1762	>	simError();
1763	>	zconsForcePolicy->setData("BYMASS");
1764	>	}
1765	>
1766	>	theInfo.addProperty(zconsForcePolicy);
1767	>
1768	>	//set zcons gap
1769	>	DoubleData* zconsGap = new DoubleData();
1770	>	zconsGap->setID(ZCONSGAP_ID);
1771	>
1772	>	if (globals->haveZConsGap()){
1773	>	zconsGap->setData(globals->getZconsGap());
1774	>	theInfo.addProperty(zconsGap);
1775	>	}
1776	>
1777	>	//set zcons fixtime
1778	>	DoubleData* zconsFixtime = new DoubleData();
1779	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
1780	>
1781	>	if (globals->haveZConsFixTime()){
1782	>	zconsFixtime->setData(globals->getZconsFixtime());
1783	>	theInfo.addProperty(zconsFixtime);
1784	>	}
1785	>
1786	>	//set zconsUsingSMD
1787	>	IntData* zconsUsingSMD = new IntData();
1788	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1789	>
1790	>	if (globals->haveZConsUsingSMD()){
1791	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1792	>	theInfo.addProperty(zconsUsingSMD);
1793	>	}
1794	>
1795	>	//Determine the name of ouput file and add it into SimInfo's property list
1796	>	//Be careful, do not use inFileName, since it is a pointer which
1797	>	//point to a string at master node, and slave nodes do not contain that string
1798	>
1799	>	string zconsOutput(theInfo.finalName);
1800	>
1801	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1802	>
1803	>	StringData* zconsFilename = new StringData();
1804	>	zconsFilename->setID(ZCONSFILENAME_ID);
1805	>	zconsFilename->setData(zconsOutput);
1806	>
1807	>	theInfo.addProperty(zconsFilename);
1808	>
1809	>	//setup index, pos and other parameters of z-constraint molecules
1810	>	nZConstraints = globals->getNzConstraints();
1811	>	theInfo.nZconstraints = nZConstraints;
1812	>
1813	>	zconStamp = globals->getZconStamp();
1814	>	ZConsParaItem tempParaItem;
1815	>
1816	>	ZConsParaData* zconsParaData = new ZConsParaData();
1817	>	zconsParaData->setID(ZCONSPARADATA_ID);
1818	>
1819	>	for (int i = 0; i < nZConstraints; i++){
1820		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1821		tempParaItem.zPos = zconStamp[i]->getZpos();
1822		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1823		tempParaItem.kRatio = zconStamp[i]->getKratio();
1824	<
1824	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1825	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1826		zconsParaData->addItem(tempParaItem);
1827	+	}
1828	+
1829	+	//check the uniqueness of index
1830	+	if(!zconsParaData->isIndexUnique()){
1831	+	sprintf(painCave.errMsg,
1832	+	"ZConstraint Error: molIndex is not unique!\n");
1833	+	painCave.isFatal = 1;
1834	+	simError();
1835	+	}
1836	+
1837	+	//sort the parameters by index of molecules
1838	+	zconsParaData->sortByIndex();
1839	+
1840	+	//push data into siminfo, therefore, we can retrieve later
1841	+	theInfo.addProperty(zconsParaData);
1842	+	}
1843	+
1844	+	void SimSetup::makeMinimizer(){
1845	+
1846	+	OOPSEMinimizer* myOOPSEMinimizer;
1847	+	MinimizerParameterSet* param;
1848	+	char minimizerName[100];
1849	+
1850	+	for (int i = 0; i < nInfo; i++){
1851	+
1852	+	//prepare parameter set for minimizer
1853	+	param = new MinimizerParameterSet();
1854	+	param->setDefaultParameter();
1855	+
1856	+	if (globals->haveMinimizer()){
1857	+	param->setFTol(globals->getMinFTol());
1858		}
1859
1860	<	//sort the parameters by index of molecules
1861	<	zconsParaData->sortByIndex();
1862	<
1639	<	//push data into siminfo, therefore, we can retrieve later
1640	<	theInfo.addProperty(zconsParaData);
1860	>	if (globals->haveMinGTol()){
1861	>	param->setGTol(globals->getMinGTol());
1862	>	}
1863
1864	<	//push zconsTol into siminfo, if user does not specify
1865	<	//value for zconsTol, a default value will be used
1644	<	DoubleData* zconsTol = new DoubleData();
1645	<	zconsTol->setID(ZCONSTOL_ID);
1646	<	if(globals->haveZconsTol()){
1647	<	zconsTol->setData(globals->getZconsTol());
1864	>	if (globals->haveMinMaxIter()){
1865	>	param->setMaxIteration(globals->getMinMaxIter());
1866		}
1649	–	else{
1650	–	double defaultZConsTol = 1E-6;
1651	–	sprintf( painCave.errMsg,
1652	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1653	–	" , default value %f is used.\n", defaultZConsTol);
1654	–	painCave.isFatal = 0;
1655	–	simError();
1867
1868	<	zconsTol->setData(defaultZConsTol);
1869	<	}
1870	<	theInfo.addProperty(zconsTol);
1871	<
1872	<	//Determine the name of ouput file and add it into SimInfo's property list
1873	<	//Be careful, do not use inFileName, since it is a pointer which
1874	<	//point to a string at master node, and slave nodes do not contain that string
1868	>	if (globals->haveMinWriteFrq()){
1869	>	param->setMaxIteration(globals->getMinMaxIter());
1870	>	}
1871	>
1872	>	if (globals->haveMinWriteFrq()){
1873	>	param->setWriteFrq(globals->getMinWriteFrq());
1874	>	}
1875
1876	<	string zconsOutput(theInfo.finalName);
1877	<
1878	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1879	<
1880	<	StringData* zconsFilename = new StringData();
1881	<	zconsFilename->setID(ZCONSFILENAME_ID);
1882	<	zconsFilename->setData(zconsOutput);
1883	<
1884	<	theInfo.addProperty(zconsFilename);
1876	>	if (globals->haveMinStepSize()){
1877	>	param->setStepSize(globals->getMinStepSize());
1878	>	}
1879	>
1880	>	if (globals->haveMinLSMaxIter()){
1881	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1882	>	}
1883	>
1884	>	if (globals->haveMinLSTol()){
1885	>	param->setLineSearchTol(globals->getMinLSTol());
1886	>	}
1887	>
1888	>	strcpy(minimizerName, globals->getMinimizer());
1889	>
1890	>	if (!strcasecmp(minimizerName, "CG")){
1891	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	>	}
1893	>	else if (!strcasecmp(minimizerName, "SD")){
1894	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1895	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1896	>	}
1897	>	else{
1898	>	sprintf(painCave.errMsg,
1899	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1900	>	painCave.isFatal = 0;
1901	>	simError();
1902	>
1903	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1904	>	}
1905	>	info[i].the_integrator = myOOPSEMinimizer;
1906	>
1907	>	//store the minimizer into simInfo
1908	>	info[i].the_minimizer = myOOPSEMinimizer;
1909	>	info[i].has_minimizer = true;
1910	>	}
1911	>
1912		}

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