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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 20 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
24	<	#define NPTfm_ENS      5
25	<	#define NVEZCONS_ENS   6
26	<	#define NVTZCONS_ENS   7
27	<	#define NPTiZCONS_ENS  8
28	<	#define NPTfZCONS_ENS  9
29	<	#define NPTimZCONS_ENS 10
30	<	#define NPTfmZCONS_ENS 11
27	>	#define NPTxyz_ENS     4
28
32	–	#define FF_DUFF 0
33	–	#define FF_LJ   1
34	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 55 | Line 79 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
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 ){
66	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
94	<	mpiEventLoop();
95	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
102	–	int i, j, k, globalAtomIndex;
103	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 110 | Line 132 | void SimSetup::createSim(void){
132		sysObjectsCreation();
133
134		// check on the post processing info
135	<
135	>
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	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();
150	<
151	<	// make the integrator
150	>
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157
126	–	makeIntegrator();
127	–
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
#	Line 132 | Line 162 | void SimSetup::createSim(void){
162		// initialize the Fortran
163
164		initFortran();
135	–
136	–
137	–
165		}
166
167
168	<	void SimSetup::makeMolecules( void ){
169	<
170	<	int k,l;
171	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174		molInit molInfo;
175		DirectionalAtom* dAtom;
176	+	RigidBody* myRB;
177	+	StuntDouble* mySD;
178		LinkedAssign* extras;
179		LinkedAssign* current_extra;
180		AtomStamp* currentAtom;
181		BondStamp* currentBond;
182		BendStamp* currentBend;
183		TorsionStamp* currentTorsion;
184	+	RigidBodyStamp* currentRigidBody;
185
186		bond_pair* theBonds;
187		bend_set* theBends;
188		torsion_set* theTorsions;
189
190	<
190	>	set<int> skipList;
191	>
192	>	double phi, theta, psi;
193	>
194		//init the forceField paramters
195
196		the_ff->readParams();
197
163	–
198		// init the atoms
199
200	<	double ux, uy, uz, u, uSqr;
167	<
168	<	for(k=0; k<nInfo; k++){
169	<
170	<	the_ff->setSimInfo( &(info[k]) );
200	>	int nMembers, nNew, rb1, rb2;
201
202	+	for (k = 0; k < nInfo; k++){
203	+	the_ff->setSimInfo(&(info[k]));
204	+
205		atomOffset = 0;
206	<	excludeOffset = 0;
207	<	for(i=0; i<info[k].n_mol; i++){
175	<
206	>
207	>	for (i = 0; i < info[k].n_mol; i++){
208		stampID = info[k].molecules[i].getStampID();
209
210	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
211	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
212	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215
216		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
185	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
186	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
187	–	molInfo.myBends = new Bend*[molInfo.nBends];
188	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
217
218	+	if (molInfo.nBonds > 0)
219	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	+	else
221	+	molInfo.myBonds = NULL;
222	+
223	+	if (molInfo.nBends > 0)
224	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	+	else
226	+	molInfo.myBends = NULL;
227	+
228	+	if (molInfo.nTorsions > 0)
229	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	+	else
231	+	molInfo.myTorsions = NULL;
232	+
233		theBonds = new bond_pair[molInfo.nBonds];
234		theBends = new bend_set[molInfo.nBends];
235		theTorsions = new torsion_set[molInfo.nTorsions];
236	<
236	>
237		// make the Atoms
238	<
239	<	for(j=0; j<molInfo.nAtoms; j++){
240	<
241	<	currentAtom = comp_stamps[stampID]->getAtom( j );
242	<	if( currentAtom->haveOrientation() ){
243	<
244	<	dAtom = new DirectionalAtom( (j + atomOffset),
245	<	info[k].getConfiguration() );
246	<	info[k].n_oriented++;
247	<	molInfo.myAtoms[j] = dAtom;
248	<
249	<	ux = currentAtom->getOrntX();
250	<	uy = currentAtom->getOrntY();
251	<	uz = currentAtom->getOrntZ();
252	<
253	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
254	<
255	<	u = sqrt( uSqr );
256	<	ux = ux / u;
257	<	uy = uy / u;
258	<	uz = uz / u;
259	<
260	<	dAtom->setSUx( ux );
261	<	dAtom->setSUy( uy );
262	<	dAtom->setSUz( uz );
263	<	}
264	<	else{
265	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
223	<	info[k].getConfiguration() );
224	<	}
225	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
226	<
238	>
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241	>
242	>	if (currentAtom->haveOrientation()){
243	>	dAtom = new DirectionalAtom((j + atomOffset),
244	>	info[k].getConfiguration());
245	>	info[k].n_oriented++;
246	>	molInfo.myAtoms[j] = dAtom;
247	>
248	>	// Directional Atoms have standard unit vectors which are oriented
249	>	// in space using the three Euler angles.  We assume the standard
250	>	// unit vector was originally along the z axis below.
251	>
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255	>
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260	>
261	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	>	}
263	>
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265	>
266		#ifdef IS_MPI
267	<
268	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
269	<
267	>
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269	>
270		#endif // is_mpi
271		}
272	<
273	<	// make the bonds
274	<	for(j=0; j<molInfo.nBonds; j++){
275	<
276	<	currentBond = comp_stamps[stampID]->getBond( j );
277	<	theBonds[j].a = currentBond->getA() + atomOffset;
278	<	theBonds[j].b = currentBond->getB() + atomOffset;
279	<
280	<	exI = theBonds[j].a;
281	<	exJ = theBonds[j].b;
243	<
244	<	// exclude_I must always be the smaller of the pair
245	<	if( exI > exJ ){
246	<	tempEx = exI;
247	<	exI = exJ;
248	<	exJ = tempEx;
249	<	}
272	>
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278	>
279	>	tempI = theBonds[j].a;
280	>	tempJ = theBonds[j].b;
281	>
282		#ifdef IS_MPI
283	<	tempEx = exI;
284	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
285	<	tempEx = exJ;
286	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
287	<
288	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
289	<	#else  // isn't MPI
290	<
259	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
260	<	#endif  //is_mpi
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289	>
290	>	info[k].excludes->addPair(exI, exJ);
291		}
292	<	excludeOffset += molInfo.nBonds;
263	<
292	>
293		//make the bends
294	<	for(j=0; j<molInfo.nBends; j++){
295	<
296	<	currentBend = comp_stamps[stampID]->getBend( j );
297	<	theBends[j].a = currentBend->getA() + atomOffset;
298	<	theBends[j].b = currentBend->getB() + atomOffset;
299	<	theBends[j].c = currentBend->getC() + atomOffset;
300	<
301	<	if( currentBend->haveExtras() ){
302	<
303	<	extras = currentBend->getExtras();
304	<	current_extra = extras;
305	<
306	<	while( current_extra != NULL ){
307	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
308	<
309	<	switch( current_extra->getType() ){
310	<
311	<	case 0:
312	<	theBends[j].ghost =
313	<	current_extra->getInt() + atomOffset;
314	<	theBends[j].isGhost = 1;
315	<	break;
316	<
317	<	case 1:
318	<	theBends[j].ghost =
319	<	(int)current_extra->getDouble() + atomOffset;
320	<	theBends[j].isGhost = 1;
321	<	break;
322	<
323	<	default:
324	<	sprintf( painCave.errMsg,
325	<	"SimSetup Error: ghostVectorSource was neither a "
326	<	"double nor an int.\n"
327	<	"-->Bend[%d] in %s\n",
328	<	j, comp_stamps[stampID]->getID() );
329	<	painCave.isFatal = 1;
330	<	simError();
331	<	}
332	<	}
333	<
334	<	else{
335	<
336	<	sprintf( painCave.errMsg,
337	<	"SimSetup Error: unhandled bend assignment:\n"
338	<	"    -->%s in Bend[%d] in %s\n",
339	<	current_extra->getlhs(),
340	<	j, comp_stamps[stampID]->getID() );
341	<	painCave.isFatal = 1;
342	<	simError();
343	<	}
344	<
345	<	current_extra = current_extra->getNext();
317	<	}
318	<	}
319	<
320	<	if( !theBends[j].isGhost ){
321	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].c;
324	<	}
325	<	else{
326	<
327	<	exI = theBends[j].a;
328	<	exJ = theBends[j].b;
329	<	}
330	<
331	<	// exclude_I must always be the smaller of the pair
332	<	if( exI > exJ ){
333	<	tempEx = exI;
334	<	exI = exJ;
335	<	exJ = tempEx;
336	<	}
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299	>
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303	>
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311	>
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317	>
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336	>
337	>	current_extra = current_extra->getNext();
338	>	}
339	>	}
340	>
341	>	if (theBends[j].isGhost) {
342	>
343	>	tempI = theBends[j].a;
344	>	tempJ = theBends[j].b;
345	>
346		#ifdef IS_MPI
347	<	tempEx = exI;
348	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	<	tempEx = exJ;
350	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	<
352	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
353	<	#else  // isn't MPI
354	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
355	<	#endif  //is_mpi
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354	>
355	>	} else {
356	>
357	>	tempI = theBends[j].a;
358	>	tempJ = theBends[j].b;
359	>	tempK = theBends[j].c;
360	>
361	>	#ifdef IS_MPI
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375		}
376	<	excludeOffset += molInfo.nBends;
377	<
378	<	for(j=0; j<molInfo.nTorsions; j++){
379	<
380	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
381	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
382	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
383	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
384	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
385	<
386	<	exI = theTorsions[j].a;
387	<	exJ = theTorsions[j].d;
388	<
361	<	// exclude_I must always be the smaller of the pair
362	<	if( exI > exJ ){
363	<	tempEx = exI;
364	<	exI = exJ;
365	<	exJ = tempEx;
366	<	}
376	>
377	>	for (j = 0; j < molInfo.nTorsions; j++){
378	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383	>
384	>	tempI = theTorsions[j].a;
385	>	tempJ = theTorsions[j].b;
386	>	tempK = theTorsions[j].c;
387	>	tempL = theTorsions[j].d;
388	>
389		#ifdef IS_MPI
390	<	tempEx = exI;
391	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
392	<	tempEx = exJ;
393	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
394	<
395	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
396	<	#else  // isn't MPI
397	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
398	<	#endif  //is_mpi
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399	>	#endif
400	>
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407		}
408	<	excludeOffset += molInfo.nTorsions;
409	<
408	>
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410	>
411	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	>	nMembers = currentRigidBody->getNMembers();
413	>
414	>	// Create the Rigid Body:
415	>
416	>	myRB = new RigidBody();
417	>
418	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
419	>
420	>	// molI is atom numbering inside this molecule
421	>	molI = currentRigidBody->getMember(rb1);
422	>
423	>	// tempI is atom numbering on local processor
424	>	tempI = molI + atomOffset;
425	>
426	>	// currentAtom is the AtomStamp (which we need for
427	>	// rigid body reference positions)
428	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
429	>
430	>	// When we add to the rigid body, add the atom itself and
431	>	// the stamp info:
432	>
433	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	>
435	>	// Add this atom to the Skip List for the integrators
436	>	#ifdef IS_MPI
437	>	slI = info[k].atoms[tempI]->getGlobalIndex();
438	>	#else
439	>	slI = tempI;
440	>	#endif
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468	>	}
469
470		// send the arrays off to the forceField for init.
471
472	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
473	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
474	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
475	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
476	<
388	<
389	<	info[k].molecules[i].initialize( molInfo );
472	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
473	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
474	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
475	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
476	>	theTorsions);
477
478	<
478	>	info[k].molecules[i].initialize(molInfo);
479	>
480	>
481		atomOffset += molInfo.nAtoms;
482		delete[] theBonds;
483		delete[] theBends;
484		delete[] theTorsions;
485		}
486	+
487	+	// build up the integrableObjects vector:
488	+
489	+	for (i = 0; i < info[k].n_atoms; i++) {
490	+
491	+	#ifdef IS_MPI
492	+	slI = info[k].atoms[i]->getGlobalIndex();
493	+	#else
494	+	slI = i;
495	+	#endif
496	+
497	+	if (skipList.find(slI) == skipList.end()) {
498	+	mySD = (StuntDouble *) info[k].atoms[i];
499	+	info[k].integrableObjects.push_back(mySD);
500	+	}
501	+	}
502	+	for (i = 0; i < info[k].rigidBodies.size(); i++) {
503	+	mySD = (StuntDouble *) info[k].rigidBodies[i];
504	+	info[k].integrableObjects.push_back(mySD);
505	+	}
506	+
507		}
508	<
508	>
509		#ifdef IS_MPI
510	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
510	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
511		MPIcheckPoint();
512		#endif // is_mpi
513	<
513	>
514		// clean up the forcefield
515
516	<	the_ff->calcRcut();
516	>	if (!globals->haveLJrcut()){
517	>
518	>	the_ff->calcRcut();
519	>
520	>	} else {
521	>
522	>	the_ff->setRcut( globals->getLJrcut() );
523	>	}
524	>
525		the_ff->cleanMe();
408	–
526		}
527
528	<	void SimSetup::initFromBass( void ){
412	<
528	>	void SimSetup::initFromBass(void){
529		int i, j, k;
530		int n_cells;
531		double cellx, celly, cellz;
#	Line 423 | Line 539 | void SimSetup::initFromBass( void ){
539		vel[1] = 0.0;
540		vel[2] = 0.0;
541
542	<	temp1 = (double)tot_nmol / 4.0;
543	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
544	<	temp3 = ceil( temp2 );
542	>	temp1 = (double) tot_nmol / 4.0;
543	>	temp2 = pow(temp1, (1.0 / 3.0));
544	>	temp3 = ceil(temp2);
545
546	<	have_extra =0;
547	<	if( temp2 < temp3 ){ // we have a non-complete lattice
548	<	have_extra =1;
546	>	have_extra = 0;
547	>	if (temp2 < temp3){
548	>	// we have a non-complete lattice
549	>	have_extra = 1;
550
551	<	n_cells = (int)temp3 - 1;
551	>	n_cells = (int) temp3 - 1;
552		cellx = info[0].boxL[0] / temp3;
553		celly = info[0].boxL[1] / temp3;
554		cellz = info[0].boxL[2] / temp3;
555	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
556	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
557	<	n_per_extra = (int)ceil( temp1 );
555	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
556	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
557	>	n_per_extra = (int) ceil(temp1);
558
559	<	if( n_per_extra > 4){
560	<	sprintf( painCave.errMsg,
561	<	"SimSetup error. There has been an error in constructing"
562	<	" the non-complete lattice.\n" );
559	>	if (n_per_extra > 4){
560	>	sprintf(painCave.errMsg,
561	>	"SimSetup error. There has been an error in constructing"
562	>	" the non-complete lattice.\n");
563		painCave.isFatal = 1;
564		simError();
565		}
566		}
567		else{
568	<	n_cells = (int)temp3;
568	>	n_cells = (int) temp3;
569		cellx = info[0].boxL[0] / temp3;
570		celly = info[0].boxL[1] / temp3;
571		cellz = info[0].boxL[2] / temp3;
#	Line 459 | Line 576 | void SimSetup::initFromBass( void ){
576		current_comp = 0;
577		current_atom_ndx = 0;
578
579	<	for( i=0; i < n_cells ; i++ ){
580	<	for( j=0; j < n_cells; j++ ){
581	<	for( k=0; k < n_cells; k++ ){
579	>	for (i = 0; i < n_cells ; i++){
580	>	for (j = 0; j < n_cells; j++){
581	>	for (k = 0; k < n_cells; k++){
582	>	makeElement(i * cellx, j * celly, k * cellz);
583
584	<	makeElement( i * cellx,
467	<	j * celly,
468	<	k * cellz );
584	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
585
586	<	makeElement( i * cellx + 0.5 * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz );
586	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
587
588	<	makeElement( i * cellx,
475	<	j * celly + 0.5 * celly,
476	<	k * cellz + 0.5 * cellz );
477	<
478	<	makeElement( i * cellx + 0.5 * cellx,
479	<	j * celly,
480	<	k * cellz + 0.5 * cellz );
588	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
589		}
590		}
591		}
592
593	<	if( have_extra ){
593	>	if (have_extra){
594		done = 0;
595
596		int start_ndx;
597	<	for( i=0; i < (n_cells+1) && !done; i++ ){
598	<	for( j=0; j < (n_cells+1) && !done; j++ ){
597	>	for (i = 0; i < (n_cells + 1) && !done; i++){
598	>	for (j = 0; j < (n_cells + 1) && !done; j++){
599	>	if (i < n_cells){
600	>	if (j < n_cells){
601	>	start_ndx = n_cells;
602	>	}
603	>	else
604	>	start_ndx = 0;
605	>	}
606	>	else
607	>	start_ndx = 0;
608
609	<	if( i < n_cells ){
609	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
610	>	makeElement(i * cellx, j * celly, k * cellz);
611	>	done = (current_mol >= tot_nmol);
612
613	<	if( j < n_cells ){
614	<	start_ndx = n_cells;
615	<	}
616	<	else start_ndx = 0;
617	<	}
499	<	else start_ndx = 0;
613	>	if (!done && n_per_extra > 1){
614	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
615	>	k * cellz);
616	>	done = (current_mol >= tot_nmol);
617	>	}
618
619	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
619	>	if (!done && n_per_extra > 2){
620	>	makeElement(i * cellx, j * celly + 0.5 * celly,
621	>	k * cellz + 0.5 * cellz);
622	>	done = (current_mol >= tot_nmol);
623	>	}
624
625	<	makeElement( i * cellx,
626	<	j * celly,
627	<	k * cellz );
628	<	done = ( current_mol >= tot_nmol );
629	<
630	<	if( !done && n_per_extra > 1 ){
509	<	makeElement( i * cellx + 0.5 * cellx,
510	<	j * celly + 0.5 * celly,
511	<	k * cellz );
512	<	done = ( current_mol >= tot_nmol );
513	<	}
514	<
515	<	if( !done && n_per_extra > 2){
516	<	makeElement( i * cellx,
517	<	j * celly + 0.5 * celly,
518	<	k * cellz + 0.5 * cellz );
519	<	done = ( current_mol >= tot_nmol );
520	<	}
521	<
522	<	if( !done && n_per_extra > 3){
523	<	makeElement( i * cellx + 0.5 * cellx,
524	<	j * celly,
525	<	k * cellz + 0.5 * cellz );
526	<	done = ( current_mol >= tot_nmol );
527	<	}
528	<	}
625	>	if (!done && n_per_extra > 3){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
627	>	k * cellz + 0.5 * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630	>	}
631		}
632		}
633		}
634
635	<	for( i=0; i<info[0].n_atoms; i++ ){
636	<	info[0].atoms[i]->setVel( vel );
635	>	for (i = 0; i < info[0].n_atoms; i++){
636	>	info[0].atoms[i]->setVel(vel);
637		}
638		}
639
640	<	void SimSetup::makeElement( double x, double y, double z ){
539	<
640	>	void SimSetup::makeElement(double x, double y, double z){
641		int k;
642		AtomStamp* current_atom;
643		DirectionalAtom* dAtom;
644		double rotMat[3][3];
645		double pos[3];
646
647	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
648	<
649	<	current_atom = comp_stamps[current_comp]->getAtom( k );
650	<	if( !current_atom->havePosition() ){
651	<	sprintf( painCave.errMsg,
652	<	"SimSetup:initFromBass error.\n"
653	<	"\tComponent %s, atom %s does not have a position specified.\n"
654	<	"\tThe initialization routine is unable to give a start"
655	<	" position.\n",
555	<	comp_stamps[current_comp]->getID(),
556	<	current_atom->getType() );
647	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
648	>	current_atom = comp_stamps[current_comp]->getAtom(k);
649	>	if (!current_atom->havePosition()){
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup:initFromBass error.\n"
652	>	"\tComponent %s, atom %s does not have a position specified.\n"
653	>	"\tThe initialization routine is unable to give a start"
654	>	" position.\n",
655	>	comp_stamps[current_comp]->getID(), current_atom->getType());
656		painCave.isFatal = 1;
657		simError();
658		}
659	<
659	>
660		pos[0] = x + current_atom->getPosX();
661		pos[1] = y + current_atom->getPosY();
662		pos[2] = z + current_atom->getPosZ();
564	–
565	–	info[0].atoms[current_atom_ndx]->setPos( pos );
663
664	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
664	>	info[0].atoms[current_atom_ndx]->setPos(pos);
665
666	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
666	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
667	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
668
669		rotMat[0][0] = 1.0;
670		rotMat[0][1] = 0.0;
#	Line 580 | Line 678 | void SimSetup::makeElement( double x, double y, double
678		rotMat[2][1] = 0.0;
679		rotMat[2][2] = 1.0;
680
681	<	dAtom->setA( rotMat );
681	>	dAtom->setA(rotMat);
682		}
683
684		current_atom_ndx++;
#	Line 589 | Line 687 | void SimSetup::makeElement( double x, double y, double
687		current_mol++;
688		current_comp_mol++;
689
690	<	if( current_comp_mol >= components_nmol[current_comp] ){
593	<
690	>	if (current_comp_mol >= components_nmol[current_comp]){
691		current_comp_mol = 0;
692		current_comp++;
693		}
694		}
695
696
697	<	void SimSetup::gatherInfo( void ){
698	<	int i,j,k;
697	>	void SimSetup::gatherInfo(void){
698	>	int i;
699
700		ensembleCase = -1;
701		ffCase = -1;
702
703		// set the easy ones first
704
705	<	for( i=0; i<nInfo; i++){
705	>	for (i = 0; i < nInfo; i++){
706		info[i].target_temp = globals->getTargetTemp();
707		info[i].dt = globals->getDt();
708		info[i].run_time = globals->getRunTime();
#	Line 615 | Line 712 | void SimSetup::gatherInfo( void ){
712
713		// get the forceField
714
715	<	strcpy( force_field, globals->getForceField() );
715	>	strcpy(force_field, globals->getForceField());
716
717	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
718	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
719	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
717	>	if (!strcasecmp(force_field, "DUFF")){
718	>	ffCase = FF_DUFF;
719	>	}
720	>	else if (!strcasecmp(force_field, "LJ")){
721	>	ffCase = FF_LJ;
722	>	}
723	>	else if (!strcasecmp(force_field, "EAM")){
724	>	ffCase = FF_EAM;
725	>	}
726	>	else if (!strcasecmp(force_field, "WATER")){
727	>	ffCase = FF_H2O;
728	>	}
729		else{
730	<	sprintf( painCave.errMsg,
731	<	"SimSetup Error. Unrecognized force field -> %s\n",
732	<	force_field );
733	<	painCave.isFatal = 1;
628	<	simError();
730	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
731	>	force_field);
732	>	painCave.isFatal = 1;
733	>	simError();
734		}
735
736	<	// get the ensemble
736	>	// get the ensemble
737
738	<	strcpy( ensemble, globals->getEnsemble() );
738	>	strcpy(ensemble, globals->getEnsemble());
739
740	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
741	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
742	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
740	>	if (!strcasecmp(ensemble, "NVE")){
741	>	ensembleCase = NVE_ENS;
742	>	}
743	>	else if (!strcasecmp(ensemble, "NVT")){
744	>	ensembleCase = NVT_ENS;
745	>	}
746	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
747		ensembleCase = NPTi_ENS;
748	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
749	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
750	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
751	<
752	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
753	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
754	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	<	ensembleCase = NPTiZCONS_ENS;
647	<	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	<	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	<
748	>	}
749	>	else if (!strcasecmp(ensemble, "NPTf")){
750	>	ensembleCase = NPTf_ENS;
751	>	}
752	>	else if (!strcasecmp(ensemble, "NPTxyz")){
753	>	ensembleCase = NPTxyz_ENS;
754	>	}
755		else{
756	<	sprintf( painCave.errMsg,
757	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
758	<	"reverting to NVE for this simulation.\n",
759	<	ensemble );
760	<	painCave.isFatal = 0;
761	<	simError();
762	<	strcpy( ensemble, "NVE" );
763	<	ensembleCase = NVE_ENS;
756	>	sprintf(painCave.errMsg,
757	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
758	>	"\treverting to NVE for this simulation.\n",
759	>	ensemble);
760	>	painCave.isFatal = 0;
761	>	simError();
762	>	strcpy(ensemble, "NVE");
763	>	ensembleCase = NVE_ENS;
764		}
661	–
662	–	for(i=0; i<nInfo; i++){
663	–
664	–	strcpy( info[i].ensemble, ensemble );
765
766	+	for (i = 0; i < nInfo; i++){
767	+	strcpy(info[i].ensemble, ensemble);
768	+
769		// get the mixing rule
770
771	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
771	>	strcpy(info[i].mixingRule, globals->getMixingRule());
772		info[i].usePBC = globals->getPBC();
773		}
774	<
774	>
775		// get the components and calculate the tot_nMol and indvidual n_mol
776	<
776	>
777		the_components = globals->getComponents();
778		components_nmol = new int[n_components];
779
780
781	<	if( !globals->haveNMol() ){
781	>	if (!globals->haveNMol()){
782		// we don't have the total number of molecules, so we assume it is
783		// given in each component
784
785		tot_nmol = 0;
786	<	for( i=0; i<n_components; i++ ){
787	<
788	<	if( !the_components[i]->haveNMol() ){
789	<	// we have a problem
790	<	sprintf( painCave.errMsg,
791	<	"SimSetup Error. No global NMol or component NMol"
792	<	" given. Cannot calculate the number of atoms.\n" );
793	<	painCave.isFatal = 1;
691	<	simError();
786	>	for (i = 0; i < n_components; i++){
787	>	if (!the_components[i]->haveNMol()){
788	>	// we have a problem
789	>	sprintf(painCave.errMsg,
790	>	"SimSetup Error. No global NMol or component NMol given.\n"
791	>	"\tCannot calculate the number of atoms.\n");
792	>	painCave.isFatal = 1;
793	>	simError();
794		}
795
796		tot_nmol += the_components[i]->getNMol();
#	Line 696 | Line 798 | void SimSetup::gatherInfo( void ){
798		}
799		}
800		else{
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup error.\n"
803	<	"\tSorry, the ability to specify total"
804	<	" nMols and then give molfractions in the components\n"
805	<	"\tis not currently supported."
806	<	" Please give nMol in the components.\n" );
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup error.\n"
803	>	"\tSorry, the ability to specify total"
804	>	" nMols and then give molfractions in the components\n"
805	>	"\tis not currently supported."
806	>	" Please give nMol in the components.\n");
807		painCave.isFatal = 1;
808		simError();
809		}
810
811	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
812	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
813	+	sprintf(painCave.errMsg,
814	+	"Sample time is not divisible by dt.\n"
815	+	"\tThis will result in samples that are not uniformly\n"
816	+	"\tdistributed in time.  If this is a problem, change\n"
817	+	"\tyour sampleTime variable.\n");
818	+	painCave.isFatal = 0;
819	+	simError();
820	+	}
821	+
822	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
823	+	sprintf(painCave.errMsg,
824	+	"Status time is not divisible by dt.\n"
825	+	"\tThis will result in status reports that are not uniformly\n"
826	+	"\tdistributed in time.  If this is a problem, change \n"
827	+	"\tyour statusTime variable.\n");
828	+	painCave.isFatal = 0;
829	+	simError();
830	+	}
831	+
832	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
833	+	sprintf(painCave.errMsg,
834	+	"Thermal time is not divisible by dt.\n"
835	+	"\tThis will result in thermalizations that are not uniformly\n"
836	+	"\tdistributed in time.  If this is a problem, change \n"
837	+	"\tyour thermalTime variable.\n");
838	+	painCave.isFatal = 0;
839	+	simError();
840	+	}
841	+
842	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
843	+	sprintf(painCave.errMsg,
844	+	"Reset time is not divisible by dt.\n"
845	+	"\tThis will result in integrator resets that are not uniformly\n"
846	+	"\tdistributed in time.  If this is a problem, change\n"
847	+	"\tyour resetTime variable.\n");
848	+	painCave.isFatal = 0;
849	+	simError();
850	+	}
851	+
852		// set the status, sample, and thermal kick times
710	–
711	–	for(i=0; i<nInfo; i++){
853
854	<	if( globals->haveSampleTime() ){
854	>	for (i = 0; i < nInfo; i++){
855	>	if (globals->haveSampleTime()){
856		info[i].sampleTime = globals->getSampleTime();
857		info[i].statusTime = info[i].sampleTime;
858		info[i].thermalTime = info[i].sampleTime;
#	Line 720 | Line 862 | void SimSetup::gatherInfo( void ){
862		info[i].statusTime = info[i].sampleTime;
863		info[i].thermalTime = info[i].sampleTime;
864		}
865	<
866	<	if( globals->haveStatusTime() ){
865	>
866	>	if (globals->haveStatusTime()){
867		info[i].statusTime = globals->getStatusTime();
868		}
869	<
870	<	if( globals->haveThermalTime() ){
869	>
870	>	if (globals->haveThermalTime()){
871		info[i].thermalTime = globals->getThermalTime();
872		}
873
874	+	info[i].resetIntegrator = 0;
875	+	if( globals->haveResetTime() ){
876	+	info[i].resetTime = globals->getResetTime();
877	+	info[i].resetIntegrator = 1;
878	+	}
879	+
880		// check for the temperature set flag
881	+
882	+	if (globals->haveTempSet())
883	+	info[i].setTemp = globals->getTempSet();
884
885	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
885	>	// check for the extended State init
886	>
887	>	info[i].useInitXSstate = globals->getUseInitXSstate();
888	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
889
736	–	// get some of the tricky things that may still be in the globals
737	–
738	–	double boxVector[3];
739	–	if( globals->haveBox() ){
740	–	boxVector[0] = globals->getBox();
741	–	boxVector[1] = globals->getBox();
742	–	boxVector[2] = globals->getBox();
743	–
744	–	info[i].setBox( boxVector );
745	–	}
746	–	else if( globals->haveDensity() ){
747	–
748	–	double vol;
749	–	vol = (double)tot_nmol / globals->getDensity();
750	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	–	boxVector[1] = boxVector[0];
752	–	boxVector[2] = boxVector[0];
753	–
754	–	info[i].setBox( boxVector );
890		}
891	<	else{
892	<	if( !globals->haveBoxX() ){
893	<	sprintf( painCave.errMsg,
894	<	"SimSetup error, no periodic BoxX size given.\n" );
895	<	painCave.isFatal = 1;
896	<	simError();
897	<	}
898	<	boxVector[0] = globals->getBoxX();
899	<
900	<	if( !globals->haveBoxY() ){
901	<	sprintf( painCave.errMsg,
902	<	"SimSetup error, no periodic BoxY size given.\n" );
903	<	painCave.isFatal = 1;
904	<	simError();
891	>
892	>	//setup seed for random number generator
893	>	int seedValue;
894	>
895	>	if (globals->haveSeed()){
896	>	seedValue = globals->getSeed();
897	>
898	>	if(seedValue / 1E9 == 0){
899	>	sprintf(painCave.errMsg,
900	>	"Seed for sprng library should contain at least 9 digits\n"
901	>	"OOPSE will generate a seed for user\n");
902	>	painCave.isFatal = 0;
903	>	simError();
904	>
905	>	//using seed generated by system instead of invalid seed set by user
906	>	#ifndef IS_MPI
907	>	seedValue = make_sprng_seed();
908	>	#else
909	>	if (worldRank == 0){
910	>	seedValue = make_sprng_seed();
911		}
912	<	boxVector[1] = globals->getBoxY();
913	<
773	<	if( !globals->haveBoxZ() ){
774	<	sprintf( painCave.errMsg,
775	<	"SimSetup error, no periodic BoxZ size given.\n" );
776	<	painCave.isFatal = 1;
777	<	simError();
778	<	}
779	<	boxVector[2] = globals->getBoxZ();
780	<
781	<	info[i].setBox( boxVector );
912	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
913	>	#endif
914		}
915	+	}//end of if branch of globals->haveSeed()
916	+	else{
917	+
918	+	#ifndef IS_MPI
919	+	seedValue = make_sprng_seed();
920	+	#else
921	+	if (worldRank == 0){
922	+	seedValue = make_sprng_seed();
923	+	}
924	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	+	#endif
926	+	}//end of globals->haveSeed()
927
928	+	for (int i = 0; i < nInfo; i++){
929	+	info[i].setSeed(seedValue);
930		}
931	<
931	>
932		#ifdef IS_MPI
933	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
933	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
934		MPIcheckPoint();
935		#endif // is_mpi
790	–
936		}
937
938
939	<	void SimSetup::finalInfoCheck( void ){
939	>	void SimSetup::finalInfoCheck(void){
940		int index;
941		int usesDipoles;
942		int i;
943
944	<	for(i=0; i<nInfo; i++){
944	>	for (i = 0; i < nInfo; i++){
945		// check electrostatic parameters
946	<
946	>
947		index = 0;
948		usesDipoles = 0;
949	<	while( (index < info[i].n_atoms) && !usesDipoles ){
949	>	while ((index < info[i].n_atoms) && !usesDipoles){
950		usesDipoles = (info[i].atoms[index])->hasDipole();
951		index++;
952		}
953	<
953	>
954		#ifdef IS_MPI
955		int myUse = usesDipoles;
956	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
956	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
957		#endif //is_mpi
958	<
958	>
959		double theEcr, theEst;
960	<
961	<	if (globals->getUseRF() ) {
960	>
961	>	if (globals->getUseRF()){
962		info[i].useReactionField = 1;
963	<
964	<	if( !globals->haveECR() ){
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Warning: using default value of 1/2 the smallest "
967	<	"box length for the electrostaticCutoffRadius.\n"
968	<	"I hope you have a very fast processor!\n");
969	<	painCave.isFatal = 0;
970	<	simError();
971	<	double smallest;
827	<	smallest = info[i].boxL[0];
828	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830	<	theEcr = 0.5 * smallest;
831	<	} else {
832	<	theEcr = globals->getECR();
963	>
964	>	if (!globals->haveECR()){
965	>	sprintf(painCave.errMsg,
966	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
967	>	"\tOOPSE will use a default value of 15.0 angstroms"
968	>	"\tfor the electrostaticCutoffRadius.\n");
969	>	painCave.isFatal = 0;
970	>	simError();
971	>	theEcr = 15.0;
972		}
973	<
974	<	if( !globals->haveEST() ){
836	<	sprintf( painCave.errMsg,
837	<	"SimSetup Warning: using default value of 0.05 * the "
838	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	<	);
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	theEst = 0.05 * theEcr;
843	<	} else {
844	<	theEst= globals->getEST();
973	>	else{
974	>	theEcr = globals->getECR();
975		}
976	<
977	<	info[i].setEcr( theEcr, theEst );
978	<
979	<	if(!globals->haveDielectric() ){
980	<	sprintf( painCave.errMsg,
981	<	"SimSetup Error: You are trying to use Reaction Field without"
982	<	"setting a dielectric constant!\n"
983	<	);
984	<	painCave.isFatal = 1;
985	<	simError();
976	>
977	>	if (!globals->haveEST()){
978	>	sprintf(painCave.errMsg,
979	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
980	>	"\tOOPSE will use a default value of\n"
981	>	"\t0.05 * electrostaticCutoffRadius\n"
982	>	"\tfor the electrostaticSkinThickness\n");
983	>	painCave.isFatal = 0;
984	>	simError();
985	>	theEst = 0.05 * theEcr;
986		}
987	<	info[i].dielectric = globals->getDielectric();
988	<	}
989	<	else {
990	<	if (usesDipoles) {
991	<
992	<	if( !globals->haveECR() ){
993	<	sprintf( painCave.errMsg,
994	<	"SimSetup Warning: using default value of 1/2 the smallest "
995	<	"box length for the electrostaticCutoffRadius.\n"
996	<	"I hope you have a very fast processor!\n");
987	>	else{
988	>	theEst = globals->getEST();
989	>	}
990	>
991	>	info[i].setDefaultEcr(theEcr, theEst);
992	>
993	>	if (!globals->haveDielectric()){
994	>	sprintf(painCave.errMsg,
995	>	"SimSetup Error: No Dielectric constant was set.\n"
996	>	"\tYou are trying to use Reaction Field without"
997	>	"\tsetting a dielectric constant!\n");
998	>	painCave.isFatal = 1;
999	>	simError();
1000	>	}
1001	>	info[i].dielectric = globals->getDielectric();
1002	>	}
1003	>	else{
1004	>	if (usesDipoles){
1005	>	if (!globals->haveECR()){
1006	>	sprintf(painCave.errMsg,
1007	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1008	>	"\tOOPSE will use a default value of 15.0 angstroms"
1009	>	"\tfor the electrostaticCutoffRadius.\n");
1010		painCave.isFatal = 0;
1011		simError();
1012	<	double smallest;
1013	<	smallest = info[i].boxL[0];
1014	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
1015	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
1016	<	theEcr = 0.5 * smallest;
874	<	} else {
875	<	theEcr = globals->getECR();
876	<	}
1012	>	theEcr = 15.0;
1013	>	}
1014	>	else{
1015	>	theEcr = globals->getECR();
1016	>	}
1017
1018	<	if( !globals->haveEST() ){
1019	<	sprintf( painCave.errMsg,
1020	<	"SimSetup Warning: using default value of 0.05 * the "
1021	<	"electrostaticCutoffRadius for the "
1022	<	"electrostaticSkinThickness\n"
1023	<	);
1024	<	painCave.isFatal = 0;
1025	<	simError();
1026	<	theEst = 0.05 * theEcr;
1027	<	} else {
1028	<	theEst= globals->getEST();
1029	<	}
1018	>	if (!globals->haveEST()){
1019	>	sprintf(painCave.errMsg,
1020	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1021	>	"\tOOPSE will use a default value of\n"
1022	>	"\t0.05 * electrostaticCutoffRadius\n"
1023	>	"\tfor the electrostaticSkinThickness\n");
1024	>	painCave.isFatal = 0;
1025	>	simError();
1026	>	theEst = 0.05 * theEcr;
1027	>	}
1028	>	else{
1029	>	theEst = globals->getEST();
1030	>	}
1031
1032	<	info[i].setEcr( theEcr, theEst );
1032	>	info[i].setDefaultEcr(theEcr, theEst);
1033		}
1034	<	}
1034	>	}
1035		}
895	–
1036		#ifdef IS_MPI
1037	<	strcpy( checkPointMsg, "post processing checks out" );
1037	>	strcpy(checkPointMsg, "post processing checks out");
1038		MPIcheckPoint();
1039		#endif // is_mpi
900	–
1040		}
902	–
903	–	void SimSetup::initSystemCoords( void ){
904	–	int i;
1041
1042	<	std::cerr << "Setting atom Coords\n";
1042	>	void SimSetup::initSystemCoords(void){
1043	>	int i;
1044
1045	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1046	<
1047	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1048	<
1049	<	if( globals->haveInitialConfig() ){
1050	<
1045	>	char* inName;
1046	>
1047	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1048	>
1049	>	for (i = 0; i < info[0].n_atoms; i++)
1050	>	info[0].atoms[i]->setCoords();
1051	>
1052	>	if (globals->haveInitialConfig()){
1053		InitializeFromFile* fileInit;
1054		#ifdef IS_MPI // is_mpi
1055	<	if( worldRank == 0 ){
1055	>	if (worldRank == 0){
1056		#endif //is_mpi
1057	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1057	>	inName = globals->getInitialConfig();
1058	>	fileInit = new InitializeFromFile(inName);
1059		#ifdef IS_MPI
1060	<	}else fileInit = new InitializeFromFile( NULL );
1060	>	}
1061	>	else
1062	>	fileInit = new InitializeFromFile(NULL);
1063		#endif
1064	<	fileInit->readInit( info ); // default velocities on
1065	<
1064	>	fileInit->readInit(info); // default velocities on
1065	>
1066		delete fileInit;
1067		}
1068		else{
1069
928	–	#ifdef IS_MPI
929	–
1070		// no init from bass
1071
1072	<	sprintf( painCave.errMsg,
1073	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1074	<	painCave.isFatal;
1072	>	sprintf(painCave.errMsg,
1073	>	"Cannot intialize a simulation without an initial configuration file.\n");
1074	>	painCave.isFatal = 1;;
1075		simError();
1076
937	–	#else
938	–
939	–	initFromBass();
940	–
941	–
942	–	#endif
1077		}
1078	<
1078	>
1079		#ifdef IS_MPI
1080	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1080	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1081		MPIcheckPoint();
1082		#endif // is_mpi
949	–
1083		}
1084
1085
1086	<	void SimSetup::makeOutNames( void ){
954	<
1086	>	void SimSetup::makeOutNames(void){
1087		int k;
1088
957	–
958	–	for(k=0; k<nInfo; k++){
1089
1090	+	for (k = 0; k < nInfo; k++){
1091		#ifdef IS_MPI
1092	<	if( worldRank == 0 ){
1092	>	if (worldRank == 0){
1093		#endif // is_mpi
1094	<
1095	<	if( globals->haveFinalConfig() ){
1096	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1094	>
1095	>	if (globals->haveFinalConfig()){
1096	>	strcpy(info[k].finalName, globals->getFinalConfig());
1097		}
1098		else{
1099	<	strcpy( info[k].finalName, inFileName );
1100	<	char* endTest;
1101	<	int nameLength = strlen( info[k].finalName );
1102	<	endTest = &(info[k].finalName[nameLength - 5]);
1103	<	if( !strcmp( endTest, ".bass" ) ){
1104	<	strcpy( endTest, ".eor" );
1105	<	}
1106	<	else if( !strcmp( endTest, ".BASS" ) ){
1107	<	strcpy( endTest, ".eor" );
1108	<	}
1109	<	else{
1110	<	endTest = &(info[k].finalName[nameLength - 4]);
1111	<	if( !strcmp( endTest, ".bss" ) ){
1112	<	strcpy( endTest, ".eor" );
1113	<	}
1114	<	else if( !strcmp( endTest, ".mdl" ) ){
1115	<	strcpy( endTest, ".eor" );
1116	<	}
1117	<	else{
1118	<	strcat( info[k].finalName, ".eor" );
1119	<	}
1120	<	}
1099	>	strcpy(info[k].finalName, inFileName);
1100	>	char* endTest;
1101	>	int nameLength = strlen(info[k].finalName);
1102	>	endTest = &(info[k].finalName[nameLength - 5]);
1103	>	if (!strcmp(endTest, ".bass")){
1104	>	strcpy(endTest, ".eor");
1105	>	}
1106	>	else if (!strcmp(endTest, ".BASS")){
1107	>	strcpy(endTest, ".eor");
1108	>	}
1109	>	else{
1110	>	endTest = &(info[k].finalName[nameLength - 4]);
1111	>	if (!strcmp(endTest, ".bss")){
1112	>	strcpy(endTest, ".eor");
1113	>	}
1114	>	else if (!strcmp(endTest, ".mdl")){
1115	>	strcpy(endTest, ".eor");
1116	>	}
1117	>	else{
1118	>	strcat(info[k].finalName, ".eor");
1119	>	}
1120	>	}
1121		}
1122	<
1122	>
1123		// make the sample and status out names
1124	<
1125	<	strcpy( info[k].sampleName, inFileName );
1124	>
1125	>	strcpy(info[k].sampleName, inFileName);
1126		char* endTest;
1127	<	int nameLength = strlen( info[k].sampleName );
1127	>	int nameLength = strlen(info[k].sampleName);
1128		endTest = &(info[k].sampleName[nameLength - 5]);
1129	<	if( !strcmp( endTest, ".bass" ) ){
1130	<	strcpy( endTest, ".dump" );
1129	>	if (!strcmp(endTest, ".bass")){
1130	>	strcpy(endTest, ".dump");
1131		}
1132	<	else if( !strcmp( endTest, ".BASS" ) ){
1133	<	strcpy( endTest, ".dump" );
1132	>	else if (!strcmp(endTest, ".BASS")){
1133	>	strcpy(endTest, ".dump");
1134		}
1135		else{
1136	<	endTest = &(info[k].sampleName[nameLength - 4]);
1137	<	if( !strcmp( endTest, ".bss" ) ){
1138	<	strcpy( endTest, ".dump" );
1139	<	}
1140	<	else if( !strcmp( endTest, ".mdl" ) ){
1141	<	strcpy( endTest, ".dump" );
1142	<	}
1143	<	else{
1144	<	strcat( info[k].sampleName, ".dump" );
1145	<	}
1136	>	endTest = &(info[k].sampleName[nameLength - 4]);
1137	>	if (!strcmp(endTest, ".bss")){
1138	>	strcpy(endTest, ".dump");
1139	>	}
1140	>	else if (!strcmp(endTest, ".mdl")){
1141	>	strcpy(endTest, ".dump");
1142	>	}
1143	>	else{
1144	>	strcat(info[k].sampleName, ".dump");
1145	>	}
1146		}
1147	<
1148	<	strcpy( info[k].statusName, inFileName );
1149	<	nameLength = strlen( info[k].statusName );
1147	>
1148	>	strcpy(info[k].statusName, inFileName);
1149	>	nameLength = strlen(info[k].statusName);
1150		endTest = &(info[k].statusName[nameLength - 5]);
1151	<	if( !strcmp( endTest, ".bass" ) ){
1152	<	strcpy( endTest, ".stat" );
1151	>	if (!strcmp(endTest, ".bass")){
1152	>	strcpy(endTest, ".stat");
1153		}
1154	<	else if( !strcmp( endTest, ".BASS" ) ){
1155	<	strcpy( endTest, ".stat" );
1154	>	else if (!strcmp(endTest, ".BASS")){
1155	>	strcpy(endTest, ".stat");
1156		}
1157		else{
1158	<	endTest = &(info[k].statusName[nameLength - 4]);
1159	<	if( !strcmp( endTest, ".bss" ) ){
1160	<	strcpy( endTest, ".stat" );
1161	<	}
1162	<	else if( !strcmp( endTest, ".mdl" ) ){
1163	<	strcpy( endTest, ".stat" );
1164	<	}
1165	<	else{
1166	<	strcat( info[k].statusName, ".stat" );
1167	<	}
1158	>	endTest = &(info[k].statusName[nameLength - 4]);
1159	>	if (!strcmp(endTest, ".bss")){
1160	>	strcpy(endTest, ".stat");
1161	>	}
1162	>	else if (!strcmp(endTest, ".mdl")){
1163	>	strcpy(endTest, ".stat");
1164	>	}
1165	>	else{
1166	>	strcat(info[k].statusName, ".stat");
1167	>	}
1168		}
1169	<
1169	>
1170		#ifdef IS_MPI
1171	+
1172		}
1173		#endif // is_mpi
1174		}
1175		}
1176
1177
1178	<	void SimSetup::sysObjectsCreation( void ){
1179	<
1180	<	int i,k;
1049	<
1178	>	void SimSetup::sysObjectsCreation(void){
1179	>	int i, k;
1180	>
1181		// create the forceField
1182	<
1182	>
1183		createFF();
1184
1185		// extract componentList
#	Line 1061 | Line 1192 | void SimSetup::sysObjectsCreation( void ){
1192
1193		#ifdef IS_MPI
1194		// divide the molecules among the processors
1195	<
1195	>
1196		mpiMolDivide();
1197		#endif //is_mpi
1198	<
1198	>
1199		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1200	<
1200	>
1201		makeSysArrays();
1202
1203		// make and initialize the molecules (all but atomic coordinates)
1204	<
1204	>
1205		makeMolecules();
1206	<
1207	<	for(k=0; k<nInfo; k++){
1206	>
1207	>	for (k = 0; k < nInfo; k++){
1208		info[k].identArray = new int[info[k].n_atoms];
1209	<	for(i=0; i<info[k].n_atoms; i++){
1209	>	for (i = 0; i < info[k].n_atoms; i++){
1210		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1211		}
1212		}
1213		}
1214
1215
1216	<	void SimSetup::createFF( void ){
1216	>	void SimSetup::createFF(void){
1217	>	switch (ffCase){
1218	>	case FF_DUFF:
1219	>	the_ff = new DUFF();
1220	>	break;
1221
1222	<	switch( ffCase ){
1222	>	case FF_LJ:
1223	>	the_ff = new LJFF();
1224	>	break;
1225
1226	<	case FF_DUFF:
1227	<	the_ff = new DUFF();
1228	<	break;
1226	>	case FF_EAM:
1227	>	the_ff = new EAM_FF();
1228	>	break;
1229
1230	<	case FF_LJ:
1231	<	the_ff = new LJFF();
1232	<	break;
1230	>	case FF_H2O:
1231	>	the_ff = new WATER();
1232	>	break;
1233
1234	<	case FF_EAM:
1235	<	the_ff = new EAM_FF();
1236	<	break;
1237	<
1238	<	default:
1102	<	sprintf( painCave.errMsg,
1103	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1104	<	painCave.isFatal = 1;
1105	<	simError();
1234	>	default:
1235	>	sprintf(painCave.errMsg,
1236	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1237	>	painCave.isFatal = 1;
1238	>	simError();
1239		}
1240
1241		#ifdef IS_MPI
1242	<	strcpy( checkPointMsg, "ForceField creation successful" );
1242	>	strcpy(checkPointMsg, "ForceField creation successful");
1243		MPIcheckPoint();
1244		#endif // is_mpi
1112	–
1245		}
1246
1247
1248	<	void SimSetup::compList( void ){
1117	<
1248	>	void SimSetup::compList(void){
1249		int i;
1250		char* id;
1251		LinkedMolStamp* headStamp = new LinkedMolStamp();
1252		LinkedMolStamp* currentStamp = NULL;
1253	<	comp_stamps = new MoleculeStamp*[n_components];
1254	<
1253	>	comp_stamps = new MoleculeStamp * [n_components];
1254	>
1255		// make an array of molecule stamps that match the components used.
1256		// also extract the used stamps out into a separate linked list
1257	<
1258	<	for(i=0; i<nInfo; i++){
1257	>
1258	>	for (i = 0; i < nInfo; i++){
1259		info[i].nComponents = n_components;
1260		info[i].componentsNmol = components_nmol;
1261		info[i].compStamps = comp_stamps;
1262		info[i].headStamp = headStamp;
1263		}
1133	–
1264
1135	–	for( i=0; i<n_components; i++ ){
1265
1266	+	for (i = 0; i < n_components; i++){
1267		id = the_components[i]->getType();
1268		comp_stamps[i] = NULL;
1269	<
1269	>
1270		// check to make sure the component isn't already in the list
1271
1272	<	comp_stamps[i] = headStamp->match( id );
1273	<	if( comp_stamps[i] == NULL ){
1144	<
1272	>	comp_stamps[i] = headStamp->match(id);
1273	>	if (comp_stamps[i] == NULL){
1274		// extract the component from the list;
1275	<
1276	<	currentStamp = stamps->extractMolStamp( id );
1277	<	if( currentStamp == NULL ){
1278	<	sprintf( painCave.errMsg,
1279	<	"SimSetup error: Component \"%s\" was not found in the "
1280	<	"list of declared molecules\n",
1281	<	id );
1282	<	painCave.isFatal = 1;
1283	<	simError();
1275	>
1276	>	currentStamp = stamps->extractMolStamp(id);
1277	>	if (currentStamp == NULL){
1278	>	sprintf(painCave.errMsg,
1279	>	"SimSetup error: Component \"%s\" was not found in the "
1280	>	"list of declared molecules\n",
1281	>	id);
1282	>	painCave.isFatal = 1;
1283	>	simError();
1284		}
1285	<
1286	<	headStamp->add( currentStamp );
1287	<	comp_stamps[i] = headStamp->match( id );
1285	>
1286	>	headStamp->add(currentStamp);
1287	>	comp_stamps[i] = headStamp->match(id);
1288		}
1289		}
1290
1291		#ifdef IS_MPI
1292	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1292	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1293		MPIcheckPoint();
1294		#endif // is_mpi
1295	+	}
1296
1297	+	void SimSetup::calcSysValues(void){
1298	+	int i;
1299
1300	<	}
1300	>	int* molMembershipArray;
1301
1170	–	void SimSetup::calcSysValues( void ){
1171	–	int i, j, k;
1172	–
1173	–	int *molMembershipArray;
1174	–
1302		tot_atoms = 0;
1303		tot_bonds = 0;
1304		tot_bends = 0;
1305		tot_torsions = 0;
1306	<	for( i=0; i<n_components; i++ ){
1307	<
1308	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1309	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1310	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1306	>	tot_rigid = 0;
1307	>	for (i = 0; i < n_components; i++){
1308	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1309	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1310	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1311		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1312	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1313		}
1314
1315		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1316		molMembershipArray = new int[tot_atoms];
1317	<
1318	<	for(i=0; i<nInfo; i++){
1317	>
1318	>	for (i = 0; i < nInfo; i++){
1319		info[i].n_atoms = tot_atoms;
1320		info[i].n_bonds = tot_bonds;
1321		info[i].n_bends = tot_bends;
1322		info[i].n_torsions = tot_torsions;
1323		info[i].n_SRI = tot_SRI;
1324		info[i].n_mol = tot_nmol;
1325	<
1325	>
1326		info[i].molMembershipArray = molMembershipArray;
1327	<	}
1327	>	}
1328		}
1329
1330		#ifdef IS_MPI
1331
1332	<	void SimSetup::mpiMolDivide( void ){
1205	<
1332	>	void SimSetup::mpiMolDivide(void){
1333		int i, j, k;
1334		int localMol, allMol;
1335		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1336	+	int local_rigid;
1337
1338	<	mpiSim = new mpiSimulation( info );
1339	<
1338	>	mpiSim = new mpiSimulation(info);
1339	>
1340		globalIndex = mpiSim->divideLabor();
1341
1342		// set up the local variables
1343	<
1343	>
1344		mol2proc = mpiSim->getMolToProcMap();
1345		molCompType = mpiSim->getMolComponentType();
1346	<
1346	>
1347		allMol = 0;
1348		localMol = 0;
1349		local_atoms = 0;
1350		local_bonds = 0;
1351		local_bends = 0;
1352		local_torsions = 0;
1353	+	local_rigid = 0;
1354		globalAtomIndex = 0;
1355
1356	<
1357	<	for( i=0; i<n_components; i++ ){
1358	<
1359	<	for( j=0; j<components_nmol[i]; j++ ){
1360	<
1361	<	if( mol2proc[allMol] == worldRank ){
1362	<
1363	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1364	<	local_bonds +=    comp_stamps[i]->getNBonds();
1236	<	local_bends +=    comp_stamps[i]->getNBends();
1237	<	local_torsions += comp_stamps[i]->getNTorsions();
1238	<	localMol++;
1356	>	for (i = 0; i < n_components; i++){
1357	>	for (j = 0; j < components_nmol[i]; j++){
1358	>	if (mol2proc[allMol] == worldRank){
1359	>	local_atoms += comp_stamps[i]->getNAtoms();
1360	>	local_bonds += comp_stamps[i]->getNBonds();
1361	>	local_bends += comp_stamps[i]->getNBends();
1362	>	local_torsions += comp_stamps[i]->getNTorsions();
1363	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1364	>	localMol++;
1365		}
1366	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1366	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1367		info[0].molMembershipArray[globalAtomIndex] = allMol;
1368		globalAtomIndex++;
1369		}
1370
1371	<	allMol++;
1371	>	allMol++;
1372		}
1373		}
1374		local_SRI = local_bonds + local_bends + local_torsions;
1375	<
1375	>
1376		info[0].n_atoms = mpiSim->getMyNlocal();
1377
1378	<	if( local_atoms != info[0].n_atoms ){
1379	<	sprintf( painCave.errMsg,
1380	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1381	<	" localAtom (%d) are not equal.\n",
1382	<	info[0].n_atoms,
1383	<	local_atoms );
1378	>
1379	>	if (local_atoms != info[0].n_atoms){
1380	>	sprintf(painCave.errMsg,
1381	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1382	>	"\tlocalAtom (%d) are not equal.\n",
1383	>	info[0].n_atoms, local_atoms);
1384		painCave.isFatal = 1;
1385		simError();
1386		}
#	Line 1265 | Line 1391 | void SimSetup::mpiMolDivide( void ){
1391		info[0].n_SRI = local_SRI;
1392		info[0].n_mol = localMol;
1393
1394	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1394	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1395		MPIcheckPoint();
1396		}
1397	<
1397	>
1398		#endif // is_mpi
1399
1400
1401	<	void SimSetup::makeSysArrays( void ){
1402	<	int i, j, k, l;
1401	>	void SimSetup::makeSysArrays(void){
1402	>
1403	>	#ifndef IS_MPI
1404	>	int k, j;
1405	>	#endif // is_mpi
1406	>	int i, l;
1407
1408		Atom** the_atoms;
1409		Molecule* the_molecules;
1280	–	Exclude** the_excludes;
1410
1411	<
1283	<	for(l=0; l<nInfo; l++){
1284	<
1411	>	for (l = 0; l < nInfo; l++){
1412		// create the atom and short range interaction arrays
1413	<
1414	<	the_atoms = new Atom*[info[l].n_atoms];
1413	>
1414	>	the_atoms = new Atom * [info[l].n_atoms];
1415		the_molecules = new Molecule[info[l].n_mol];
1416		int molIndex;
1417
1418		// initialize the molecule's stampID's
1419	<
1419	>
1420		#ifdef IS_MPI
1421	<
1422	<
1421	>
1422	>
1423		molIndex = 0;
1424	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1425	<
1426	<	if(mol2proc[i] == worldRank ){
1427	<	the_molecules[molIndex].setStampID( molCompType[i] );
1428	<	the_molecules[molIndex].setMyIndex( molIndex );
1429	<	the_molecules[molIndex].setGlobalIndex( i );
1303	<	molIndex++;
1424	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1425	>	if (mol2proc[i] == worldRank){
1426	>	the_molecules[molIndex].setStampID(molCompType[i]);
1427	>	the_molecules[molIndex].setMyIndex(molIndex);
1428	>	the_molecules[molIndex].setGlobalIndex(i);
1429	>	molIndex++;
1430		}
1431		}
1432	<
1432	>
1433		#else // is_mpi
1434	<
1434	>
1435		molIndex = 0;
1436		globalAtomIndex = 0;
1437	<	for(i=0; i<n_components; i++){
1438	<	for(j=0; j<components_nmol[i]; j++ ){
1439	<	the_molecules[molIndex].setStampID( i );
1440	<	the_molecules[molIndex].setMyIndex( molIndex );
1441	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1442	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1443	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1444	<	globalAtomIndex++;
1445	<	}
1446	<	molIndex++;
1437	>	for (i = 0; i < n_components; i++){
1438	>	for (j = 0; j < components_nmol[i]; j++){
1439	>	the_molecules[molIndex].setStampID(i);
1440	>	the_molecules[molIndex].setMyIndex(molIndex);
1441	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1442	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1443	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1444	>	globalAtomIndex++;
1445	>	}
1446	>	molIndex++;
1447		}
1448		}
1323	–
1324	–
1325	–	#endif // is_mpi
1449
1450
1451	<	if( info[l].n_SRI ){
1329	<
1330	<	Exclude::createArray(info[l].n_SRI);
1331	<	the_excludes = new Exclude*[info[l].n_SRI];
1332	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1333	<	the_excludes[ex] = new Exclude(ex);
1334	<	}
1335	<	info[l].globalExcludes = new int;
1336	<	info[l].n_exclude = info[l].n_SRI;
1337	<	}
1338	<	else{
1339	<
1340	<	Exclude::createArray( 1 );
1341	<	the_excludes = new Exclude*;
1342	<	the_excludes[0] = new Exclude(0);
1343	<	the_excludes[0]->setPair( 0,0 );
1344	<	info[l].globalExcludes = new int;
1345	<	info[l].globalExcludes[0] = 0;
1346	<	info[l].n_exclude = 0;
1347	<	}
1451	>	#endif // is_mpi
1452
1453	+	info[l].globalExcludes = new int;
1454	+	info[l].globalExcludes[0] = 0;
1455	+
1456		// set the arrays into the SimInfo object
1457
1458		info[l].atoms = the_atoms;
1459		info[l].molecules = the_molecules;
1460		info[l].nGlobalExcludes = 0;
1354	–	info[l].excludes = the_excludes;
1461
1462	<	the_ff->setSimInfo( info );
1357	<
1462	>	the_ff->setSimInfo(info);
1463		}
1464		}
1465
1466	<	void SimSetup::makeIntegrator( void ){
1362	<
1466	>	void SimSetup::makeIntegrator(void){
1467		int k;
1468
1469	<	NVT<RealIntegrator>*  myNVT = NULL;
1470	<	NPTi<RealIntegrator>* myNPTi = NULL;
1471	<	NPTf<RealIntegrator>* myNPTf = NULL;
1472	<	NPTim<RealIntegrator>* myNPTim = NULL;
1473	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1474	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1475	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1476	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1477	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1478	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1479	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1480	<
1481	<	for(k=0; k<nInfo; k++){
1482	<
1483	<	switch( ensembleCase ){
1484	<
1485	<	case NVE_ENS:
1486	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1487	<	break;
1488	<
1489	<	case NVT_ENS:
1490	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1491	<	myNVT->setTargetTemp(globals->getTargetTemp());
1492	<
1493	<	if (globals->haveTauThermostat())
1494	<	myNVT->setTauThermostat(globals->getTauThermostat());
1495	<
1496	<	else {
1497	<	sprintf( painCave.errMsg,
1498	<	"SimSetup error: If you use the NVT\n"
1499	<	"    ensemble, you must set tauThermostat.\n");
1500	<	painCave.isFatal = 1;
1501	<	simError();
1502	<	}
1503	<	break;
1504	<
1505	<	case NPTi_ENS:
1506	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1507	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1508	<
1509	<	if (globals->haveTargetPressure())
1510	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1511	<	else {
1512	<	sprintf( painCave.errMsg,
1513	<	"SimSetup error: If you use a constant pressure\n"
1514	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1515	<	painCave.isFatal = 1;
1516	<	simError();
1517	<	}
1518	<
1519	<	if( globals->haveTauThermostat() )
1520	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1521	<	else{
1522	<	sprintf( painCave.errMsg,
1523	<	"SimSetup error: If you use an NPT\n"
1524	<	"    ensemble, you must set tauThermostat.\n");
1525	<	painCave.isFatal = 1;
1526	<	simError();
1527	<	}
1528	<
1529	<	if( globals->haveTauBarostat() )
1530	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1531	<	else{
1532	<	sprintf( painCave.errMsg,
1533	<	"SimSetup error: If you use an NPT\n"
1534	<	"    ensemble, you must set tauBarostat.\n");
1535	<	painCave.isFatal = 1;
1536	<	simError();
1537	<	}
1538	<	break;
1539	<
1540	<	case NPTf_ENS:
1541	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1542	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1543	<
1544	<	if (globals->haveTargetPressure())
1545	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1546	<	else {
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use a constant pressure\n"
1549	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1553	<
1554	<	if( globals->haveTauThermostat() )
1555	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1556	<	else{
1557	<	sprintf( painCave.errMsg,
1558	<	"SimSetup error: If you use an NPT\n"
1559	<	"    ensemble, you must set tauThermostat.\n");
1560	<	painCave.isFatal = 1;
1561	<	simError();
1562	<	}
1563	<
1564	<	if( globals->haveTauBarostat() )
1565	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1566	<	else{
1567	<	sprintf( painCave.errMsg,
1568	<	"SimSetup error: If you use an NPT\n"
1569	<	"    ensemble, you must set tauBarostat.\n");
1570	<	painCave.isFatal = 1;
1571	<	simError();
1572	<	}
1573	<	break;
1574	<
1575	<	case NPTim_ENS:
1576	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1577	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1578	<
1579	<	if (globals->haveTargetPressure())
1580	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1581	<	else {
1582	<	sprintf( painCave.errMsg,
1583	<	"SimSetup error: If you use a constant pressure\n"
1584	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1585	<	painCave.isFatal = 1;
1586	<	simError();
1587	<	}
1588	<
1589	<	if( globals->haveTauThermostat() )
1590	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1591	<	else{
1592	<	sprintf( painCave.errMsg,
1593	<	"SimSetup error: If you use an NPT\n"
1594	<	"    ensemble, you must set tauThermostat.\n");
1595	<	painCave.isFatal = 1;
1596	<	simError();
1597	<	}
1598	<
1599	<	if( globals->haveTauBarostat() )
1600	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1601	<	else{
1602	<	sprintf( painCave.errMsg,
1603	<	"SimSetup error: If you use an NPT\n"
1604	<	"    ensemble, you must set tauBarostat.\n");
1605	<	painCave.isFatal = 1;
1606	<	simError();
1607	<	}
1608	<	break;
1609	<
1610	<	case NPTfm_ENS:
1611	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1612	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1613	<
1614	<	if (globals->haveTargetPressure())
1615	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1616	<	else {
1617	<	sprintf( painCave.errMsg,
1618	<	"SimSetup error: If you use a constant pressure\n"
1619	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1620	<	painCave.isFatal = 1;
1621	<	simError();
1622	<	}
1623	<
1624	<	if( globals->haveTauThermostat() )
1625	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1626	<	else{
1627	<	sprintf( painCave.errMsg,
1628	<	"SimSetup error: If you use an NPT\n"
1629	<	"    ensemble, you must set tauThermostat.\n");
1630	<	painCave.isFatal = 1;
1631	<	simError();
1632	<	}
1633	<
1634	<	if( globals->haveTauBarostat() )
1635	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1636	<	else{
1637	<	sprintf( painCave.errMsg,
1638	<	"SimSetup error: If you use an NPT\n"
1639	<	"    ensemble, you must set tauBarostat.\n");
1640	<	painCave.isFatal = 1;
1641	<	simError();
1642	<	}
1643	<	break;
1644	<
1645	<	case NVEZCONS_ENS:
1646	<
1647	<
1544	<	//setup index of z-constraint molecules, z-constraint sampel time
1545	<	//and z-constraint force output name. These parameter should be known
1546	<	//before constructing the z-constraint integrator
1547	<	setupZConstraint();
1548	<
1549	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	<
1551	<	break;
1552	<
1553	<
1554	<	case NVTZCONS_ENS:
1555	<
1556	<	setupZConstraint();
1557	<
1558	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	<
1561	<	if (globals->haveTauThermostat())
1562	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	<
1564	<	else {
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use the NVT\n"
1567	<	"    ensemble, you must set tauThermostat.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1570	<	}
1571	<	break;
1572	<
1573	<	case NPTiZCONS_ENS:
1574	<
1575	<	setupZConstraint();
1576	<
1577	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	<
1580	<	if (globals->haveTargetPressure())
1581	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	<	else {
1583	<	sprintf( painCave.errMsg,
1584	<	"SimSetup error: If you use a constant pressure\n"
1585	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	<	painCave.isFatal = 1;
1587	<	simError();
1588	<	}
1589	<
1590	<	if( globals->haveTauThermostat() )
1591	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	<	else{
1593	<	sprintf( painCave.errMsg,
1594	<	"SimSetup error: If you use an NPT\n"
1595	<	"    ensemble, you must set tauThermostat.\n");
1596	<	painCave.isFatal = 1;
1597	<	simError();
1598	<	}
1599	<
1600	<	if( globals->haveTauBarostat() )
1601	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	<	else{
1603	<	sprintf( painCave.errMsg,
1604	<	"SimSetup error: If you use an NPT\n"
1605	<	"    ensemble, you must set tauBarostat.\n");
1606	<	painCave.isFatal = 1;
1607	<	simError();
1608	<	}
1609	<
1610	<	break;
1611	<
1612	<	case NPTfZCONS_ENS:
1613	<
1614	<	setupZConstraint();
1615	<
1616	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	<
1619	<	if (globals->haveTargetPressure())
1620	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	<	else {
1622	<	sprintf( painCave.errMsg,
1623	<	"SimSetup error: If you use a constant pressure\n"
1624	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	<	painCave.isFatal = 1;
1626	<	simError();
1627	<	}
1628	<
1629	<	if( globals->haveTauThermostat() )
1630	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	<	else{
1632	<	sprintf( painCave.errMsg,
1633	<	"SimSetup error: If you use an NPT\n"
1634	<	"    ensemble, you must set tauThermostat.\n");
1635	<	painCave.isFatal = 1;
1636	<	simError();
1637	<	}
1638	<
1639	<	if( globals->haveTauBarostat() )
1640	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	<	else{
1642	<	sprintf( painCave.errMsg,
1643	<	"SimSetup error: If you use an NPT\n"
1644	<	"    ensemble, you must set tauBarostat.\n");
1645	<	painCave.isFatal = 1;
1646	<	simError();
1647	<	}
1648	<
1649	<	break;
1650	<
1651	<	case NPTimZCONS_ENS:
1652	<
1653	<	setupZConstraint();
1654	<
1655	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	<
1658	<	if (globals->haveTargetPressure())
1659	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	<	else {
1661	<	sprintf( painCave.errMsg,
1662	<	"SimSetup error: If you use a constant pressure\n"
1663	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	<	painCave.isFatal = 1;
1665	<	simError();
1666	<	}
1667	<
1668	<	if( globals->haveTauThermostat() )
1669	<	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	<	else{
1671	<	sprintf( painCave.errMsg,
1672	<	"SimSetup error: If you use an NPT\n"
1673	<	"    ensemble, you must set tauThermostat.\n");
1674	<	painCave.isFatal = 1;
1675	<	simError();
1676	<	}
1677	<
1678	<	if( globals->haveTauBarostat() )
1679	<	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	<	else{
1681	<	sprintf( painCave.errMsg,
1682	<	"SimSetup error: If you use an NPT\n"
1683	<	"    ensemble, you must set tauBarostat.\n");
1684	<	painCave.isFatal = 1;
1685	<	simError();
1686	<	}
1687	<
1688	<	break;
1689	<
1690	<	case NPTfmZCONS_ENS:
1691	<
1692	<	setupZConstraint();
1693	<
1694	<	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	<	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	<
1697	<	if (globals->haveTargetPressure())
1698	<	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	<	else {
1700	<	sprintf( painCave.errMsg,
1701	<	"SimSetup error: If you use a constant pressure\n"
1702	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	<	painCave.isFatal = 1;
1704	<	simError();
1705	<	}
1706	<
1707	<	if( globals->haveTauThermostat() )
1708	<	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	<	else{
1710	<	sprintf( painCave.errMsg,
1711	<	"SimSetup error: If you use an NPT\n"
1712	<	"    ensemble, you must set tauThermostat.\n");
1713	<	painCave.isFatal = 1;
1714	<	simError();
1715	<	}
1716	<
1717	<	if( globals->haveTauBarostat() )
1718	<	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	<	else{
1720	<	sprintf( painCave.errMsg,
1721	<	"SimSetup error: If you use an NPT\n"
1722	<	"    ensemble, you must set tauBarostat.\n");
1723	<	painCave.isFatal = 1;
1724	<	simError();
1725	<	}
1726	<	break;
1727	<
1728	<
1729	<
1730	<	default:
1731	<	sprintf( painCave.errMsg,
1732	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733	<	painCave.isFatal = 1;
1734	<	simError();
1469	>	NVE<RealIntegrator>* myNVE = NULL;
1470	>	NVT<RealIntegrator>* myNVT = NULL;
1471	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1472	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1473	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1474	>
1475	>	for (k = 0; k < nInfo; k++){
1476	>	switch (ensembleCase){
1477	>	case NVE_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1481	>	}
1482	>	else{
1483	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1484	>	}
1485	>
1486	>	info->the_integrator = myNVE;
1487	>	break;
1488	>
1489	>	case NVT_ENS:
1490	>	if (globals->haveZconstraints()){
1491	>	setupZConstraint(info[k]);
1492	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1493	>	}
1494	>	else
1495	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1496	>
1497	>	myNVT->setTargetTemp(globals->getTargetTemp());
1498	>
1499	>	if (globals->haveTauThermostat())
1500	>	myNVT->setTauThermostat(globals->getTauThermostat());
1501	>	else{
1502	>	sprintf(painCave.errMsg,
1503	>	"SimSetup error: If you use the NVT\n"
1504	>	"\tensemble, you must set tauThermostat.\n");
1505	>	painCave.isFatal = 1;
1506	>	simError();
1507	>	}
1508	>
1509	>	info->the_integrator = myNVT;
1510	>	break;
1511	>
1512	>	case NPTi_ENS:
1513	>	if (globals->haveZconstraints()){
1514	>	setupZConstraint(info[k]);
1515	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1516	>	}
1517	>	else
1518	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1519	>
1520	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1521	>
1522	>	if (globals->haveTargetPressure())
1523	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1524	>	else{
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup error: If you use a constant pressure\n"
1527	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1528	>	painCave.isFatal = 1;
1529	>	simError();
1530	>	}
1531	>
1532	>	if (globals->haveTauThermostat())
1533	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1534	>	else{
1535	>	sprintf(painCave.errMsg,
1536	>	"SimSetup error: If you use an NPT\n"
1537	>	"\tensemble, you must set tauThermostat.\n");
1538	>	painCave.isFatal = 1;
1539	>	simError();
1540	>	}
1541	>
1542	>	if (globals->haveTauBarostat())
1543	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1544	>	else{
1545	>	sprintf(painCave.errMsg,
1546	>	"SimSetup error: If you use an NPT\n"
1547	>	"\tensemble, you must set tauBarostat.\n");
1548	>	painCave.isFatal = 1;
1549	>	simError();
1550	>	}
1551	>
1552	>	info->the_integrator = myNPTi;
1553	>	break;
1554	>
1555	>	case NPTf_ENS:
1556	>	if (globals->haveZconstraints()){
1557	>	setupZConstraint(info[k]);
1558	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1559	>	}
1560	>	else
1561	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1562	>
1563	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1564	>
1565	>	if (globals->haveTargetPressure())
1566	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1567	>	else{
1568	>	sprintf(painCave.errMsg,
1569	>	"SimSetup error: If you use a constant pressure\n"
1570	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1571	>	painCave.isFatal = 1;
1572	>	simError();
1573	>	}
1574	>
1575	>	if (globals->haveTauThermostat())
1576	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1577	>
1578	>	else{
1579	>	sprintf(painCave.errMsg,
1580	>	"SimSetup error: If you use an NPT\n"
1581	>	"\tensemble, you must set tauThermostat.\n");
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585	>
1586	>	if (globals->haveTauBarostat())
1587	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1588	>
1589	>	else{
1590	>	sprintf(painCave.errMsg,
1591	>	"SimSetup error: If you use an NPT\n"
1592	>	"\tensemble, you must set tauBarostat.\n");
1593	>	painCave.isFatal = 1;
1594	>	simError();
1595	>	}
1596	>
1597	>	info->the_integrator = myNPTf;
1598	>	break;
1599	>
1600	>	case NPTxyz_ENS:
1601	>	if (globals->haveZconstraints()){
1602	>	setupZConstraint(info[k]);
1603	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1604	>	}
1605	>	else
1606	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1607	>
1608	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1609	>
1610	>	if (globals->haveTargetPressure())
1611	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1612	>	else{
1613	>	sprintf(painCave.errMsg,
1614	>	"SimSetup error: If you use a constant pressure\n"
1615	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1616	>	painCave.isFatal = 1;
1617	>	simError();
1618	>	}
1619	>
1620	>	if (globals->haveTauThermostat())
1621	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1622	>	else{
1623	>	sprintf(painCave.errMsg,
1624	>	"SimSetup error: If you use an NPT\n"
1625	>	"\tensemble, you must set tauThermostat.\n");
1626	>	painCave.isFatal = 1;
1627	>	simError();
1628	>	}
1629	>
1630	>	if (globals->haveTauBarostat())
1631	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1632	>	else{
1633	>	sprintf(painCave.errMsg,
1634	>	"SimSetup error: If you use an NPT\n"
1635	>	"\tensemble, you must set tauBarostat.\n");
1636	>	painCave.isFatal = 1;
1637	>	simError();
1638	>	}
1639	>
1640	>	info->the_integrator = myNPTxyz;
1641	>	break;
1642	>
1643	>	default:
1644	>	sprintf(painCave.errMsg,
1645	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1646	>	painCave.isFatal = 1;
1647	>	simError();
1648		}
1649		}
1650		}
1651
1652	<	void SimSetup::initFortran( void ){
1740	<
1652	>	void SimSetup::initFortran(void){
1653		info[0].refreshSim();
1654	<
1655	<	if( !strcmp( info[0].mixingRule, "standard") ){
1656	<	the_ff->initForceField( LB_MIXING_RULE );
1654	>
1655	>	if (!strcmp(info[0].mixingRule, "standard")){
1656	>	the_ff->initForceField(LB_MIXING_RULE);
1657		}
1658	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1659	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1658	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1659	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1660		}
1661		else{
1662	<	sprintf( painCave.errMsg,
1663	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	<	info[0].mixingRule );
1662	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1663	>	info[0].mixingRule);
1664		painCave.isFatal = 1;
1665		simError();
1666		}
1667
1668
1669		#ifdef IS_MPI
1670	<	strcpy( checkPointMsg,
1760	<	"Successfully intialized the mixingRule for Fortran." );
1670	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1671		MPIcheckPoint();
1672		#endif // is_mpi
1673	+	}
1674
1675	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1676	+	int nZConstraints;
1677	+	ZconStamp** zconStamp;
1678	+
1679	+	if (globals->haveZconstraintTime()){
1680	+	//add sample time of z-constraint  into SimInfo's property list
1681	+	DoubleData* zconsTimeProp = new DoubleData();
1682	+	zconsTimeProp->setID(ZCONSTIME_ID);
1683	+	zconsTimeProp->setData(globals->getZconsTime());
1684	+	theInfo.addProperty(zconsTimeProp);
1685	+	}
1686	+	else{
1687	+	sprintf(painCave.errMsg,
1688	+	"ZConstraint error: If you use a ZConstraint,\n"
1689	+	"\tyou must set zconsTime.\n");
1690	+	painCave.isFatal = 1;
1691	+	simError();
1692	+	}
1693	+
1694	+	//push zconsTol into siminfo, if user does not specify
1695	+	//value for zconsTol, a default value will be used
1696	+	DoubleData* zconsTol = new DoubleData();
1697	+	zconsTol->setID(ZCONSTOL_ID);
1698	+	if (globals->haveZconsTol()){
1699	+	zconsTol->setData(globals->getZconsTol());
1700	+	}
1701	+	else{
1702	+	double defaultZConsTol = 0.01;
1703	+	sprintf(painCave.errMsg,
1704	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1705	+	"\tOOPSE will use a default value of %f.\n"
1706	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1707	+	defaultZConsTol);
1708	+	painCave.isFatal = 0;
1709	+	simError();
1710	+
1711	+	zconsTol->setData(defaultZConsTol);
1712	+	}
1713	+	theInfo.addProperty(zconsTol);
1714	+
1715	+	//set Force Subtraction Policy
1716	+	StringData* zconsForcePolicy = new StringData();
1717	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1718	+
1719	+	if (globals->haveZconsForcePolicy()){
1720	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1721	+	}
1722	+	else{
1723	+	sprintf(painCave.errMsg,
1724	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1725	+	"\tOOPSE will use PolicyByMass.\n"
1726	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1727	+	painCave.isFatal = 0;
1728	+	simError();
1729	+	zconsForcePolicy->setData("BYMASS");
1730	+	}
1731	+
1732	+	theInfo.addProperty(zconsForcePolicy);
1733	+
1734	+	//set zcons gap
1735	+	DoubleData* zconsGap = new DoubleData();
1736	+	zconsGap->setID(ZCONSGAP_ID);
1737	+
1738	+	if (globals->haveZConsGap()){
1739	+	zconsGap->setData(globals->getZconsGap());
1740	+	theInfo.addProperty(zconsGap);
1741	+	}
1742	+
1743	+	//set zcons fixtime
1744	+	DoubleData* zconsFixtime = new DoubleData();
1745	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1746	+
1747	+	if (globals->haveZConsFixTime()){
1748	+	zconsFixtime->setData(globals->getZconsFixtime());
1749	+	theInfo.addProperty(zconsFixtime);
1750	+	}
1751	+
1752	+	//set zconsUsingSMD
1753	+	IntData* zconsUsingSMD = new IntData();
1754	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1755	+
1756	+	if (globals->haveZConsUsingSMD()){
1757	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1758	+	theInfo.addProperty(zconsUsingSMD);
1759	+	}
1760	+
1761	+	//Determine the name of ouput file and add it into SimInfo's property list
1762	+	//Be careful, do not use inFileName, since it is a pointer which
1763	+	//point to a string at master node, and slave nodes do not contain that string
1764	+
1765	+	string zconsOutput(theInfo.finalName);
1766	+
1767	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1768	+
1769	+	StringData* zconsFilename = new StringData();
1770	+	zconsFilename->setID(ZCONSFILENAME_ID);
1771	+	zconsFilename->setData(zconsOutput);
1772	+
1773	+	theInfo.addProperty(zconsFilename);
1774	+
1775	+	//setup index, pos and other parameters of z-constraint molecules
1776	+	nZConstraints = globals->getNzConstraints();
1777	+	theInfo.nZconstraints = nZConstraints;
1778	+
1779	+	zconStamp = globals->getZconStamp();
1780	+	ZConsParaItem tempParaItem;
1781	+
1782	+	ZConsParaData* zconsParaData = new ZConsParaData();
1783	+	zconsParaData->setID(ZCONSPARADATA_ID);
1784	+
1785	+	for (int i = 0; i < nZConstraints; i++){
1786	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1787	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1788	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1789	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1790	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1791	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1792	+	zconsParaData->addItem(tempParaItem);
1793	+	}
1794	+
1795	+	//check the uniqueness of index
1796	+	if(!zconsParaData->isIndexUnique()){
1797	+	sprintf(painCave.errMsg,
1798	+	"ZConstraint Error: molIndex is not unique!\n");
1799	+	painCave.isFatal = 1;
1800	+	simError();
1801	+	}
1802	+
1803	+	//sort the parameters by index of molecules
1804	+	zconsParaData->sortByIndex();
1805	+
1806	+	//push data into siminfo, therefore, we can retrieve later
1807	+	theInfo.addProperty(zconsParaData);
1808		}
1809
1810	<	void SimSetup::setupZConstraint()
1767	<	{
1768	<	int k;
1810	>	void SimSetup::makeMinimizer(){
1811
1812	<	for(k=0; k<nInfo; k++){
1812	>	OOPSEMinimizer* myOOPSEMinimizer;
1813	>	MinimizerParameterSet* param;
1814	>	char minimizerName[100];
1815	>
1816	>	for (int i = 0; i < nInfo; i++){
1817
1818	<	if(globals->haveZConsTime()){
1819	<
1820	<	//add sample time of z-constraint  into SimInfo's property list
1821	<	DoubleData* zconsTimeProp = new DoubleData();
1822	<	zconsTimeProp->setID("zconstime");
1823	<	zconsTimeProp->setData(globals->getZConsTime());
1778	<	info[k].addProperty(zconsTimeProp);
1818	>	//prepare parameter set for minimizer
1819	>	param = new MinimizerParameterSet();
1820	>	param->setDefaultParameter();
1821	>
1822	>	if (globals->haveMinimizer()){
1823	>	param->setFTol(globals->getMinFTol());
1824		}
1825	<	else{
1826	<	sprintf( painCave.errMsg,
1827	<	"ZConstraint error: If you use an ZConstraint\n"
1783	<	" , you must set sample time.\n");
1784	<	painCave.isFatal = 1;
1785	<	simError();
1825	>
1826	>	if (globals->haveMinGTol()){
1827	>	param->setGTol(globals->getMinGTol());
1828		}
1829	+
1830	+	if (globals->haveMinMaxIter()){
1831	+	param->setMaxIteration(globals->getMinMaxIter());
1832	+	}
1833	+
1834	+	if (globals->haveMinWriteFrq()){
1835	+	param->setMaxIteration(globals->getMinMaxIter());
1836	+	}
1837	+
1838	+	if (globals->haveMinWriteFrq()){
1839	+	param->setWriteFrq(globals->getMinWriteFrq());
1840	+	}
1841
1842	<	if(globals->haveIndexOfAllZConsMols()){
1843	<
1790	<	//add index of z-constraint molecules into SimInfo's property list
1791	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792	<
1793	<	//sort the index
1794	<	sort(tempIndex.begin(), tempIndex.end());
1795	<
1796	<	IndexData* zconsIndex = new IndexData();
1797	<	zconsIndex->setID("zconsindex");
1798	<	zconsIndex->setIndexData(tempIndex);
1799	<	info[k].addProperty(zconsIndex);
1842	>	if (globals->haveMinStepSize()){
1843	>	param->setStepSize(globals->getMinStepSize());
1844		}
1845	+
1846	+	if (globals->haveMinLSMaxIter()){
1847	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinLSTol()){
1851	+	param->setLineSearchTol(globals->getMinLSTol());
1852	+	}
1853	+
1854	+	strcpy(minimizerName, globals->getMinimizer());
1855	+
1856	+	if (!strcasecmp(minimizerName, "CG")){
1857	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1858	+	}
1859	+	else if (!strcasecmp(minimizerName, "SD")){
1860	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1861	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1862	+	}
1863		else{
1864	<	sprintf( painCave.errMsg,
1865	<	"SimSetup error: If you use an ZConstraint\n"
1866	<	" , you must set index of z-constraint molecules.\n");
1867	<	painCave.isFatal = 1;
1868	<	simError();
1869	<
1864	>	sprintf(painCave.errMsg,
1865	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1866	>	painCave.isFatal = 0;
1867	>	simError();
1868	>
1869	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870		}
1871	<
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
1875	<
1814	<	string zconsOutput(info[k].finalName);
1815	<
1816	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1817	<
1818	<	StringData* zconsFilename = new StringData();
1819	<	zconsFilename->setID("zconsfilename");
1820	<	zconsFilename->setData(zconsOutput);
1821	<
1822	<	info[k].addProperty(zconsFilename);
1871	>	info[i].the_integrator = myOOPSEMinimizer;
1872	>
1873	>	//store the minimizer into simInfo
1874	>	info[i].the_minimizer = myOOPSEMinimizer;
1875	>	info[i].has_minimizer = true;
1876		}
1877	+
1878		}

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