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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC vs.
Revision 999 by chrisfen, Fri Jan 30 15:01:09 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"
#	Line 21 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
24	>	#define NPTxyz_ENS     4
25
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#define FF_EAM  2
26
27	+	#define FF_DUFF  0
28	+	#define FF_LJ    1
29	+	#define FF_EAM   2
30	+	#define FF_H2O 3
31	+
32		using namespace std;
33
34	+	/**
35	+	* Check whether dividend is divisble by divisor or not
36	+	*/
37	+	bool isDivisible(double dividend, double divisor){
38	+	double tolerance = 0.000001;
39	+	double quotient;
40	+	double diff;
41	+	int intQuotient;
42	+
43	+	quotient = dividend / divisor;
44	+
45	+	if (quotient < 0)
46	+	quotient = -quotient;
47	+
48	+	intQuotient = int (quotient + tolerance);
49	+
50	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
51	+
52	+	if (diff <= tolerance)
53	+	return true;
54	+	else
55	+	return false;
56	+	}
57	+
58		SimSetup::SimSetup(){
59
60	+	initSuspend = false;
61		isInfoArray = 0;
62		nInfo = 1;
63	<
63	>
64		stamps = new MakeStamps();
65		globals = new Globals();
66	<
67	<
66	>
67	>
68		#ifdef IS_MPI
69	<	strcpy( checkPointMsg, "SimSetup creation successful" );
69	>	strcpy(checkPointMsg, "SimSetup creation successful");
70		MPIcheckPoint();
71		#endif // IS_MPI
72		}
#	Line 50 | Line 76 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
76		delete globals;
77		}
78
79	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
80	<	info = the_info;
81	<	nInfo = theNinfo;
82	<	isInfoArray = 1;
79	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
80	>	info = the_info;
81	>	nInfo = theNinfo;
82	>	isInfoArray = 1;
83	>	initSuspend = true;
84		}
85
86
87	<	void SimSetup::parseFile( char* fileName ){
61	<
87	>	void SimSetup::parseFile(char* fileName){
88		#ifdef IS_MPI
89	<	if( worldRank == 0 ){
89	>	if (worldRank == 0){
90		#endif // is_mpi
91	<
91	>
92		inFileName = fileName;
93	<	set_interface_stamps( stamps, globals );
94	<
93	>	set_interface_stamps(stamps, globals);
94	>
95		#ifdef IS_MPI
96		mpiEventInit();
97		#endif
98
99	<	yacc_BASS( fileName );
99	>	yacc_BASS(fileName);
100
101		#ifdef IS_MPI
102		throwMPIEvent(NULL);
103		}
104	<	else receiveParse();
104	>	else{
105	>	receiveParse();
106	>	}
107		#endif
108
109		}
110
111		#ifdef IS_MPI
112		void SimSetup::receiveParse(void){
113	<
114	<	set_interface_stamps( stamps, globals );
115	<	mpiEventInit();
116	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
113	>	set_interface_stamps(stamps, globals);
114	>	mpiEventInit();
115	>	MPIcheckPoint();
116	>	mpiEventLoop();
117		}
118
119		#endif // is_mpi
120
121		void SimSetup::createSim(void){
122
97	–	int i, j, k, globalAtomIndex;
98	–
123		// gather all of the information from the Bass file
124
125		gatherInfo();
#	Line 110 | Line 134 | void SimSetup::createSim(void){
134
135		// initialize the system coordinates
136
137	<	if( !isInfoArray ) initSystemCoords();
137	>	if ( !initSuspend ){
138	>	initSystemCoords();
139
140	+	if( !(globals->getUseInitTime()) )
141	+	info[0].currentTime = 0.0;
142	+	}
143	+
144		// make the output filenames
145
146		makeOutNames();
147	<
147	>
148		// make the integrator
149	<
149	>
150		makeIntegrator();
151	<
151	>
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 127 | Line 156 | void SimSetup::createSim(void){
156		// initialize the Fortran
157
158		initFortran();
130	–
131	–
132	–
159		}
160
161
162	<	void SimSetup::makeMolecules( void ){
163	<
138	<	int k,l;
162	>	void SimSetup::makeMolecules(void){
163	>	int k;
164		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
165		molInit molInfo;
166		DirectionalAtom* dAtom;
#	Line 150 | Line 175 | void SimSetup::makeMolecules( void ){
175		bend_set* theBends;
176		torsion_set* theTorsions;
177
153	–
178		//init the forceField paramters
179
180		the_ff->readParams();
181
182	<
182	>
183		// init the atoms
184
185	+	double phi, theta, psi;
186	+	double sux, suy, suz;
187	+	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
188		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
189
190	+	for (k = 0; k < nInfo; k++){
191	+	the_ff->setSimInfo(&(info[k]));
192	+
193		atomOffset = 0;
194		excludeOffset = 0;
195	<	for(i=0; i<info[k].n_mol; i++){
170	<
195	>	for (i = 0; i < info[k].n_mol; i++){
196		stampID = info[k].molecules[i].getStampID();
197
198	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
199	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
200	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
198	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
199	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
200	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
201		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
202		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
203	<
203	>
204		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
205		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
206	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
207	<	molInfo.myBends = new Bend*[molInfo.nBends];
208	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
206	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
207	>	molInfo.myBends = new Bend * [molInfo.nBends];
208	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
209
210		theBonds = new bond_pair[molInfo.nBonds];
211		theBends = new bend_set[molInfo.nBends];
212		theTorsions = new torsion_set[molInfo.nTorsions];
213	<
213	>
214		// make the Atoms
215	<
216	<	for(j=0; j<molInfo.nAtoms; j++){
217	<
218	<	currentAtom = comp_stamps[stampID]->getAtom( j );
219	<	if( currentAtom->haveOrientation() ){
220	<
221	<	dAtom = new DirectionalAtom( (j + atomOffset),
222	<	info[k].getConfiguration() );
223	<	info[k].n_oriented++;
224	<	molInfo.myAtoms[j] = dAtom;
225	<
226	<	ux = currentAtom->getOrntX();
227	<	uy = currentAtom->getOrntY();
228	<	uz = currentAtom->getOrntZ();
229	<
230	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
231	<
232	<	u = sqrt( uSqr );
233	<	ux = ux / u;
234	<	uy = uy / u;
235	<	uz = uz / u;
236	<
237	<	dAtom->setSUx( ux );
238	<	dAtom->setSUy( uy );
239	<	dAtom->setSUz( uz );
240	<	}
241	<	else{
242	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
243	<	info[k].getConfiguration() );
244	<	}
245	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
246	<
215	>
216	>	for (j = 0; j < molInfo.nAtoms; j++){
217	>	currentAtom = comp_stamps[stampID]->getAtom(j);
218	>	if (currentAtom->haveOrientation()){
219	>	dAtom = new DirectionalAtom((j + atomOffset),
220	>	info[k].getConfiguration());
221	>	info[k].n_oriented++;
222	>	molInfo.myAtoms[j] = dAtom;
223	>
224	>	// Directional Atoms have standard unit vectors which are oriented
225	>	// in space using the three Euler angles.  We assume the standard
226	>	// unit vector was originally along the z axis below.
227	>
228	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
229	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
230	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
231	>
232	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
233	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
234	>	Axz = sin(theta) * sin(psi);
235	>
236	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
237	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
238	>	Ayz = sin(theta) * cos(psi);
239	>
240	>	Azx = sin(phi) * sin(theta);
241	>	Azy = -cos(phi) * sin(theta);
242	>	Azz = cos(theta);
243	>
244	>	sux = 0.0;
245	>	suy = 0.0;
246	>	suz = 1.0;
247	>
248	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
249	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
250	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
251	>
252	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
253	>
254	>	u = sqrt(uSqr);
255	>	ux = ux / u;
256	>	uy = uy / u;
257	>	uz = uz / u;
258	>
259	>	dAtom->setSUx(ux);
260	>	dAtom->setSUy(uy);
261	>	dAtom->setSUz(uz);
262	>	}
263	>	else{
264	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265	>	info[k].getConfiguration());
266	>	}
267	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
268	>
269		#ifdef IS_MPI
270	<
271	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
272	<
270	>
271	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
272	>
273		#endif // is_mpi
274		}
275	<
276	<	// make the bonds
277	<	for(j=0; j<molInfo.nBonds; j++){
278	<
279	<	currentBond = comp_stamps[stampID]->getBond( j );
280	<	theBonds[j].a = currentBond->getA() + atomOffset;
281	<	theBonds[j].b = currentBond->getB() + atomOffset;
282	<
283	<	exI = theBonds[j].a;
284	<	exJ = theBonds[j].b;
285	<
286	<	// exclude_I must always be the smaller of the pair
287	<	if( exI > exJ ){
288	<	tempEx = exI;
289	<	exI = exJ;
290	<	exJ = tempEx;
244	<	}
275	>
276	>	// make the bonds
277	>	for (j = 0; j < molInfo.nBonds; j++){
278	>	currentBond = comp_stamps[stampID]->getBond(j);
279	>	theBonds[j].a = currentBond->getA() + atomOffset;
280	>	theBonds[j].b = currentBond->getB() + atomOffset;
281	>
282	>	exI = theBonds[j].a;
283	>	exJ = theBonds[j].b;
284	>
285	>	// exclude_I must always be the smaller of the pair
286	>	if (exI > exJ){
287	>	tempEx = exI;
288	>	exI = exJ;
289	>	exJ = tempEx;
290	>	}
291		#ifdef IS_MPI
292	<	tempEx = exI;
293	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
294	<	tempEx = exJ;
295	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
296	<
297	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
292	>	tempEx = exI;
293	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
294	>	tempEx = exJ;
295	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
296	>
297	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
298		#else  // isn't MPI
299	<
300	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
299	>
300	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
301		#endif  //is_mpi
302		}
303		excludeOffset += molInfo.nBonds;
304	<
304	>
305		//make the bends
306	<	for(j=0; j<molInfo.nBends; j++){
307	<
308	<	currentBend = comp_stamps[stampID]->getBend( j );
309	<	theBends[j].a = currentBend->getA() + atomOffset;
310	<	theBends[j].b = currentBend->getB() + atomOffset;
311	<	theBends[j].c = currentBend->getC() + atomOffset;
312	<
313	<	if( currentBend->haveExtras() ){
314	<
315	<	extras = currentBend->getExtras();
316	<	current_extra = extras;
317	<
318	<	while( current_extra != NULL ){
319	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
320	<
321	<	switch( current_extra->getType() ){
322	<
323	<	case 0:
324	<	theBends[j].ghost =
325	<	current_extra->getInt() + atomOffset;
326	<	theBends[j].isGhost = 1;
327	<	break;
328	<
329	<	case 1:
330	<	theBends[j].ghost =
331	<	(int)current_extra->getDouble() + atomOffset;
332	<	theBends[j].isGhost = 1;
333	<	break;
334	<
335	<	default:
336	<	sprintf( painCave.errMsg,
337	<	"SimSetup Error: ghostVectorSource was neither a "
338	<	"double nor an int.\n"
339	<	"-->Bend[%d] in %s\n",
340	<	j, comp_stamps[stampID]->getID() );
341	<	painCave.isFatal = 1;
342	<	simError();
306	>	for (j = 0; j < molInfo.nBends; j++){
307	>	currentBend = comp_stamps[stampID]->getBend(j);
308	>	theBends[j].a = currentBend->getA() + atomOffset;
309	>	theBends[j].b = currentBend->getB() + atomOffset;
310	>	theBends[j].c = currentBend->getC() + atomOffset;
311	>
312	>	if (currentBend->haveExtras()){
313	>	extras = currentBend->getExtras();
314	>	current_extra = extras;
315	>
316	>	while (current_extra != NULL){
317	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
318	>	switch (current_extra->getType()){
319	>	case 0:
320	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
321	>	theBends[j].isGhost = 1;
322	>	break;
323	>
324	>	case 1:
325	>	theBends[j].ghost = (int) current_extra->getDouble() +
326	>	atomOffset;
327	>	theBends[j].isGhost = 1;
328	>	break;
329	>
330	>	default:
331	>	sprintf(painCave.errMsg,
332	>	"SimSetup Error: ghostVectorSource was neither a "
333	>	"double nor an int.\n"
334	>	"-->Bend[%d] in %s\n",
335	>	j, comp_stamps[stampID]->getID());
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>	}
340	>	else{
341	>	sprintf(painCave.errMsg,
342	>	"SimSetup Error: unhandled bend assignment:\n"
343	>	"    -->%s in Bend[%d] in %s\n",
344	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
345	>	painCave.isFatal = 1;
346	>	simError();
347	>	}
348	>
349	>	current_extra = current_extra->getNext();
350	>	}
351		}
352	<	}
353	<
354	<	else{
355	<
356	<	sprintf( painCave.errMsg,
357	<	"SimSetup Error: unhandled bend assignment:\n"
358	<	"    -->%s in Bend[%d] in %s\n",
359	<	current_extra->getlhs(),
360	<	j, comp_stamps[stampID]->getID() );
361	<	painCave.isFatal = 1;
362	<	simError();
363	<	}
364	<
365	<	current_extra = current_extra->getNext();
366	<	}
367	<	}
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	<	}
352	>
353	>	if (!theBends[j].isGhost){
354	>	exI = theBends[j].a;
355	>	exJ = theBends[j].c;
356	>	}
357	>	else{
358	>	exI = theBends[j].a;
359	>	exJ = theBends[j].b;
360	>	}
361	>
362	>	// exclude_I must always be the smaller of the pair
363	>	if (exI > exJ){
364	>	tempEx = exI;
365	>	exI = exJ;
366	>	exJ = tempEx;
367	>	}
368		#ifdef IS_MPI
369	<	tempEx = exI;
370	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
371	<	tempEx = exJ;
372	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	<
374	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	>	tempEx = exI;
370	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
371	>	tempEx = exJ;
372	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>
374	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
375		#else  // isn't MPI
376	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
376	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
377		#endif  //is_mpi
378		}
379		excludeOffset += molInfo.nBends;
380	<
381	<	for(j=0; j<molInfo.nTorsions; j++){
382	<
383	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
384	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
385	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
386	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
387	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
388	<
389	<	exI = theTorsions[j].a;
390	<	exJ = theTorsions[j].d;
391	<
392	<	// exclude_I must always be the smaller of the pair
393	<	if( exI > exJ ){
394	<	tempEx = exI;
395	<	exI = exJ;
396	<	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	>	exI = theTorsions[j].a;
389	>	exJ = theTorsions[j].d;
390	>
391	>	// exclude_I must always be the smaller of the pair
392	>	if (exI > exJ){
393	>	tempEx = exI;
394	>	exI = exJ;
395	>	exJ = tempEx;
396	>	}
397		#ifdef IS_MPI
398	<	tempEx = exI;
399	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
400	<	tempEx = exJ;
401	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	<
403	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
398	>	tempEx = exI;
399	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
400	>	tempEx = exJ;
401	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	>
403	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
404		#else  // isn't MPI
405	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
405	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
406		#endif  //is_mpi
407		}
408		excludeOffset += molInfo.nTorsions;
409	<
410	<
409	>
410	>
411		// send the arrays off to the forceField for init.
377	–
378	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	–
383	–
384	–	info[k].molecules[i].initialize( molInfo );
412
413	<
413	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
414	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
415	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
416	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
417	>	theTorsions);
418	>
419	>
420	>	info[k].molecules[i].initialize(molInfo);
421	>
422	>
423		atomOffset += molInfo.nAtoms;
424		delete[] theBonds;
425		delete[] theBends;
426		delete[] theTorsions;
427		}
428		}
429	<
429	>
430		#ifdef IS_MPI
431	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
431	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
432		MPIcheckPoint();
433		#endif // is_mpi
434	<
434	>
435		// clean up the forcefield
436
437		the_ff->calcRcut();
438		the_ff->cleanMe();
403	–
439		}
440
441	<	void SimSetup::initFromBass( void ){
407	<
441	>	void SimSetup::initFromBass(void){
442		int i, j, k;
443		int n_cells;
444		double cellx, celly, cellz;
#	Line 418 | Line 452 | void SimSetup::initFromBass( void ){
452		vel[1] = 0.0;
453		vel[2] = 0.0;
454
455	<	temp1 = (double)tot_nmol / 4.0;
456	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
457	<	temp3 = ceil( temp2 );
455	>	temp1 = (double) tot_nmol / 4.0;
456	>	temp2 = pow(temp1, (1.0 / 3.0));
457	>	temp3 = ceil(temp2);
458
459	<	have_extra =0;
460	<	if( temp2 < temp3 ){ // we have a non-complete lattice
461	<	have_extra =1;
459	>	have_extra = 0;
460	>	if (temp2 < temp3){
461	>	// we have a non-complete lattice
462	>	have_extra = 1;
463
464	<	n_cells = (int)temp3 - 1;
464	>	n_cells = (int) temp3 - 1;
465		cellx = info[0].boxL[0] / temp3;
466		celly = info[0].boxL[1] / temp3;
467		cellz = info[0].boxL[2] / temp3;
468	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
469	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
470	<	n_per_extra = (int)ceil( temp1 );
468	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
469	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
470	>	n_per_extra = (int) ceil(temp1);
471
472	<	if( n_per_extra > 4){
473	<	sprintf( painCave.errMsg,
474	<	"SimSetup error. There has been an error in constructing"
475	<	" the non-complete lattice.\n" );
472	>	if (n_per_extra > 4){
473	>	sprintf(painCave.errMsg,
474	>	"SimSetup error. There has been an error in constructing"
475	>	" the non-complete lattice.\n");
476		painCave.isFatal = 1;
477		simError();
478		}
479		}
480		else{
481	<	n_cells = (int)temp3;
481	>	n_cells = (int) temp3;
482		cellx = info[0].boxL[0] / temp3;
483		celly = info[0].boxL[1] / temp3;
484		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 489 | void SimSetup::initFromBass( void ){
489		current_comp = 0;
490		current_atom_ndx = 0;
491
492	<	for( i=0; i < n_cells ; i++ ){
493	<	for( j=0; j < n_cells; j++ ){
494	<	for( k=0; k < n_cells; k++ ){
492	>	for (i = 0; i < n_cells ; i++){
493	>	for (j = 0; j < n_cells; j++){
494	>	for (k = 0; k < n_cells; k++){
495	>	makeElement(i * cellx, j * celly, k * cellz);
496
497	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
497	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
498
499	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
499	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
500
501	<	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 );
501	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
502		}
503		}
504		}
505
506	<	if( have_extra ){
506	>	if (have_extra){
507		done = 0;
508
509		int start_ndx;
510	<	for( i=0; i < (n_cells+1) && !done; i++ ){
511	<	for( j=0; j < (n_cells+1) && !done; j++ ){
510	>	for (i = 0; i < (n_cells + 1) && !done; i++){
511	>	for (j = 0; j < (n_cells + 1) && !done; j++){
512	>	if (i < n_cells){
513	>	if (j < n_cells){
514	>	start_ndx = n_cells;
515	>	}
516	>	else
517	>	start_ndx = 0;
518	>	}
519	>	else
520	>	start_ndx = 0;
521
522	<	if( i < n_cells ){
522	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
523	>	makeElement(i * cellx, j * celly, k * cellz);
524	>	done = (current_mol >= tot_nmol);
525
526	<	if( j < n_cells ){
527	<	start_ndx = n_cells;
528	<	}
529	<	else start_ndx = 0;
530	<	}
494	<	else start_ndx = 0;
526	>	if (!done && n_per_extra > 1){
527	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
528	>	k * cellz);
529	>	done = (current_mol >= tot_nmol);
530	>	}
531
532	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
532	>	if (!done && n_per_extra > 2){
533	>	makeElement(i * cellx, j * celly + 0.5 * celly,
534	>	k * cellz + 0.5 * cellz);
535	>	done = (current_mol >= tot_nmol);
536	>	}
537
538	<	makeElement( i * cellx,
539	<	j * celly,
540	<	k * cellz );
541	<	done = ( current_mol >= tot_nmol );
542	<
543	<	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	<	}
538	>	if (!done && n_per_extra > 3){
539	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
540	>	k * cellz + 0.5 * cellz);
541	>	done = (current_mol >= tot_nmol);
542	>	}
543	>	}
544		}
545		}
546		}
547
548	<	for( i=0; i<info[0].n_atoms; i++ ){
549	<	info[0].atoms[i]->setVel( vel );
548	>	for (i = 0; i < info[0].n_atoms; i++){
549	>	info[0].atoms[i]->setVel(vel);
550		}
551		}
552
553	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
553	>	void SimSetup::makeElement(double x, double y, double z){
554		int k;
555		AtomStamp* current_atom;
556		DirectionalAtom* dAtom;
557		double rotMat[3][3];
558		double pos[3];
559
560	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
561	<
562	<	current_atom = comp_stamps[current_comp]->getAtom( k );
563	<	if( !current_atom->havePosition() ){
564	<	sprintf( painCave.errMsg,
565	<	"SimSetup:initFromBass error.\n"
566	<	"\tComponent %s, atom %s does not have a position specified.\n"
567	<	"\tThe initialization routine is unable to give a start"
568	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
560	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
561	>	current_atom = comp_stamps[current_comp]->getAtom(k);
562	>	if (!current_atom->havePosition()){
563	>	sprintf(painCave.errMsg,
564	>	"SimSetup:initFromBass error.\n"
565	>	"\tComponent %s, atom %s does not have a position specified.\n"
566	>	"\tThe initialization routine is unable to give a start"
567	>	" position.\n",
568	>	comp_stamps[current_comp]->getID(), current_atom->getType());
569		painCave.isFatal = 1;
570		simError();
571		}
572	<
572	>
573		pos[0] = x + current_atom->getPosX();
574		pos[1] = y + current_atom->getPosY();
575		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
576
577	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
577	>	info[0].atoms[current_atom_ndx]->setPos(pos);
578
579	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
579	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
580	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
581
582		rotMat[0][0] = 1.0;
583		rotMat[0][1] = 0.0;
#	Line 575 | Line 591 | void SimSetup::makeElement( double x, double y, double
591		rotMat[2][1] = 0.0;
592		rotMat[2][2] = 1.0;
593
594	<	dAtom->setA( rotMat );
594	>	dAtom->setA(rotMat);
595		}
596
597		current_atom_ndx++;
#	Line 584 | Line 600 | void SimSetup::makeElement( double x, double y, double
600		current_mol++;
601		current_comp_mol++;
602
603	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
603	>	if (current_comp_mol >= components_nmol[current_comp]){
604		current_comp_mol = 0;
605		current_comp++;
606		}
607		}
608
609
610	<	void SimSetup::gatherInfo( void ){
611	<	int i,j,k;
610	>	void SimSetup::gatherInfo(void){
611	>	int i;
612
613		ensembleCase = -1;
614		ffCase = -1;
615
616		// set the easy ones first
617
618	<	for( i=0; i<nInfo; i++){
618	>	for (i = 0; i < nInfo; i++){
619		info[i].target_temp = globals->getTargetTemp();
620		info[i].dt = globals->getDt();
621		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 625 | void SimSetup::gatherInfo( void ){
625
626		// get the forceField
627
628	<	strcpy( force_field, globals->getForceField() );
628	>	strcpy(force_field, globals->getForceField());
629
630	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
631	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
632	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
630	>	if (!strcasecmp(force_field, "DUFF")){
631	>	ffCase = FF_DUFF;
632	>	}
633	>	else if (!strcasecmp(force_field, "LJ")){
634	>	ffCase = FF_LJ;
635	>	}
636	>	else if (!strcasecmp(force_field, "EAM")){
637	>	ffCase = FF_EAM;
638	>	}
639	>	else if (!strcasecmp(force_field, "WATER")){
640	>	ffCase = FF_H2O;
641	>	}
642		else{
643	<	sprintf( painCave.errMsg,
644	<	"SimSetup Error. Unrecognized force field -> %s\n",
645	<	force_field );
646	<	painCave.isFatal = 1;
623	<	simError();
643	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
644	>	force_field);
645	>	painCave.isFatal = 1;
646	>	simError();
647		}
648
649	<	// get the ensemble
649	>	// get the ensemble
650
651	<	strcpy( ensemble, globals->getEnsemble() );
651	>	strcpy(ensemble, globals->getEnsemble());
652
653	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
654	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
655	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
653	>	if (!strcasecmp(ensemble, "NVE")){
654	>	ensembleCase = NVE_ENS;
655	>	}
656	>	else if (!strcasecmp(ensemble, "NVT")){
657	>	ensembleCase = NVT_ENS;
658	>	}
659	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
660		ensembleCase = NPTi_ENS;
661	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
662	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
663	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
661	>	}
662	>	else if (!strcasecmp(ensemble, "NPTf")){
663	>	ensembleCase = NPTf_ENS;
664	>	}
665	>	else if (!strcasecmp(ensemble, "NPTxyz")){
666	>	ensembleCase = NPTxyz_ENS;
667	>	}
668		else{
669	<	sprintf( painCave.errMsg,
670	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
671	<	"reverting to NVE for this simulation.\n",
672	<	ensemble );
673	<	painCave.isFatal = 0;
674	<	simError();
675	<	strcpy( ensemble, "NVE" );
676	<	ensembleCase = NVE_ENS;
669	>	sprintf(painCave.errMsg,
670	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
671	>	"\treverting to NVE for this simulation.\n",
672	>	ensemble);
673	>	painCave.isFatal = 0;
674	>	simError();
675	>	strcpy(ensemble, "NVE");
676	>	ensembleCase = NVE_ENS;
677		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
678
679	+	for (i = 0; i < nInfo; i++){
680	+	strcpy(info[i].ensemble, ensemble);
681	+
682		// get the mixing rule
683
684	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
684	>	strcpy(info[i].mixingRule, globals->getMixingRule());
685		info[i].usePBC = globals->getPBC();
686		}
687	<
687	>
688		// get the components and calculate the tot_nMol and indvidual n_mol
689	<
689	>
690		the_components = globals->getComponents();
691		components_nmol = new int[n_components];
692
693
694	<	if( !globals->haveNMol() ){
694	>	if (!globals->haveNMol()){
695		// we don't have the total number of molecules, so we assume it is
696		// given in each component
697
698		tot_nmol = 0;
699	<	for( i=0; i<n_components; i++ ){
700	<
701	<	if( !the_components[i]->haveNMol() ){
702	<	// we have a problem
703	<	sprintf( painCave.errMsg,
704	<	"SimSetup Error. No global NMol or component NMol"
705	<	" given. Cannot calculate the number of atoms.\n" );
706	<	painCave.isFatal = 1;
677	<	simError();
699	>	for (i = 0; i < n_components; i++){
700	>	if (!the_components[i]->haveNMol()){
701	>	// we have a problem
702	>	sprintf(painCave.errMsg,
703	>	"SimSetup Error. No global NMol or component NMol given.\n"
704	>	"\tCannot calculate the number of atoms.\n");
705	>	painCave.isFatal = 1;
706	>	simError();
707		}
708
709		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 711 | void SimSetup::gatherInfo( void ){
711		}
712		}
713		else{
714	<	sprintf( painCave.errMsg,
715	<	"SimSetup error.\n"
716	<	"\tSorry, the ability to specify total"
717	<	" nMols and then give molfractions in the components\n"
718	<	"\tis not currently supported."
719	<	" Please give nMol in the components.\n" );
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error.\n"
716	>	"\tSorry, the ability to specify total"
717	>	" nMols and then give molfractions in the components\n"
718	>	"\tis not currently supported."
719	>	" Please give nMol in the components.\n");
720		painCave.isFatal = 1;
721		simError();
722		}
723
724	<	// set the status, sample, and thermal kick times
725	<
726	<	for(i=0; i<nInfo; i++){
724	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
725	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
726	>	sprintf(painCave.errMsg,
727	>	"Sample time is not divisible by dt.\n"
728	>	"\tThis will result in samples that are not uniformly\n"
729	>	"\tdistributed in time.  If this is a problem, change\n"
730	>	"\tyour sampleTime variable.\n");
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734
735	<	if( globals->haveSampleTime() ){
735	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
736	>	sprintf(painCave.errMsg,
737	>	"Status time is not divisible by dt.\n"
738	>	"\tThis will result in status reports that are not uniformly\n"
739	>	"\tdistributed in time.  If this is a problem, change \n"
740	>	"\tyour statusTime variable.\n");
741	>	painCave.isFatal = 0;
742	>	simError();
743	>	}
744	>
745	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
746	>	sprintf(painCave.errMsg,
747	>	"Thermal time is not divisible by dt.\n"
748	>	"\tThis will result in thermalizations that are not uniformly\n"
749	>	"\tdistributed in time.  If this is a problem, change \n"
750	>	"\tyour thermalTime variable.\n");
751	>	painCave.isFatal = 0;
752	>	simError();
753	>	}
754	>
755	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
756	>	sprintf(painCave.errMsg,
757	>	"Reset time is not divisible by dt.\n"
758	>	"\tThis will result in integrator resets that are not uniformly\n"
759	>	"\tdistributed in time.  If this is a problem, change\n"
760	>	"\tyour resetTime variable.\n");
761	>	painCave.isFatal = 0;
762	>	simError();
763	>	}
764	>
765	>	// set the status, sample, and thermal kick times
766	>
767	>	for (i = 0; i < nInfo; i++){
768	>	if (globals->haveSampleTime()){
769		info[i].sampleTime = globals->getSampleTime();
770		info[i].statusTime = info[i].sampleTime;
771		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 775 | void SimSetup::gatherInfo( void ){
775		info[i].statusTime = info[i].sampleTime;
776		info[i].thermalTime = info[i].sampleTime;
777		}
778	<
779	<	if( globals->haveStatusTime() ){
778	>
779	>	if (globals->haveStatusTime()){
780		info[i].statusTime = globals->getStatusTime();
781		}
782	<
783	<	if( globals->haveThermalTime() ){
782	>
783	>	if (globals->haveThermalTime()){
784		info[i].thermalTime = globals->getThermalTime();
785		}
786
787	+	info[i].resetIntegrator = 0;
788	+	if( globals->haveResetTime() ){
789	+	info[i].resetTime = globals->getResetTime();
790	+	info[i].resetIntegrator = 1;
791	+	}
792	+
793		// check for the temperature set flag
794	+
795	+	if (globals->haveTempSet())
796	+	info[i].setTemp = globals->getTempSet();
797
798	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
798	>	// check for the extended State init
799	>
800	>	info[i].useInitXSstate = globals->getUseInitXSstate();
801	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
802
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 );
803		}
804	<	else{
805	<	if( !globals->haveBoxX() ){
806	<	sprintf( painCave.errMsg,
807	<	"SimSetup error, no periodic BoxX size given.\n" );
808	<	painCave.isFatal = 1;
809	<	simError();
804	>
805	>	//setup seed for random number generator
806	>	int seedValue;
807	>
808	>	if (globals->haveSeed()){
809	>	seedValue = globals->getSeed();
810	>
811	>	if(seedValue / 1E9 == 0){
812	>	sprintf(painCave.errMsg,
813	>	"Seed for sprng library should contain at least 9 digits\n"
814	>	"OOPSE will generate a seed for user\n");
815	>	painCave.isFatal = 0;
816	>	simError();
817	>
818	>	//using seed generated by system instead of invalid seed set by user
819	>	#ifndef IS_MPI
820	>	seedValue = make_sprng_seed();
821	>	#else
822	>	if (worldRank == 0){
823	>	seedValue = make_sprng_seed();
824		}
825	<	boxVector[0] = globals->getBoxX();
826	<
751	<	if( !globals->haveBoxY() ){
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error, no periodic BoxY size given.\n" );
754	<	painCave.isFatal = 1;
755	<	simError();
756	<	}
757	<	boxVector[1] = globals->getBoxY();
758	<
759	<	if( !globals->haveBoxZ() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxZ size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
765	<	boxVector[2] = globals->getBoxZ();
766	<
767	<	info[i].setBox( boxVector );
825	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
826	>	#endif
827		}
828	+	}//end of if branch of globals->haveSeed()
829	+	else{
830	+
831	+	#ifndef IS_MPI
832	+	seedValue = make_sprng_seed();
833	+	#else
834	+	if (worldRank == 0){
835	+	seedValue = make_sprng_seed();
836	+	}
837	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
838	+	#endif
839	+	}//end of globals->haveSeed()
840
841	+	for (int i = 0; i < nInfo; i++){
842	+	info[i].setSeed(seedValue);
843		}
844	<
844	>
845		#ifdef IS_MPI
846	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
846	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
847		MPIcheckPoint();
848		#endif // is_mpi
776	–
849		}
850
851
852	<	void SimSetup::finalInfoCheck( void ){
852	>	void SimSetup::finalInfoCheck(void){
853		int index;
854		int usesDipoles;
855		int i;
856
857	<	for(i=0; i<nInfo; i++){
857	>	for (i = 0; i < nInfo; i++){
858		// check electrostatic parameters
859	<
859	>
860		index = 0;
861		usesDipoles = 0;
862	<	while( (index < info[i].n_atoms) && !usesDipoles ){
862	>	while ((index < info[i].n_atoms) && !usesDipoles){
863		usesDipoles = (info[i].atoms[index])->hasDipole();
864		index++;
865		}
866	<
866	>
867		#ifdef IS_MPI
868		int myUse = usesDipoles;
869	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
869	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
870		#endif //is_mpi
871	<
871	>
872		double theEcr, theEst;
873	<
874	<	if (globals->getUseRF() ) {
873	>
874	>	if (globals->getUseRF()){
875		info[i].useReactionField = 1;
876	<
877	<	if( !globals->haveECR() ){
878	<	sprintf( painCave.errMsg,
879	<	"SimSetup Warning: using default value of 1/2 the smallest "
880	<	"box length for the electrostaticCutoffRadius.\n"
881	<	"I hope you have a very fast processor!\n");
882	<	painCave.isFatal = 0;
883	<	simError();
884	<	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();
876	>
877	>	if (!globals->haveECR()){
878	>	sprintf(painCave.errMsg,
879	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
880	>	"\tOOPSE will use a default value of 15.0 angstroms"
881	>	"\tfor the electrostaticCutoffRadius.\n");
882	>	painCave.isFatal = 0;
883	>	simError();
884	>	theEcr = 15.0;
885		}
886	<
887	<	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();
886	>	else{
887	>	theEcr = globals->getECR();
888		}
889	<
890	<	info[i].setEcr( theEcr, theEst );
891	<
892	<	if(!globals->haveDielectric() ){
893	<	sprintf( painCave.errMsg,
894	<	"SimSetup Error: You are trying to use Reaction Field without"
895	<	"setting a dielectric constant!\n"
896	<	);
897	<	painCave.isFatal = 1;
898	<	simError();
889	>
890	>	if (!globals->haveEST()){
891	>	sprintf(painCave.errMsg,
892	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
893	>	"\tOOPSE will use a default value of\n"
894	>	"\t0.05 * electrostaticCutoffRadius\n"
895	>	"\tfor the electrostaticSkinThickness\n");
896	>	painCave.isFatal = 0;
897	>	simError();
898	>	theEst = 0.05 * theEcr;
899		}
900	<	info[i].dielectric = globals->getDielectric();
901	<	}
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 );
900	>	else{
901	>	theEst = globals->getEST();
902		}
879	–	}
880	–	}
903
904	+	info[i].setDefaultEcr(theEcr, theEst);
905	+
906	+	if (!globals->haveDielectric()){
907	+	sprintf(painCave.errMsg,
908	+	"SimSetup Error: No Dielectric constant was set.\n"
909	+	"\tYou are trying to use Reaction Field without"
910	+	"\tsetting a dielectric constant!\n");
911	+	painCave.isFatal = 1;
912	+	simError();
913	+	}
914	+	info[i].dielectric = globals->getDielectric();
915	+	}
916	+	else{
917	+	if (usesDipoles){
918	+	if (!globals->haveECR()){
919	+	sprintf(painCave.errMsg,
920	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
921	+	"\tOOPSE will use a default value of 15.0 angstroms"
922	+	"\tfor the electrostaticCutoffRadius.\n");
923	+	painCave.isFatal = 0;
924	+	simError();
925	+	theEcr = 15.0;
926	+	}
927	+	else{
928	+	theEcr = globals->getECR();
929	+	}
930	+
931	+	if (!globals->haveEST()){
932	+	sprintf(painCave.errMsg,
933	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
934	+	"\tOOPSE will use a default value of\n"
935	+	"\t0.05 * electrostaticCutoffRadius\n"
936	+	"\tfor the electrostaticSkinThickness\n");
937	+	painCave.isFatal = 0;
938	+	simError();
939	+	theEst = 0.05 * theEcr;
940	+	}
941	+	else{
942	+	theEst = globals->getEST();
943	+	}
944	+
945	+	info[i].setDefaultEcr(theEcr, theEst);
946	+	}
947	+	}
948	+	}
949		#ifdef IS_MPI
950	<	strcpy( checkPointMsg, "post processing checks out" );
950	>	strcpy(checkPointMsg, "post processing checks out");
951		MPIcheckPoint();
952		#endif // is_mpi
886	–
953		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
954
955	+	void SimSetup::initSystemCoords(void){
956	+	int i;
957	+
958		char* inName;
959
960	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
960	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
961
962	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
963	<
964	<	if( globals->haveInitialConfig() ){
965	<
962	>	for (i = 0; i < info[0].n_atoms; i++)
963	>	info[0].atoms[i]->setCoords();
964	>
965	>	if (globals->haveInitialConfig()){
966		InitializeFromFile* fileInit;
967		#ifdef IS_MPI // is_mpi
968	<	if( worldRank == 0 ){
968	>	if (worldRank == 0){
969		#endif //is_mpi
970		inName = globals->getInitialConfig();
971	<	double* tempDouble = new double[1000000];
906	<	fileInit = new InitializeFromFile( inName );
971	>	fileInit = new InitializeFromFile(inName);
972		#ifdef IS_MPI
973	<	}else fileInit = new InitializeFromFile( NULL );
973	>	}
974	>	else
975	>	fileInit = new InitializeFromFile(NULL);
976		#endif
977	<	fileInit->readInit( info ); // default velocities on
978	<
977	>	fileInit->readInit(info); // default velocities on
978	>
979		delete fileInit;
980		}
981		else{
982
916	–	#ifdef IS_MPI
917	–
983		// no init from bass
984
985	<	sprintf( painCave.errMsg,
986	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
987	<	painCave.isFatal;
985	>	sprintf(painCave.errMsg,
986	>	"Cannot intialize a simulation without an initial configuration file.\n");
987	>	painCave.isFatal = 1;;
988		simError();
989
925	–	#else
926	–
927	–	initFromBass();
928	–
929	–
930	–	#endif
990		}
991	<
991	>
992		#ifdef IS_MPI
993	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
993	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
994		MPIcheckPoint();
995		#endif // is_mpi
937	–
996		}
997
998
999	<	void SimSetup::makeOutNames( void ){
942	<
999	>	void SimSetup::makeOutNames(void){
1000		int k;
1001
945	–
946	–	for(k=0; k<nInfo; k++){
1002
1003	+	for (k = 0; k < nInfo; k++){
1004		#ifdef IS_MPI
1005	<	if( worldRank == 0 ){
1005	>	if (worldRank == 0){
1006		#endif // is_mpi
1007	<
1008	<	if( globals->haveFinalConfig() ){
1009	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1007	>
1008	>	if (globals->haveFinalConfig()){
1009	>	strcpy(info[k].finalName, globals->getFinalConfig());
1010		}
1011		else{
1012	<	strcpy( info[k].finalName, inFileName );
1013	<	char* endTest;
1014	<	int nameLength = strlen( info[k].finalName );
1015	<	endTest = &(info[k].finalName[nameLength - 5]);
1016	<	if( !strcmp( endTest, ".bass" ) ){
1017	<	strcpy( endTest, ".eor" );
1018	<	}
1019	<	else if( !strcmp( endTest, ".BASS" ) ){
1020	<	strcpy( endTest, ".eor" );
1021	<	}
1022	<	else{
1023	<	endTest = &(info[k].finalName[nameLength - 4]);
1024	<	if( !strcmp( endTest, ".bss" ) ){
1025	<	strcpy( endTest, ".eor" );
1026	<	}
1027	<	else if( !strcmp( endTest, ".mdl" ) ){
1028	<	strcpy( endTest, ".eor" );
1029	<	}
1030	<	else{
1031	<	strcat( info[k].finalName, ".eor" );
1032	<	}
1033	<	}
1012	>	strcpy(info[k].finalName, inFileName);
1013	>	char* endTest;
1014	>	int nameLength = strlen(info[k].finalName);
1015	>	endTest = &(info[k].finalName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".eor");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".eor");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].finalName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".eor");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".eor");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].finalName, ".eor");
1032	>	}
1033	>	}
1034		}
1035	<
1035	>
1036		// make the sample and status out names
1037	<
1038	<	strcpy( info[k].sampleName, inFileName );
1037	>
1038	>	strcpy(info[k].sampleName, inFileName);
1039		char* endTest;
1040	<	int nameLength = strlen( info[k].sampleName );
1040	>	int nameLength = strlen(info[k].sampleName);
1041		endTest = &(info[k].sampleName[nameLength - 5]);
1042	<	if( !strcmp( endTest, ".bass" ) ){
1043	<	strcpy( endTest, ".dump" );
1042	>	if (!strcmp(endTest, ".bass")){
1043	>	strcpy(endTest, ".dump");
1044		}
1045	<	else if( !strcmp( endTest, ".BASS" ) ){
1046	<	strcpy( endTest, ".dump" );
1045	>	else if (!strcmp(endTest, ".BASS")){
1046	>	strcpy(endTest, ".dump");
1047		}
1048		else{
1049	<	endTest = &(info[k].sampleName[nameLength - 4]);
1050	<	if( !strcmp( endTest, ".bss" ) ){
1051	<	strcpy( endTest, ".dump" );
1052	<	}
1053	<	else if( !strcmp( endTest, ".mdl" ) ){
1054	<	strcpy( endTest, ".dump" );
1055	<	}
1056	<	else{
1057	<	strcat( info[k].sampleName, ".dump" );
1058	<	}
1049	>	endTest = &(info[k].sampleName[nameLength - 4]);
1050	>	if (!strcmp(endTest, ".bss")){
1051	>	strcpy(endTest, ".dump");
1052	>	}
1053	>	else if (!strcmp(endTest, ".mdl")){
1054	>	strcpy(endTest, ".dump");
1055	>	}
1056	>	else{
1057	>	strcat(info[k].sampleName, ".dump");
1058	>	}
1059		}
1060	<
1061	<	strcpy( info[k].statusName, inFileName );
1062	<	nameLength = strlen( info[k].statusName );
1060	>
1061	>	strcpy(info[k].statusName, inFileName);
1062	>	nameLength = strlen(info[k].statusName);
1063		endTest = &(info[k].statusName[nameLength - 5]);
1064	<	if( !strcmp( endTest, ".bass" ) ){
1065	<	strcpy( endTest, ".stat" );
1064	>	if (!strcmp(endTest, ".bass")){
1065	>	strcpy(endTest, ".stat");
1066		}
1067	<	else if( !strcmp( endTest, ".BASS" ) ){
1068	<	strcpy( endTest, ".stat" );
1067	>	else if (!strcmp(endTest, ".BASS")){
1068	>	strcpy(endTest, ".stat");
1069		}
1070		else{
1071	<	endTest = &(info[k].statusName[nameLength - 4]);
1072	<	if( !strcmp( endTest, ".bss" ) ){
1073	<	strcpy( endTest, ".stat" );
1074	<	}
1075	<	else if( !strcmp( endTest, ".mdl" ) ){
1076	<	strcpy( endTest, ".stat" );
1077	<	}
1078	<	else{
1079	<	strcat( info[k].statusName, ".stat" );
1080	<	}
1071	>	endTest = &(info[k].statusName[nameLength - 4]);
1072	>	if (!strcmp(endTest, ".bss")){
1073	>	strcpy(endTest, ".stat");
1074	>	}
1075	>	else if (!strcmp(endTest, ".mdl")){
1076	>	strcpy(endTest, ".stat");
1077	>	}
1078	>	else{
1079	>	strcat(info[k].statusName, ".stat");
1080	>	}
1081		}
1082	<
1082	>
1083		#ifdef IS_MPI
1084	+
1085		}
1086		#endif // is_mpi
1087		}
1088		}
1089
1090
1091	<	void SimSetup::sysObjectsCreation( void ){
1092	<
1093	<	int i,k;
1037	<
1091	>	void SimSetup::sysObjectsCreation(void){
1092	>	int i, k;
1093	>
1094		// create the forceField
1095
1096		createFF();
#	Line 1049 | Line 1105 | void SimSetup::sysObjectsCreation( void ){
1105
1106		#ifdef IS_MPI
1107		// divide the molecules among the processors
1108	<
1108	>
1109		mpiMolDivide();
1110		#endif //is_mpi
1111	<
1111	>
1112		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1113	<
1113	>
1114		makeSysArrays();
1115
1116		// make and initialize the molecules (all but atomic coordinates)
1117	<
1118	<	makeMolecules();
1119	<
1120	<	for(k=0; k<nInfo; k++){
1117	>
1118	>	makeMolecules();
1119	>
1120	>	for (k = 0; k < nInfo; k++){
1121		info[k].identArray = new int[info[k].n_atoms];
1122	<	for(i=0; i<info[k].n_atoms; i++){
1122	>	for (i = 0; i < info[k].n_atoms; i++){
1123		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1124		}
1125		}
1126		}
1127
1128
1129	<	void SimSetup::createFF( void ){
1129	>	void SimSetup::createFF(void){
1130	>	switch (ffCase){
1131	>	case FF_DUFF:
1132	>	the_ff = new DUFF();
1133	>	break;
1134
1135	<	switch( ffCase ){
1135	>	case FF_LJ:
1136	>	the_ff = new LJFF();
1137	>	break;
1138
1139	<	case FF_DUFF:
1140	<	the_ff = new DUFF();
1141	<	break;
1139	>	case FF_EAM:
1140	>	the_ff = new EAM_FF();
1141	>	break;
1142
1143	<	case FF_LJ:
1144	<	the_ff = new LJFF();
1145	<	break;
1143	>	case FF_H2O:
1144	>	the_ff = new WATER();
1145	>	break;
1146
1147	<	case FF_EAM:
1148	<	the_ff = new EAM_FF();
1149	<	break;
1150	<
1151	<	default:
1090	<	sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	<	painCave.isFatal = 1;
1093	<	simError();
1147	>	default:
1148	>	sprintf(painCave.errMsg,
1149	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1150	>	painCave.isFatal = 1;
1151	>	simError();
1152		}
1153
1154		#ifdef IS_MPI
1155	<	strcpy( checkPointMsg, "ForceField creation successful" );
1155	>	strcpy(checkPointMsg, "ForceField creation successful");
1156		MPIcheckPoint();
1157		#endif // is_mpi
1100	–
1158		}
1159
1160
1161	<	void SimSetup::compList( void ){
1105	<
1161	>	void SimSetup::compList(void){
1162		int i;
1163		char* id;
1164		LinkedMolStamp* headStamp = new LinkedMolStamp();
1165		LinkedMolStamp* currentStamp = NULL;
1166	<	comp_stamps = new MoleculeStamp*[n_components];
1167	<
1166	>	comp_stamps = new MoleculeStamp * [n_components];
1167	>
1168		// make an array of molecule stamps that match the components used.
1169		// also extract the used stamps out into a separate linked list
1170	<
1171	<	for(i=0; i<nInfo; i++){
1170	>
1171	>	for (i = 0; i < nInfo; i++){
1172		info[i].nComponents = n_components;
1173		info[i].componentsNmol = components_nmol;
1174		info[i].compStamps = comp_stamps;
1175		info[i].headStamp = headStamp;
1176		}
1121	–
1177
1123	–	for( i=0; i<n_components; i++ ){
1178
1179	+	for (i = 0; i < n_components; i++){
1180		id = the_components[i]->getType();
1181		comp_stamps[i] = NULL;
1182	<
1182	>
1183		// check to make sure the component isn't already in the list
1184
1185	<	comp_stamps[i] = headStamp->match( id );
1186	<	if( comp_stamps[i] == NULL ){
1132	<
1185	>	comp_stamps[i] = headStamp->match(id);
1186	>	if (comp_stamps[i] == NULL){
1187		// extract the component from the list;
1188	<
1189	<	currentStamp = stamps->extractMolStamp( id );
1190	<	if( currentStamp == NULL ){
1191	<	sprintf( painCave.errMsg,
1192	<	"SimSetup error: Component \"%s\" was not found in the "
1193	<	"list of declared molecules\n",
1194	<	id );
1195	<	painCave.isFatal = 1;
1196	<	simError();
1188	>
1189	>	currentStamp = stamps->extractMolStamp(id);
1190	>	if (currentStamp == NULL){
1191	>	sprintf(painCave.errMsg,
1192	>	"SimSetup error: Component \"%s\" was not found in the "
1193	>	"list of declared molecules\n",
1194	>	id);
1195	>	painCave.isFatal = 1;
1196	>	simError();
1197		}
1198	<
1199	<	headStamp->add( currentStamp );
1200	<	comp_stamps[i] = headStamp->match( id );
1198	>
1199	>	headStamp->add(currentStamp);
1200	>	comp_stamps[i] = headStamp->match(id);
1201		}
1202		}
1203
1204		#ifdef IS_MPI
1205	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1205	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1206		MPIcheckPoint();
1207		#endif // is_mpi
1208	+	}
1209
1210	+	void SimSetup::calcSysValues(void){
1211	+	int i;
1212
1213	<	}
1213	>	int* molMembershipArray;
1214
1158	–	void SimSetup::calcSysValues( void ){
1159	–	int i, j, k;
1160	–
1161	–	int *molMembershipArray;
1162	–
1215		tot_atoms = 0;
1216		tot_bonds = 0;
1217		tot_bends = 0;
1218		tot_torsions = 0;
1219	<	for( i=0; i<n_components; i++ ){
1220	<
1221	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1222	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1219	>	for (i = 0; i < n_components; i++){
1220	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1221	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1222	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1223		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1224		}
1225	<
1225	>
1226		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1227		molMembershipArray = new int[tot_atoms];
1228	<
1229	<	for(i=0; i<nInfo; i++){
1228	>
1229	>	for (i = 0; i < nInfo; i++){
1230		info[i].n_atoms = tot_atoms;
1231		info[i].n_bonds = tot_bonds;
1232		info[i].n_bends = tot_bends;
1233		info[i].n_torsions = tot_torsions;
1234		info[i].n_SRI = tot_SRI;
1235		info[i].n_mol = tot_nmol;
1236	<
1236	>
1237		info[i].molMembershipArray = molMembershipArray;
1238	<	}
1238	>	}
1239		}
1240
1241		#ifdef IS_MPI
1242
1243	<	void SimSetup::mpiMolDivide( void ){
1193	<
1243	>	void SimSetup::mpiMolDivide(void){
1244		int i, j, k;
1245		int localMol, allMol;
1246		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1247
1248	<	mpiSim = new mpiSimulation( info );
1249	<
1248	>	mpiSim = new mpiSimulation(info);
1249	>
1250		globalIndex = mpiSim->divideLabor();
1251
1252		// set up the local variables
1253	<
1253	>
1254		mol2proc = mpiSim->getMolToProcMap();
1255		molCompType = mpiSim->getMolComponentType();
1256	<
1256	>
1257		allMol = 0;
1258		localMol = 0;
1259		local_atoms = 0;
#	Line 1213 | Line 1263 | void SimSetup::mpiMolDivide( void ){
1263		globalAtomIndex = 0;
1264
1265
1266	<	for( i=0; i<n_components; i++ ){
1267	<
1268	<	for( j=0; j<components_nmol[i]; j++ ){
1269	<
1270	<	if( mol2proc[allMol] == worldRank ){
1271	<
1272	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1273	<	local_bonds +=    comp_stamps[i]->getNBonds();
1224	<	local_bends +=    comp_stamps[i]->getNBends();
1225	<	local_torsions += comp_stamps[i]->getNTorsions();
1226	<	localMol++;
1266	>	for (i = 0; i < n_components; i++){
1267	>	for (j = 0; j < components_nmol[i]; j++){
1268	>	if (mol2proc[allMol] == worldRank){
1269	>	local_atoms += comp_stamps[i]->getNAtoms();
1270	>	local_bonds += comp_stamps[i]->getNBonds();
1271	>	local_bends += comp_stamps[i]->getNBends();
1272	>	local_torsions += comp_stamps[i]->getNTorsions();
1273	>	localMol++;
1274		}
1275	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1275	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1276		info[0].molMembershipArray[globalAtomIndex] = allMol;
1277		globalAtomIndex++;
1278		}
1279
1280	<	allMol++;
1280	>	allMol++;
1281		}
1282		}
1283		local_SRI = local_bonds + local_bends + local_torsions;
1284	<
1284	>
1285		info[0].n_atoms = mpiSim->getMyNlocal();
1286	<
1287	<	if( local_atoms != info[0].n_atoms ){
1288	<	sprintf( painCave.errMsg,
1289	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1290	<	" localAtom (%d) are not equal.\n",
1291	<	info[0].n_atoms,
1245	<	local_atoms );
1286	>
1287	>	if (local_atoms != info[0].n_atoms){
1288	>	sprintf(painCave.errMsg,
1289	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1290	>	"\tlocalAtom (%d) are not equal.\n",
1291	>	info[0].n_atoms, local_atoms);
1292		painCave.isFatal = 1;
1293		simError();
1294		}
#	Line 1253 | Line 1299 | void SimSetup::mpiMolDivide( void ){
1299		info[0].n_SRI = local_SRI;
1300		info[0].n_mol = localMol;
1301
1302	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1302	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1303		MPIcheckPoint();
1304		}
1305	<
1305	>
1306		#endif // is_mpi
1307
1308
1309	<	void SimSetup::makeSysArrays( void ){
1310	<	int i, j, k, l;
1309	>	void SimSetup::makeSysArrays(void){
1310	>
1311	>	#ifndef IS_MPI
1312	>	int k, j;
1313	>	#endif // is_mpi
1314	>	int i, l;
1315
1316		Atom** the_atoms;
1317		Molecule* the_molecules;
1318		Exclude** the_excludes;
1319
1320	<
1321	<	for(l=0; l<nInfo; l++){
1272	<
1320	>
1321	>	for (l = 0; l < nInfo; l++){
1322		// create the atom and short range interaction arrays
1323	<
1324	<	the_atoms = new Atom*[info[l].n_atoms];
1323	>
1324	>	the_atoms = new Atom * [info[l].n_atoms];
1325		the_molecules = new Molecule[info[l].n_mol];
1326		int molIndex;
1327
1328		// initialize the molecule's stampID's
1329	<
1329	>
1330		#ifdef IS_MPI
1331	<
1332	<
1331	>
1332	>
1333		molIndex = 0;
1334	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1335	<
1336	<	if(mol2proc[i] == worldRank ){
1337	<	the_molecules[molIndex].setStampID( molCompType[i] );
1338	<	the_molecules[molIndex].setMyIndex( molIndex );
1339	<	the_molecules[molIndex].setGlobalIndex( i );
1291	<	molIndex++;
1334	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1335	>	if (mol2proc[i] == worldRank){
1336	>	the_molecules[molIndex].setStampID(molCompType[i]);
1337	>	the_molecules[molIndex].setMyIndex(molIndex);
1338	>	the_molecules[molIndex].setGlobalIndex(i);
1339	>	molIndex++;
1340		}
1341		}
1342	<
1342	>
1343		#else // is_mpi
1344	<
1344	>
1345		molIndex = 0;
1346		globalAtomIndex = 0;
1347	<	for(i=0; i<n_components; i++){
1348	<	for(j=0; j<components_nmol[i]; j++ ){
1349	<	the_molecules[molIndex].setStampID( i );
1350	<	the_molecules[molIndex].setMyIndex( molIndex );
1351	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1352	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1353	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1354	<	globalAtomIndex++;
1355	<	}
1356	<	molIndex++;
1347	>	for (i = 0; i < n_components; i++){
1348	>	for (j = 0; j < components_nmol[i]; j++){
1349	>	the_molecules[molIndex].setStampID(i);
1350	>	the_molecules[molIndex].setMyIndex(molIndex);
1351	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1352	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1353	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1354	>	globalAtomIndex++;
1355	>	}
1356	>	molIndex++;
1357		}
1358		}
1359	<
1360	<
1359	>
1360	>
1361		#endif // is_mpi
1362
1363
1364	<	if( info[l].n_SRI ){
1317	<
1364	>	if (info[l].n_SRI){
1365		Exclude::createArray(info[l].n_SRI);
1366	<	the_excludes = new Exclude*[info[l].n_SRI];
1367	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1368	<	the_excludes[ex] = new Exclude(ex);
1366	>	the_excludes = new Exclude * [info[l].n_SRI];
1367	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1368	>	the_excludes[ex] = new Exclude(ex);
1369		}
1370		info[l].globalExcludes = new int;
1371		info[l].n_exclude = info[l].n_SRI;
1372		}
1373		else{
1374	<
1375	<	Exclude::createArray( 1 );
1329	<	the_excludes = new Exclude*;
1374	>	Exclude::createArray(1);
1375	>	the_excludes = new Exclude * ;
1376		the_excludes[0] = new Exclude(0);
1377	<	the_excludes[0]->setPair( 0,0 );
1377	>	the_excludes[0]->setPair(0, 0);
1378		info[l].globalExcludes = new int;
1379		info[l].globalExcludes[0] = 0;
1380		info[l].n_exclude = 0;
#	Line 1341 | Line 1387 | void SimSetup::makeSysArrays( void ){
1387		info[l].nGlobalExcludes = 0;
1388		info[l].excludes = the_excludes;
1389
1390	<	the_ff->setSimInfo( info );
1345	<
1390	>	the_ff->setSimInfo(info);
1391		}
1392		}
1393
1394	<	void SimSetup::makeIntegrator( void ){
1350	<
1394	>	void SimSetup::makeIntegrator(void){
1395		int k;
1396
1397	<	NVT<RealIntegrator>*  myNVT = NULL;
1398	<	NPTi<RealIntegrator>* myNPTi = NULL;
1399	<	NPTf<RealIntegrator>* myNPTf = NULL;
1400	<	NPTim<RealIntegrator>* myNPTim = NULL;
1401	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1402	<
1403	<	for(k=0; k<nInfo; k++){
1404	<
1405	<	switch( ensembleCase ){
1406	<
1407	<	case NVE_ENS:
1408	<	if (globals->haveZconstraints()){
1409	<	setupZConstraint(info[k]);
1410	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1411	<	}
1397	>	NVE<RealIntegrator>* myNVE = NULL;
1398	>	NVT<RealIntegrator>* myNVT = NULL;
1399	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1400	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1401	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1402	>
1403	>	for (k = 0; k < nInfo; k++){
1404	>	switch (ensembleCase){
1405	>	case NVE_ENS:
1406	>	if (globals->haveZconstraints()){
1407	>	setupZConstraint(info[k]);
1408	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1409	>	}
1410	>	else{
1411	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1412	>	}
1413	>
1414	>	info->the_integrator = myNVE;
1415	>	break;
1416
1417	<	else
1418	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1419	<	break;
1420	<
1421	<	case NVT_ENS:
1422	<	if (globals->haveZconstraints()){
1423	<	setupZConstraint(info[k]);
1376	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	<	}
1378	<	else
1379	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1417	>	case NVT_ENS:
1418	>	if (globals->haveZconstraints()){
1419	>	setupZConstraint(info[k]);
1420	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1421	>	}
1422	>	else
1423	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1424
1425		myNVT->setTargetTemp(globals->getTargetTemp());
1426	<
1427	<	if (globals->haveTauThermostat())
1426	>
1427	>	if (globals->haveTauThermostat())
1428		myNVT->setTauThermostat(globals->getTauThermostat());
1429	<
1430	<	else {
1431	<	sprintf( painCave.errMsg,
1432	<	"SimSetup error: If you use the NVT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1429	>	else{
1430	>	sprintf(painCave.errMsg,
1431	>	"SimSetup error: If you use the NVT\n"
1432	>	"\tensemble, you must set tauThermostat.\n");
1433		painCave.isFatal = 1;
1434		simError();
1435		}
1436	+
1437	+	info->the_integrator = myNVT;
1438		break;
1394	–
1395	–	case NPTi_ENS:
1396	–	if (globals->haveZconstraints()){
1397	–	setupZConstraint(info[k]);
1398	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	–	}
1400	–	else
1401	–	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1439
1440	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1441	<
1442	<	if (globals->haveTargetPressure())
1443	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1444	<	else {
1445	<	sprintf( painCave.errMsg,
1446	<	"SimSetup error: If you use a constant pressure\n"
1410	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	<	painCave.isFatal = 1;
1412	<	simError();
1413	<	}
1414	<
1415	<	if( globals->haveTauThermostat() )
1416	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	<	else{
1418	<	sprintf( painCave.errMsg,
1419	<	"SimSetup error: If you use an NPT\n"
1420	<	"    ensemble, you must set tauThermostat.\n");
1421	<	painCave.isFatal = 1;
1422	<	simError();
1423	<	}
1424	<
1425	<	if( globals->haveTauBarostat() )
1426	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	<	else{
1428	<	sprintf( painCave.errMsg,
1429	<	"SimSetup error: If you use an NPT\n"
1430	<	"    ensemble, you must set tauBarostat.\n");
1431	<	painCave.isFatal = 1;
1432	<	simError();
1433	<	}
1434	<	break;
1435	<
1436	<	case NPTf_ENS:
1437	<	if (globals->haveZconstraints()){
1438	<	setupZConstraint(info[k]);
1439	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	<	}
1441	<	else
1442	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	>	case NPTi_ENS:
1441	>	if (globals->haveZconstraints()){
1442	>	setupZConstraint(info[k]);
1443	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1444	>	}
1445	>	else
1446	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1447
1448	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1449	<
1450	<	if (globals->haveTargetPressure())
1451	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1452	<	else {
1453	<	sprintf( painCave.errMsg,
1448	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1449	>
1450	>	if (globals->haveTargetPressure())
1451	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1452	>	else{
1453	>	sprintf(painCave.errMsg,
1454		"SimSetup error: If you use a constant pressure\n"
1455	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1456	<	painCave.isFatal = 1;
1457	<	simError();
1458	<	}
1459	<
1460	<	if( globals->haveTauThermostat() )
1461	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1462	<	else{
1463	<	sprintf( painCave.errMsg,
1460	<	"SimSetup error: If you use an NPT\n"
1461	<	"    ensemble, you must set tauThermostat.\n");
1462	<	painCave.isFatal = 1;
1463	<	simError();
1464	<	}
1465	<
1466	<	if( globals->haveTauBarostat() )
1467	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	<	else{
1469	<	sprintf( painCave.errMsg,
1455	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if (globals->haveTauThermostat())
1461	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1462	>	else{
1463	>	sprintf(painCave.errMsg,
1464		"SimSetup error: If you use an NPT\n"
1465	<	"    ensemble, you must set tauBarostat.\n");
1466	<	painCave.isFatal = 1;
1467	<	simError();
1468	<	}
1475	<	break;
1476	<
1477	<	case NPTim_ENS:
1478	<	if (globals->haveZconstraints()){
1479	<	setupZConstraint(info[k]);
1480	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	<	}
1482	<	else
1483	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1465	>	"\tensemble, you must set tauThermostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469
1470	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1471	<
1472	<	if (globals->haveTargetPressure())
1473	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	<	else {
1490	<	sprintf( painCave.errMsg,
1491	<	"SimSetup error: If you use a constant pressure\n"
1492	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	<	painCave.isFatal = 1;
1494	<	simError();
1495	<	}
1496	<
1497	<	if( globals->haveTauThermostat() )
1498	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	<	else{
1500	<	sprintf( painCave.errMsg,
1470	>	if (globals->haveTauBarostat())
1471	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1472	>	else{
1473	>	sprintf(painCave.errMsg,
1474		"SimSetup error: If you use an NPT\n"
1475	<	"    ensemble, you must set tauThermostat.\n");
1476	<	painCave.isFatal = 1;
1477	<	simError();
1478	<	}
1506	<
1507	<	if( globals->haveTauBarostat() )
1508	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	<	else{
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup error: If you use an NPT\n"
1512	<	"    ensemble, you must set tauBarostat.\n");
1513	<	painCave.isFatal = 1;
1514	<	simError();
1515	<	}
1516	<	break;
1517	<
1518	<	case NPTfm_ENS:
1519	<	if (globals->haveZconstraints()){
1520	<	setupZConstraint(info[k]);
1521	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	<	}
1523	<	else
1524	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1475	>	"\tensemble, you must set tauBarostat.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479
1480	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1480	>	info->the_integrator = myNPTi;
1481	>	break;
1482
1483	<	if (globals->haveTargetPressure())
1484	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1485	<	else {
1486	<	sprintf( painCave.errMsg,
1483	>	case NPTf_ENS:
1484	>	if (globals->haveZconstraints()){
1485	>	setupZConstraint(info[k]);
1486	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1487	>	}
1488	>	else
1489	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1490	>
1491	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1492	>
1493	>	if (globals->haveTargetPressure())
1494	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1495	>	else{
1496	>	sprintf(painCave.errMsg,
1497		"SimSetup error: If you use a constant pressure\n"
1498	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1499	<	painCave.isFatal = 1;
1500	<	simError();
1501	<	}
1498	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1499	>	painCave.isFatal = 1;
1500	>	simError();
1501	>	}
1502
1503	<	if( globals->haveTauThermostat() )
1504	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1505	<	else{
1506	<	sprintf( painCave.errMsg,
1503	>	if (globals->haveTauThermostat())
1504	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1505	>
1506	>	else{
1507	>	sprintf(painCave.errMsg,
1508		"SimSetup error: If you use an NPT\n"
1509	<	"    ensemble, you must set tauThermostat.\n");
1510	<	painCave.isFatal = 1;
1511	<	simError();
1512	<	}
1509	>	"\tensemble, you must set tauThermostat.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513
1514	<	if( globals->haveTauBarostat() )
1515	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1516	<	else{
1517	<	sprintf( painCave.errMsg,
1514	>	if (globals->haveTauBarostat())
1515	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1516	>
1517	>	else{
1518	>	sprintf(painCave.errMsg,
1519		"SimSetup error: If you use an NPT\n"
1520	<	"    ensemble, you must set tauBarostat.\n");
1520	>	"\tensemble, you must set tauBarostat.\n");
1521	>	painCave.isFatal = 1;
1522	>	simError();
1523	>	}
1524	>
1525	>	info->the_integrator = myNPTf;
1526	>	break;
1527	>
1528	>	case NPTxyz_ENS:
1529	>	if (globals->haveZconstraints()){
1530	>	setupZConstraint(info[k]);
1531	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1532	>	}
1533	>	else
1534	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1535	>
1536	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1537	>
1538	>	if (globals->haveTargetPressure())
1539	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1540	>	else{
1541	>	sprintf(painCave.errMsg,
1542	>	"SimSetup error: If you use a constant pressure\n"
1543	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if (globals->haveTauThermostat())
1549	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1550	>	else{
1551	>	sprintf(painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"\tensemble, you must set tauThermostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>
1558	>	if (globals->haveTauBarostat())
1559	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1560	>	else{
1561	>	sprintf(painCave.errMsg,
1562	>	"SimSetup error: If you use an NPT\n"
1563	>	"\tensemble, you must set tauBarostat.\n");
1564	>	painCave.isFatal = 1;
1565	>	simError();
1566	>	}
1567	>
1568	>	info->the_integrator = myNPTxyz;
1569	>	break;
1570	>
1571	>	default:
1572	>	sprintf(painCave.errMsg,
1573	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1574		painCave.isFatal = 1;
1575		simError();
1556	–	}
1557	–	break;
1558	–
1559	–	default:
1560	–	sprintf( painCave.errMsg,
1561	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562	–	painCave.isFatal = 1;
1563	–	simError();
1576		}
1577		}
1578		}
1579
1580	<	void SimSetup::initFortran( void ){
1569	<
1580	>	void SimSetup::initFortran(void){
1581		info[0].refreshSim();
1582	<
1583	<	if( !strcmp( info[0].mixingRule, "standard") ){
1584	<	the_ff->initForceField( LB_MIXING_RULE );
1582	>
1583	>	if (!strcmp(info[0].mixingRule, "standard")){
1584	>	the_ff->initForceField(LB_MIXING_RULE);
1585		}
1586	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1587	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1587	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1588		}
1589		else{
1590	<	sprintf( painCave.errMsg,
1591	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info[0].mixingRule );
1590	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1591	>	info[0].mixingRule);
1592		painCave.isFatal = 1;
1593		simError();
1594		}
1595
1596
1597		#ifdef IS_MPI
1598	<	strcpy( checkPointMsg,
1589	<	"Successfully intialized the mixingRule for Fortran." );
1598	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1599		MPIcheckPoint();
1600		#endif // is_mpi
1592	–
1601		}
1602
1603	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	<	{
1603	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1604		int nZConstraints;
1605		ZconStamp** zconStamp;
1606
1607	<	if(globals->haveZconstraintTime()){
1601	<
1607	>	if (globals->haveZconstraintTime()){
1608		//add sample time of z-constraint  into SimInfo's property list
1609		DoubleData* zconsTimeProp = new DoubleData();
1610		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1606 | Line 1612 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1612		theInfo.addProperty(zconsTimeProp);
1613		}
1614		else{
1615	<	sprintf( painCave.errMsg,
1616	<	"ZConstraint error: If you use an ZConstraint\n"
1617	<	" , you must set sample time.\n");
1615	>	sprintf(painCave.errMsg,
1616	>	"ZConstraint error: If you use a ZConstraint,\n"
1617	>	"\tyou must set zconsTime.\n");
1618		painCave.isFatal = 1;
1619	<	simError();
1619	>	simError();
1620		}
1621
1622		//push zconsTol into siminfo, if user does not specify
1623		//value for zconsTol, a default value will be used
1624		DoubleData* zconsTol = new DoubleData();
1625		zconsTol->setID(ZCONSTOL_ID);
1626	<	if(globals->haveZconsTol()){
1626	>	if (globals->haveZconsTol()){
1627		zconsTol->setData(globals->getZconsTol());
1628		}
1629		else{
1630	<	double defaultZConsTol = 0.01;
1631	<	sprintf( painCave.errMsg,
1632	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1633	<	" , default value %f is used.\n", defaultZConsTol);
1630	>	double defaultZConsTol = 0.01;
1631	>	sprintf(painCave.errMsg,
1632	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1633	>	"\tOOPSE will use a default value of %f.\n"
1634	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1635	>	defaultZConsTol);
1636		painCave.isFatal = 0;
1637		simError();
1638
#	Line 1632 | Line 1640 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1640		}
1641		theInfo.addProperty(zconsTol);
1642
1643	<	//set Force Substraction Policy
1644	<	StringData* zconsForcePolicy =  new StringData();
1643	>	//set Force Subtraction Policy
1644	>	StringData* zconsForcePolicy = new StringData();
1645		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1646	<
1647	<	if(globals->haveZconsForcePolicy()){
1646	>
1647	>	if (globals->haveZconsForcePolicy()){
1648		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1649	<	}
1649	>	}
1650		else{
1651	<	sprintf( painCave.errMsg,
1652	<	"ZConstraint Warning: User does not set force substraction policy, "
1653	<	"average force substraction policy is used\n");
1654	<	painCave.isFatal = 0;
1655	<	simError();
1656	<	zconsForcePolicy->setData("BYNUMBER");
1651	>	sprintf(painCave.errMsg,
1652	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1653	>	"\tOOPSE will use PolicyByMass.\n"
1654	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1655	>	painCave.isFatal = 0;
1656	>	simError();
1657	>	zconsForcePolicy->setData("BYMASS");
1658		}
1659	<
1660	<	theInfo.addProperty(zconsForcePolicy);
1661	<
1659	>
1660	>	theInfo.addProperty(zconsForcePolicy);
1661	>
1662		//Determine the name of ouput file and add it into SimInfo's property list
1663		//Be careful, do not use inFileName, since it is a pointer which
1664		//point to a string at master node, and slave nodes do not contain that string
1665	<
1665	>
1666		string zconsOutput(theInfo.finalName);
1667	<
1667	>
1668		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1669	<
1669	>
1670		StringData* zconsFilename = new StringData();
1671		zconsFilename->setID(ZCONSFILENAME_ID);
1672		zconsFilename->setData(zconsOutput);
1673	<
1673	>
1674		theInfo.addProperty(zconsFilename);
1675	<
1675	>
1676		//setup index, pos and other parameters of z-constraint molecules
1677		nZConstraints = globals->getNzConstraints();
1678		theInfo.nZconstraints = nZConstraints;
#	Line 1673 | Line 1682 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1682
1683		ZConsParaData* zconsParaData = new ZConsParaData();
1684		zconsParaData->setID(ZCONSPARADATA_ID);
1685	<
1686	<	for(int i = 0; i < nZConstraints; i++){
1685	>
1686	>	for (int i = 0; i < nZConstraints; i++){
1687		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1688		tempParaItem.zPos = zconStamp[i]->getZpos();
1689		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1683 | Line 1692 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1692		zconsParaData->addItem(tempParaItem);
1693		}
1694
1695	+	//check the uniqueness of index
1696	+	if(!zconsParaData->isIndexUnique()){
1697	+	sprintf(painCave.errMsg,
1698	+	"ZConstraint Error: molIndex is not unique!\n");
1699	+	painCave.isFatal = 1;
1700	+	simError();
1701	+	}
1702	+
1703		//sort the parameters by index of molecules
1704		zconsParaData->sortByIndex();
1705
1706		//push data into siminfo, therefore, we can retrieve later
1707		theInfo.addProperty(zconsParaData);
1691	–
1708		}

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