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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 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"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 20 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#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
24	>	#define NPTxyz_ENS     4
25
32	–	#define FF_DUFF 0
33	–	#define FF_LJ   1
34	–	#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 55 | 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;
83	<	}
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 ){
66	<
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();
94	<	mpiEventLoop();
95	<
113	>	set_interface_stamps(stamps, globals);
114	>	mpiEventInit();
115	>	MPIcheckPoint();
116	>	mpiEventLoop();
117		}
118
119		#endif // is_mpi
120
121	<	void SimSetup::createSim( void ){
121	>	void SimSetup::createSim(void){
122
102	–	int i, j, k, globalAtomIndex;
103	–
123		// gather all of the information from the Bass file
124	<
124	>
125		gatherInfo();
126
127		// creation of complex system objects
#	Line 110 | Line 129 | void SimSetup::createSim( void ){
129		sysObjectsCreation();
130
131		// check on the post processing info
132	<
132	>
133		finalInfoCheck();
134
135		// initialize the system coordinates
136
137	<	initSystemCoords();
138	<
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 133 | Line 156 | void SimSetup::createSim( void ){
156		// initialize the Fortran
157
158		initFortran();
136	–
137	–
138	–
159		}
160
161
162	<	void SimSetup::makeMolecules( void ){
163	<
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 155 | Line 175 | void SimSetup::makeMolecules( void ){
175		bend_set* theBends;
176		torsion_set* theTorsions;
177
158	–
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;
167	–
168	–	atomOffset = 0;
169	–	excludeOffset = 0;
170	–	for(i=0; i<info->n_mol; i++){
171	–
172	–	stampID = the_molecules[i].getStampID();
189
190	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
191	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
190	>	for (k = 0; k < nInfo; k++){
191	>	the_ff->setSimInfo(&(info[k]));
192
193	<	molInfo.myAtoms = &the_atoms[atomOffset];
194	<	molInfo.myExcludes = &the_excludes[excludeOffset];
195	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
196	<	molInfo.myBends = new Bend*[molInfo.nBends];
184	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
193	>	atomOffset = 0;
194	>	excludeOffset = 0;
195	>	for (i = 0; i < info[k].n_mol; i++){
196	>	stampID = info[k].molecules[i].getStampID();
197
198	<	theBonds = new bond_pair[molInfo.nBonds];
199	<	theBends = new bend_set[molInfo.nBends];
200	<	theTorsions = new torsion_set[molInfo.nTorsions];
201	<
202	<	// make the Atoms
203	<
204	<	for(j=0; j<molInfo.nAtoms; j++){
205	<
206	<	currentAtom = comp_stamps[stampID]->getAtom( j );
207	<	if( currentAtom->haveOrientation() ){
208	<
209	<	dAtom = new DirectionalAtom(j + atomOffset);
210	<	info->n_oriented++;
211	<	molInfo.myAtoms[j] = dAtom;
212	<
213	<	ux = currentAtom->getOrntX();
214	<	uy = currentAtom->getOrntY();
215	<	uz = currentAtom->getOrntZ();
216	<
217	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
218	<
219	<	u = sqrt( uSqr );
220	<	ux = ux / u;
221	<	uy = uy / u;
222	<	uz = uz / u;
223	<
224	<	dAtom->setSUx( ux );
225	<	dAtom->setSUy( uy );
226	<	dAtom->setSUz( uz );
227	<	}
228	<	else{
229	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
230	<	}
231	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
232	<
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	>
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];
209	>
210	>	theBonds = new bond_pair[molInfo.nBonds];
211	>	theBends = new bend_set[molInfo.nBends];
212	>	theTorsions = new torsion_set[molInfo.nTorsions];
213	>
214	>	// make the Atoms
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	<	}
227	<
228	<	// make the bonds
229	<	for(j=0; j<molInfo.nBonds; j++){
230	<
231	<	currentBond = comp_stamps[stampID]->getBond( j );
232	<	theBonds[j].a = currentBond->getA() + atomOffset;
233	<	theBonds[j].b = currentBond->getB() + atomOffset;
274	>	}
275
276	<	exI = theBonds[j].a;
277	<	exJ = theBonds[j].b;
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	<	// exclude_I must always be the smaller of the pair
283	<	if( exI > exJ ){
284	<	tempEx = exI;
285	<	exI = exJ;
286	<	exJ = tempEx;
287	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
294	<	tempEx = exJ;
295	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
296	<
297	<	the_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	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
300	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
301		#endif  //is_mpi
255	–	}
256	–	excludeOffset += molInfo.nBonds;
257	–
258	–	//make the bends
259	–	for(j=0; j<molInfo.nBends; j++){
260	–
261	–	currentBend = comp_stamps[stampID]->getBend( j );
262	–	theBends[j].a = currentBend->getA() + atomOffset;
263	–	theBends[j].b = currentBend->getB() + atomOffset;
264	–	theBends[j].c = currentBend->getC() + atomOffset;
265	–
266	–	if( currentBend->haveExtras() ){
267	–
268	–	extras = currentBend->getExtras();
269	–	current_extra = extras;
270	–
271	–	while( current_extra != NULL ){
272	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	–
274	–	switch( current_extra->getType() ){
275	–
276	–	case 0:
277	–	theBends[j].ghost =
278	–	current_extra->getInt() + atomOffset;
279	–	theBends[j].isGhost = 1;
280	–	break;
281	–
282	–	case 1:
283	–	theBends[j].ghost =
284	–	(int)current_extra->getDouble() + atomOffset;
285	–	theBends[j].isGhost = 1;
286	–	break;
287	–
288	–	default:
289	–	sprintf( painCave.errMsg,
290	–	"SimSetup Error: ghostVectorSource was neither a "
291	–	"double nor an int.\n"
292	–	"-->Bend[%d] in %s\n",
293	–	j, comp_stamps[stampID]->getID() );
294	–	painCave.isFatal = 1;
295	–	simError();
296	–	}
297	–	}
298	–
299	–	else{
300	–
301	–	sprintf( painCave.errMsg,
302	–	"SimSetup Error: unhandled bend assignment:\n"
303	–	"    -->%s in Bend[%d] in %s\n",
304	–	current_extra->getlhs(),
305	–	j, comp_stamps[stampID]->getID() );
306	–	painCave.isFatal = 1;
307	–	simError();
308	–	}
309	–
310	–	current_extra = current_extra->getNext();
311	–	}
302		}
303	<
304	<	if( !theBends[j].isGhost ){
305	<
306	<	exI = theBends[j].a;
307	<	exJ = theBends[j].c;
308	<	}
309	<	else{
310	<
311	<	exI = theBends[j].a;
312	<	exJ = theBends[j].b;
313	<	}
314	<
315	<	// exclude_I must always be the smaller of the pair
316	<	if( exI > exJ ){
317	<	tempEx = exI;
318	<	exI = exJ;
319	<	exJ = tempEx;
320	<	}
303	>	excludeOffset += molInfo.nBonds;
304	>
305	>	//make the bends
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	>	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 = the_atoms[tempEx]->getGlobalIndex() + 1;
371	<	tempEx = exJ;
372	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
373	<
374	<	the_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	<	the_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;
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;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
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	<	// exclude_I must always be the smaller of the pair
389	<	if( exI > exJ ){
390	<	tempEx = exI;
391	<	exI = exJ;
392	<	exJ = tempEx;
393	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
400	<	tempEx = exJ;
401	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
402	<
403	<	the_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	<	the_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;
407	>	}
408	>	excludeOffset += molInfo.nTorsions;
409
374	–
375	–	// send the arrays off to the forceField for init.
410
411	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
411	>	// send the arrays off to the forceField for init.
412
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
383	–	the_molecules[i].initialize( molInfo );
419
420	+	info[k].molecules[i].initialize(molInfo);
421
422	<	atomOffset += molInfo.nAtoms;
423	<	delete[] theBonds;
424	<	delete[] theBends;
425	<	delete[] theTorsions;
422	>
423	>	atomOffset += molInfo.nAtoms;
424	>	delete[] theBonds;
425	>	delete[] theBends;
426	>	delete[] theTorsions;
427	>	}
428		}
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
435		// clean up the forcefield
436	+
437		the_ff->calcRcut();
438		the_ff->cleanMe();
400	–
439		}
440
441	<	void SimSetup::initFromBass( void ){
404	<
441	>	void SimSetup::initFromBass(void){
442		int i, j, k;
443		int n_cells;
444		double cellx, celly, cellz;
#	Line 410 | Line 447 | void SimSetup::initFromBass( void ){
447		int n_extra;
448		int have_extra, done;
449
450	<	temp1 = (double)tot_nmol / 4.0;
451	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
452	<	temp3 = ceil( temp2 );
450	>	double vel[3];
451	>	vel[0] = 0.0;
452	>	vel[1] = 0.0;
453	>	vel[2] = 0.0;
454
455	<	have_extra =0;
456	<	if( temp2 < temp3 ){ // we have a non-complete lattice
457	<	have_extra =1;
455	>	temp1 = (double) tot_nmol / 4.0;
456	>	temp2 = pow(temp1, (1.0 / 3.0));
457	>	temp3 = ceil(temp2);
458
459	<	n_cells = (int)temp3 - 1;
460	<	cellx = info->boxL[0] / temp3;
461	<	celly = info->boxL[1] / temp3;
462	<	cellz = info->boxL[2] / temp3;
425	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
426	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
427	<	n_per_extra = (int)ceil( temp1 );
459	>	have_extra = 0;
460	>	if (temp2 < temp3){
461	>	// we have a non-complete lattice
462	>	have_extra = 1;
463
464	<	if( n_per_extra > 4){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error. There has been an error in constructing"
467	<	" the non-complete lattice.\n" );
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);
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");
476		painCave.isFatal = 1;
477		simError();
478		}
479		}
480		else{
481	<	n_cells = (int)temp3;
482	<	cellx = info->boxL[0] / temp3;
483	<	celly = info->boxL[1] / temp3;
484	<	cellz = info->boxL[2] / 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;
485		}
486
487		current_mol = 0;
#	Line 446 | 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,
454	<	j * celly,
455	<	k * cellz );
497	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
498
499	<	makeElement( i * cellx + 0.5 * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz );
499	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
500
501	<	makeElement( i * cellx,
462	<	j * celly + 0.5 * celly,
463	<	k * cellz + 0.5 * cellz );
464	<
465	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly,
467	<	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	<	}
486	<	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 ){
496	<	makeElement( i * cellx + 0.5 * cellx,
497	<	j * celly + 0.5 * celly,
498	<	k * cellz );
499	<	done = ( current_mol >= tot_nmol );
500	<	}
501	<
502	<	if( !done && n_per_extra > 2){
503	<	makeElement( i * cellx,
504	<	j * celly + 0.5 * celly,
505	<	k * cellz + 0.5 * cellz );
506	<	done = ( current_mol >= tot_nmol );
507	<	}
508	<
509	<	if( !done && n_per_extra > 3){
510	<	makeElement( i * cellx + 0.5 * cellx,
511	<	j * celly,
512	<	k * cellz + 0.5 * cellz );
513	<	done = ( current_mol >= tot_nmol );
514	<	}
515	<	}
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	<
549	<	for( i=0; i<info->n_atoms; i++ ){
522	<	info->atoms[i]->set_vx( 0.0 );
523	<	info->atoms[i]->set_vy( 0.0 );
524	<	info->atoms[i]->set_vz( 0.0 );
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 ){
529	<
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",
544	<	comp_stamps[current_comp]->getID(),
545	<	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
573	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
574	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
575	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
573	>	pos[0] = x + current_atom->getPosX();
574	>	pos[1] = y + current_atom->getPosY();
575	>	pos[2] = z + current_atom->getPosZ();
576
577	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
577	>	info[0].atoms[current_atom_ndx]->setPos(pos);
578
579	<	dAtom = (DirectionalAtom *)the_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 567 | 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 576 | 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] ){
580	<
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
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
616		// set the easy ones first
617	<	info->target_temp = globals->getTargetTemp();
618	<	info->dt = globals->getDt();
619	<	info->run_time = globals->getRunTime();
617	>
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();
622	>	}
623		n_components = globals->getNComponents();
624
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;
616	<	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;
624	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
626	<	ensembleCase = NPTi_ENS;
627	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
628	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
629	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
630	<
631	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634	<	ensembleCase = NPTiZCONS_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	<	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	<
639	<	else{
640	<	sprintf( painCave.errMsg,
641	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
642	<	"reverting to NVE for this simulation.\n",
643	<	ensemble );
644	<	painCave.isFatal = 0;
645	<	simError();
646	<	strcpy( ensemble, "NVE" );
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	+	}
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 \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		}
649	–	strcpy( info->ensemble, ensemble );
678
679	<	// get the mixing rule
679	>	for (i = 0; i < nInfo; i++){
680	>	strcpy(info[i].ensemble, ensemble);
681
682	<	strcpy( info->mixingRule, globals->getMixingRule() );
683	<	info->usePBC = globals->getPBC();
684	<
685	<
682	>	// get the mixing rule
683	>
684	>	strcpy(info[i].mixingRule, globals->getMixingRule());
685	>	info[i].usePBC = globals->getPBC();
686	>	}
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;
676	<	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 681 | 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	<	if( globals->haveSampleTime() ){
727	<	info->sampleTime = globals->getSampleTime();
728	<	info->statusTime = info->sampleTime;
729	<	info->thermalTime = info->sampleTime;
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		}
701	–	else{
702	–	info->sampleTime = globals->getRunTime();
703	–	info->statusTime = info->sampleTime;
704	–	info->thermalTime = info->sampleTime;
705	–	}
734
735	<	if( globals->haveStatusTime() ){
736	<	info->statusTime = globals->getStatusTime();
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() ){
746	<	info->thermalTime = globals->getThermalTime();
747	<	}
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	<	// check for the temperature set flag
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	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
765	>	// set the status, sample, and thermal kick times
766
767	<	// get some of the tricky things that may still be in the globals
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;
772	>	}
773	>	else{
774	>	info[i].sampleTime = globals->getRunTime();
775	>	info[i].statusTime = info[i].sampleTime;
776	>	info[i].thermalTime = info[i].sampleTime;
777	>	}
778
779	<	double boxVector[3];
780	<	if( globals->haveBox() ){
723	<	boxVector[0] = globals->getBox();
724	<	boxVector[1] = globals->getBox();
725	<	boxVector[2] = globals->getBox();
726	<
727	<	info->setBox( boxVector );
728	<	}
729	<	else if( globals->haveDensity() ){
730	<
731	<	double vol;
732	<	vol = (double)tot_nmol / globals->getDensity();
733	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	<	boxVector[1] = boxVector[0];
735	<	boxVector[2] = boxVector[0];
736	<
737	<	info->setBox( boxVector );
738	<	}
739	<	else{
740	<	if( !globals->haveBoxX() ){
741	<	sprintf( painCave.errMsg,
742	<	"SimSetup error, no periodic BoxX size given.\n" );
743	<	painCave.isFatal = 1;
744	<	simError();
779	>	if (globals->haveStatusTime()){
780	>	info[i].statusTime = globals->getStatusTime();
781		}
746	–	boxVector[0] = globals->getBoxX();
782
783	<	if( !globals->haveBoxY() ){
784	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
783	>	if (globals->haveThermalTime()){
784	>	info[i].thermalTime = globals->getThermalTime();
785		}
754	–	boxVector[1] = globals->getBoxY();
786
787	<	if( !globals->haveBoxZ() ){
788	<	sprintf( painCave.errMsg,
789	<	"SimSetup error, no periodic BoxZ size given.\n" );
790	<	painCave.isFatal = 1;
760	<	simError();
787	>	info[i].resetIntegrator = 0;
788	>	if( globals->haveResetTime() ){
789	>	info[i].resetTime = globals->getResetTime();
790	>	info[i].resetIntegrator = 1;
791		}
762	–	boxVector[2] = globals->getBoxZ();
792
793	<	info->setBox( boxVector );
765	<	}
766	<
767	<
793	>	// check for the temperature set flag
794
795	<	#ifdef IS_MPI
796	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
771	<	MPIcheckPoint();
772	<	#endif // is_mpi
795	>	if (globals->haveTempSet())
796	>	info[i].setTemp = globals->getTempSet();
797
798	<	}
798	>	// check for the extended State init
799
800	<
801	<	void SimSetup::finalInfoCheck( void ){
802	<	int index;
779	<	int usesDipoles;
780	<
781	<
782	<	// check electrostatic parameters
783	<
784	<	index = 0;
785	<	usesDipoles = 0;
786	<	while( (index < info->n_atoms) && !usesDipoles ){
787	<	usesDipoles = ((info->atoms)[index])->hasDipole();
788	<	index++;
800	>	info[i].useInitXSstate = globals->getUseInitXSstate();
801	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
802	>
803		}
804
805	<	#ifdef IS_MPI
806	<	int myUse = usesDipoles;
793	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
794	<	#endif //is_mpi
805	>	//setup seed for random number generator
806	>	int seedValue;
807
808	<	double theEcr, theEst;
808	>	if (globals->haveSeed()){
809	>	seedValue = globals->getSeed();
810
811	<	if (globals->getUseRF() ) {
812	<	info->useReactionField = 1;
813	<
814	<	if( !globals->haveECR() ){
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Warning: using default value of 1/2 the smallest "
804	<	"box length for the electrostaticCutoffRadius.\n"
805	<	"I hope you have a very fast processor!\n");
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();
808	–	double smallest;
809	–	smallest = info->boxL[0];
810	–	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	–	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	–	theEcr = 0.5 * smallest;
813	–	} else {
814	–	theEcr = globals->getECR();
815	–	}
817
818	<	if( !globals->haveEST() ){
819	<	sprintf( painCave.errMsg,
820	<	"SimSetup Warning: using default value of 0.05 * the "
821	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
822	<	);
823	<	painCave.isFatal = 0;
824	<	simError();
825	<	theEst = 0.05 * theEcr;
826	<	} else {
826	<	theEst= globals->getEST();
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	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
826	>	#endif
827		}
828	<
829	<	info->setEcr( theEcr, theEst );
828	>	}//end of if branch of globals->haveSeed()
829	>	else{
830
831	<	if(!globals->haveDielectric() ){
832	<	sprintf( painCave.errMsg,
833	<	"SimSetup Error: You are trying to use Reaction Field without"
834	<	"setting a dielectric constant!\n"
835	<	);
836	<	painCave.isFatal = 1;
837	<	simError();
831	>	#ifndef IS_MPI
832	>	seedValue = make_sprng_seed();
833	>	#else
834	>	if (worldRank == 0){
835	>	seedValue = make_sprng_seed();
836		}
837	<	info->dielectric = globals->getDielectric();
838	<	}
839	<	else {
842	<	if (usesDipoles) {
843	<
844	<	if( !globals->haveECR() ){
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Warning: using default value of 1/2 the smallest "
847	<	"box length for the electrostaticCutoffRadius.\n"
848	<	"I hope you have a very fast processor!\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	double smallest;
852	<	smallest = info->boxL[0];
853	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
854	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
855	<	theEcr = 0.5 * smallest;
856	<	} else {
857	<	theEcr = globals->getECR();
858	<	}
859	<
860	<	if( !globals->haveEST() ){
861	<	sprintf( painCave.errMsg,
862	<	"SimSetup Warning: using default value of 0.05 * the "
863	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
865	<	);
866	<	painCave.isFatal = 0;
867	<	simError();
868	<	theEst = 0.05 * theEcr;
869	<	} else {
870	<	theEst= globals->getEST();
871	<	}
837	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
838	>	#endif
839	>	}//end of globals->haveSeed()
840
841	<	info->setEcr( theEcr, theEst );
842	<	}
843	<	}
841	>	for (int i = 0; i < nInfo; i++){
842	>	info[i].setSeed(seedValue);
843	>	}
844
845		#ifdef IS_MPI
846	<	strcpy( checkPointMsg, "post processing checks out" );
846	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
847		MPIcheckPoint();
848		#endif // is_mpi
881	–
849		}
850
884	–	void SimSetup::initSystemCoords( void ){
851
852	<	if( globals->haveInitialConfig() ){
853	<
854	<	InitializeFromFile* fileInit;
855	<	#ifdef IS_MPI // is_mpi
856	<	if( worldRank == 0 ){
857	<	#endif //is_mpi
858	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
852	>	void SimSetup::finalInfoCheck(void){
853	>	int index;
854	>	int usesDipoles;
855	>	int i;
856	>
857	>	for (i = 0; i < nInfo; i++){
858	>	// check electrostatic parameters
859	>
860	>	index = 0;
861	>	usesDipoles = 0;
862	>	while ((index < info[i].n_atoms) && !usesDipoles){
863	>	usesDipoles = (info[i].atoms[index])->hasDipole();
864	>	index++;
865	>	}
866	>
867		#ifdef IS_MPI
868	<	}else fileInit = new InitializeFromFile( NULL );
869	<	#endif
870	<	fileInit->readInit( info ); // default velocities on
868	>	int myUse = usesDipoles;
869	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
870	>	#endif //is_mpi
871
872	<	delete fileInit;
899	<	}
900	<	else{
872	>	double theEcr, theEst;
873
874	<	#ifdef IS_MPI
874	>	if (globals->getUseRF()){
875	>	info[i].useReactionField = 1;
876
877	<	// no init from bass
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	>	else{
887	>	theEcr = globals->getECR();
888	>	}
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	>	else{
901	>	theEst = globals->getEST();
902	>	}
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");
951	>	MPIcheckPoint();
952	>	#endif // is_mpi
953	>	}
954
955	<	sprintf( painCave.errMsg,
956	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
908	<	painCave.isFatal;
909	<	simError();
910	<
911	<	#else
955	>	void SimSetup::initSystemCoords(void){
956	>	int i;
957
958	<	initFromBass();
958	>	char* inName;
959
960	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
961
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){
969	+	#endif //is_mpi
970	+	inName = globals->getInitialConfig();
971	+	fileInit = new InitializeFromFile(inName);
972	+	#ifdef IS_MPI
973	+	}
974	+	else
975	+	fileInit = new InitializeFromFile(NULL);
976		#endif
977	<	}
977	>	fileInit->readInit(info); // default velocities on
978
979	+	delete fileInit;
980	+	}
981	+	else{
982	+
983	+	// no init from bass
984	+
985	+	sprintf(painCave.errMsg,
986	+	"Cannot intialize a simulation without an initial configuration file.\n");
987	+	painCave.isFatal = 1;;
988	+	simError();
989	+
990	+	}
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
923	–
996		}
997
998
999	<	void SimSetup::makeOutNames( void ){
999	>	void SimSetup::makeOutNames(void){
1000	>	int k;
1001
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->finalName, globals->getFinalConfig() );
935	<	}
936	<	else{
937	<	strcpy( info->finalName, inFileName );
938	<	char* endTest;
939	<	int nameLength = strlen( info->finalName );
940	<	endTest = &(info->finalName[nameLength - 5]);
941	<	if( !strcmp( endTest, ".bass" ) ){
942	<	strcpy( endTest, ".eor" );
1007	>
1008	>	if (globals->haveFinalConfig()){
1009	>	strcpy(info[k].finalName, globals->getFinalConfig());
1010		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
1011		else{
1012	<	endTest = &(info->finalName[nameLength - 4]);
1013	<	if( !strcmp( endTest, ".bss" ) ){
1014	<	strcpy( endTest, ".eor" );
1015	<	}
1016	<	else if( !strcmp( endTest, ".mdl" ) ){
1017	<	strcpy( endTest, ".eor" );
1018	<	}
1019	<	else{
1020	<	strcat( info->finalName, ".eor" );
1021	<	}
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	<	}
1036	<
1037	<	// make the sample and status out names
1038	<
1039	<	strcpy( info->sampleName, inFileName );
1040	<	char* endTest;
1041	<	int nameLength = strlen( info->sampleName );
1042	<	endTest = &(info->sampleName[nameLength - 5]);
1043	<	if( !strcmp( endTest, ".bass" ) ){
968	<	strcpy( endTest, ".dump" );
969	<	}
970	<	else if( !strcmp( endTest, ".BASS" ) ){
971	<	strcpy( endTest, ".dump" );
972	<	}
973	<	else{
974	<	endTest = &(info->sampleName[nameLength - 4]);
975	<	if( !strcmp( endTest, ".bss" ) ){
976	<	strcpy( endTest, ".dump" );
1035	>
1036	>	// make the sample and status out names
1037	>
1038	>	strcpy(info[k].sampleName, inFileName);
1039	>	char* endTest;
1040	>	int nameLength = strlen(info[k].sampleName);
1041	>	endTest = &(info[k].sampleName[nameLength - 5]);
1042	>	if (!strcmp(endTest, ".bass")){
1043	>	strcpy(endTest, ".dump");
1044		}
1045	<	else if( !strcmp( endTest, ".mdl" ) ){
1046	<	strcpy( endTest, ".dump" );
1045	>	else if (!strcmp(endTest, ".BASS")){
1046	>	strcpy(endTest, ".dump");
1047		}
1048		else{
1049	<	strcat( info->sampleName, ".dump" );
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	<
1062	<	strcpy( info->statusName, inFileName );
1063	<	nameLength = strlen( info->statusName );
1064	<	endTest = &(info->statusName[nameLength - 5]);
1065	<	if( !strcmp( endTest, ".bass" ) ){
990	<	strcpy( endTest, ".stat" );
991	<	}
992	<	else if( !strcmp( endTest, ".BASS" ) ){
993	<	strcpy( endTest, ".stat" );
994	<	}
995	<	else{
996	<	endTest = &(info->statusName[nameLength - 4]);
997	<	if( !strcmp( endTest, ".bss" ) ){
998	<	strcpy( endTest, ".stat" );
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");
1066		}
1067	<	else if( !strcmp( endTest, ".mdl" ) ){
1068	<	strcpy( endTest, ".stat" );
1067	>	else if (!strcmp(endTest, ".BASS")){
1068	>	strcpy(endTest, ".stat");
1069		}
1070		else{
1071	<	strcat( info->statusName, ".stat" );
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	<	}
1007	<
1082	>
1083		#ifdef IS_MPI
1009	–	}
1010	–	#endif // is_mpi
1084
1085	+	}
1086	+	#endif // is_mpi
1087	+	}
1088		}
1089
1090
1091	<	void SimSetup::sysObjectsCreation( void ){
1091	>	void SimSetup::sysObjectsCreation(void){
1092	>	int i, k;
1093
1017	–	int i;
1018	–
1094		// create the forceField
1095
1096		createFF();
#	Line 1030 | 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	<
1117	>
1118		makeMolecules();
1044	–	info->identArray = new int[info->n_atoms];
1045	–	for(i=0; i<info->n_atoms; i++){
1046	–	info->identArray[i] = the_atoms[i]->getIdent();
1047	–	}
1048	–
1119
1120	<
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++){
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:
1071	<	sprintf( painCave.errMsg,
1072	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1073	<	painCave.isFatal = 1;
1074	<	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
1081	–
1158		}
1159
1160
1161	<	void SimSetup::compList( void ){
1086	<
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
1089	–	comp_stamps = new MoleculeStamp*[n_components];
1090	–
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	<	info->nComponents = n_components;
1172	<	info->componentsNmol = components_nmol;
1173	<	info->compStamps = comp_stamps;
1174	<	info->headStamp = new LinkedMolStamp();
1175	<
1176	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1102	<	for( i=0; i<n_components; i++ ){
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	>	}
1177
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 ){
1111	<
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
1133	–
1134	–
1208		}
1209
1210	<	void SimSetup::calcSysValues( void ){
1211	<	int i, j, k;
1210	>	void SimSetup::calcSysValues(void){
1211	>	int i;
1212
1213	+	int* molMembershipArray;
1214
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();
1149	<	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
1226		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1227	+	molMembershipArray = new int[tot_atoms];
1228
1229	<	info->n_atoms = tot_atoms;
1230	<	info->n_bonds = tot_bonds;
1231	<	info->n_bends = tot_bends;
1232	<	info->n_torsions = tot_torsions;
1233	<	info->n_SRI = tot_SRI;
1234	<	info->n_mol = tot_nmol;
1235	<
1236	<	info->molMembershipArray = new int[tot_atoms];
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	>
1237	>	info[i].molMembershipArray = molMembershipArray;
1238	>	}
1239		}
1240
1165	–
1241		#ifdef IS_MPI
1242
1243	<	void SimSetup::mpiMolDivide( void ){
1169	<
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 1189 | 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();
1200	<	local_bends +=    comp_stamps[i]->getNBends();
1201	<	local_torsions += comp_stamps[i]->getNTorsions();
1202	<	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++) {
1276	<	info->molMembershipArray[globalAtomIndex] = allMol;
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	<
1285	<	info->n_atoms = mpiSim->getMyNlocal();
1286	<
1287	<	if( local_atoms != info->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->n_atoms,
1221	<	local_atoms );
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\n"
1290	>	"\tlocalAtom (%d) are not equal.\n",
1291	>	info[0].n_atoms, local_atoms);
1292		painCave.isFatal = 1;
1293		simError();
1294		}
1295
1296	<	info->n_bonds = local_bonds;
1297	<	info->n_bends = local_bends;
1298	<	info->n_torsions = local_torsions;
1299	<	info->n_SRI = local_SRI;
1300	<	info->n_mol = localMol;
1296	>	info[0].n_bonds = local_bonds;
1297	>	info[0].n_bends = local_bends;
1298	>	info[0].n_torsions = local_torsions;
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;
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
1243	–	// create the atom and short range interaction arrays
1320
1321	<	Atom::createArrays(info->n_atoms);
1322	<	the_atoms = new Atom*[info->n_atoms];
1247	<	the_molecules = new Molecule[info->n_mol];
1248	<	int molIndex;
1321	>	for (l = 0; l < nInfo; l++){
1322	>	// create the atom and short range interaction arrays
1323
1324	<	// initialize the molecule's stampID's
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	+
1330		#ifdef IS_MPI
1253	–
1331
1332	<	molIndex = 0;
1333	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1334	<
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++;
1332	>
1333	>	molIndex = 0;
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		}
1264	–	}
1342
1343		#else // is_mpi
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->molMembershipArray[globalAtomIndex] = molIndex;
1354	<	globalAtomIndex++;
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++;
1357		}
1279	–	molIndex++;
1358		}
1281	–	}
1282	–
1359
1360	+
1361		#endif // is_mpi
1362
1363
1364	<	if( info->n_SRI ){
1365	<
1366	<	Exclude::createArray(info->n_SRI);
1367	<	the_excludes = new Exclude*[info->n_SRI];
1368	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1369	<	info->globalExcludes = new int;
1370	<	info->n_exclude = info->n_SRI;
1371	<	}
1372	<	else{
1373	<
1374	<	Exclude::createArray( 1 );
1375	<	the_excludes = new Exclude*;
1376	<	the_excludes[0] = new Exclude(0);
1377	<	the_excludes[0]->setPair( 0,0 );
1378	<	info->globalExcludes = new int;
1379	<	info->globalExcludes[0] = 0;
1380	<	info->n_exclude = 0;
1381	<	}
1305	<
1306	<	// set the arrays into the SimInfo object
1307	<
1308	<	info->atoms = the_atoms;
1309	<	info->molecules = the_molecules;
1310	<	info->nGlobalExcludes = 0;
1311	<	info->excludes = the_excludes;
1312	<
1313	<	the_ff->setSimInfo( info );
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);
1369	>	}
1370	>	info[l].globalExcludes = new int;
1371	>	info[l].n_exclude = info[l].n_SRI;
1372	>	}
1373	>	else{
1374	>	Exclude::createArray(1);
1375	>	the_excludes = new Exclude * ;
1376	>	the_excludes[0] = new Exclude(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;
1381	>	}
1382
1383	+	// set the arrays into the SimInfo object
1384	+
1385	+	info[l].atoms = the_atoms;
1386	+	info[l].molecules = the_molecules;
1387	+	info[l].nGlobalExcludes = 0;
1388	+	info[l].excludes = the_excludes;
1389	+
1390	+	the_ff->setSimInfo(info);
1391	+	}
1392		}
1393
1394	<	void SimSetup::makeIntegrator( void ){
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;
1324	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330	<
1331	<	cerr << "setting integrator" <<endl;
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	<	switch( ensembleCase ){
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	<	case NVE_ENS:
1418	<	new NVE<RealIntegrator>( info, the_ff );
1419	<	break;
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	<	case NVT_ENS:
1340	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1341	<	myNVT->setTargetTemp(globals->getTargetTemp());
1425	>	myNVT->setTargetTemp(globals->getTargetTemp());
1426
1427	<	if (globals->haveTauThermostat())
1428	<	myNVT->setTauThermostat(globals->getTauThermostat());
1427	>	if (globals->haveTauThermostat())
1428	>	myNVT->setTauThermostat(globals->getTauThermostat());
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	<	else {
1438	<	sprintf( painCave.errMsg,
1348	<	"SimSetup error: If you use the NVT\n"
1349	<	"    ensemble, you must set tauThermostat.\n");
1350	<	painCave.isFatal = 1;
1351	<	simError();
1352	<	}
1353	<	break;
1437	>	info->the_integrator = myNVT;
1438	>	break;
1439
1440	<	case NPTi_ENS:
1441	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1442	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
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	<	if (globals->haveTargetPressure())
1360	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1361	<	else {
1362	<	sprintf( painCave.errMsg,
1363	<	"SimSetup error: If you use a constant pressure\n"
1364	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1365	<	painCave.isFatal = 1;
1366	<	simError();
1367	<	}
1368	<
1369	<	if( globals->haveTauThermostat() )
1370	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1371	<	else{
1372	<	sprintf( painCave.errMsg,
1373	<	"SimSetup error: If you use an NPT\n"
1374	<	"    ensemble, you must set tauThermostat.\n");
1375	<	painCave.isFatal = 1;
1376	<	simError();
1377	<	}
1448	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1449
1450	<	if( globals->haveTauBarostat() )
1451	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1452	<	else{
1453	<	sprintf( painCave.errMsg,
1454	<	"SimSetup error: If you use an NPT\n"
1455	<	"    ensemble, you must set tauBarostat.\n");
1456	<	painCave.isFatal = 1;
1457	<	simError();
1458	<	}
1388	<	break;
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	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459
1460	<	case NPTf_ENS:
1461	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1462	<	myNPTf->setTargetTemp( globals->getTargetTemp());
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	>	"\tensemble, you must set tauThermostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469
1470	<	if (globals->haveTargetPressure())
1471	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	<	else {
1473	<	sprintf( painCave.errMsg,
1474	<	"SimSetup error: If you use a constant pressure\n"
1475	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	<	painCave.isFatal = 1;
1477	<	simError();
1478	<	}
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	>	"\tensemble, you must set tauBarostat.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479
1480	<	if( globals->haveTauThermostat() )
1481	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1406	<	else{
1407	<	sprintf( painCave.errMsg,
1408	<	"SimSetup error: If you use an NPT\n"
1409	<	"    ensemble, you must set tauThermostat.\n");
1410	<	painCave.isFatal = 1;
1411	<	simError();
1412	<	}
1480	>	info->the_integrator = myNPTi;
1481	>	break;
1482
1483	<	if( globals->haveTauBarostat() )
1484	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1485	<	else{
1486	<	sprintf( painCave.errMsg,
1487	<	"SimSetup error: If you use an NPT\n"
1488	<	"    ensemble, you must set tauBarostat.\n");
1489	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1423	<	break;
1424	<
1425	<	case NPTim_ENS:
1426	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	<	myNPTim->setTargetTemp( globals->getTargetTemp());
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	<	if (globals->haveTargetPressure())
1430	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1431	<	else {
1432	<	sprintf( painCave.errMsg,
1433	<	"SimSetup error: If you use a constant pressure\n"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1437	<	}
1438	<
1439	<	if( globals->haveTauThermostat() )
1440	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1441	<	else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1447	<	}
1491	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1492
1493	<	if( globals->haveTauBarostat() )
1494	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1495	<	else{
1496	<	sprintf( painCave.errMsg,
1497	<	"SimSetup error: If you use an NPT\n"
1498	<	"    ensemble, you must set tauBarostat.\n");
1499	<	painCave.isFatal = 1;
1500	<	simError();
1501	<	}
1458	<	break;
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	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1499	>	painCave.isFatal = 1;
1500	>	simError();
1501	>	}
1502
1503	<	case NPTfm_ENS:
1504	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1462	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1503	>	if (globals->haveTauThermostat())
1504	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1505
1506	<	if (globals->haveTargetPressure())
1507	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1508	<	else {
1509	<	sprintf( painCave.errMsg,
1510	<	"SimSetup error: If you use a constant pressure\n"
1511	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1512	<	painCave.isFatal = 1;
1471	<	simError();
1472	<	}
1473	<
1474	<	if( globals->haveTauThermostat() )
1475	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1476	<	else{
1477	<	sprintf( painCave.errMsg,
1478	<	"SimSetup error: If you use an NPT\n"
1479	<	"    ensemble, you must set tauThermostat.\n");
1480	<	painCave.isFatal = 1;
1481	<	simError();
1482	<	}
1506	>	else{
1507	>	sprintf(painCave.errMsg,
1508	>	"SimSetup error: If you use an NPT\n"
1509	>	"\tensemble, you must set tauThermostat.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513
1514	<	if( globals->haveTauBarostat() )
1515	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	<	else{
1487	<	sprintf( painCave.errMsg,
1488	<	"SimSetup error: If you use an NPT\n"
1489	<	"    ensemble, you must set tauBarostat.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<	break;
1494	<
1495	<	case NVEZCONS_ENS:
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	+	"\tensemble, you must set tauBarostat.\n");
1521	+	painCave.isFatal = 1;
1522	+	simError();
1523	+	}
1524
1525	<	//setup index of z-constraint molecules, z-constraint sampel time
1526	<	//and z-constraint force output name. These parameter should be known
1500	<	//before constructing the z-constraint integrator
1501	<	setupZConstraint();
1502	<
1503	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1504	<
1505	<	break;
1506	<
1507	<
1508	<	case NVTZCONS_ENS:
1509	<
1510	<	setupZConstraint();
1511	<
1512	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1525	>	info->the_integrator = myNPTf;
1526	>	break;
1527
1528	<	if (globals->haveTauThermostat())
1529	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
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	<	else {
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use the NVT\n"
1521	<	"    ensemble, you must set tauThermostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1525	<	break;
1526	<
1527	<	case NPTiZCONS_ENS:
1528	<
1529	<	setupZConstraint();
1530	<
1531	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1536	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1537
1538	<	if (globals->haveTargetPressure())
1539	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1540	<	else {
1541	<	sprintf( painCave.errMsg,
1542	<	"SimSetup error: If you use a constant pressure\n"
1543	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1544	<	painCave.isFatal = 1;
1545	<	simError();
1546	<	}
1543	<
1544	<	if( globals->haveTauThermostat() )
1545	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546	<	else{
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use an NPT\n"
1549	<	"    ensemble, you must set tauThermostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
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->haveTauBarostat() )
1549	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1550	<	else{
1551	<	sprintf( painCave.errMsg,
1552	<	"SimSetup error: If you use an NPT\n"
1553	<	"    ensemble, you must set tauBarostat.\n");
1554	<	painCave.isFatal = 1;
1555	<	simError();
1556	<	}
1563	<
1564	<	break;
1565	<
1566	<	case NPTfZCONS_ENS:
1567	<
1568	<	setupZConstraint();
1569	<
1570	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
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->haveTargetPressure())
1559	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1560	<	else {
1561	<	sprintf( painCave.errMsg,
1562	<	"SimSetup error: If you use a constant pressure\n"
1563	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1564	<	painCave.isFatal = 1;
1565	<	simError();
1566	<	}
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	<	if( globals->haveTauThermostat() )
1569	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585	<	else{
1586	<	sprintf( painCave.errMsg,
1587	<	"SimSetup error: If you use an NPT\n"
1588	<	"    ensemble, you must set tauThermostat.\n");
1589	<	painCave.isFatal = 1;
1590	<	simError();
1591	<	}
1568	>	info->the_integrator = myNPTxyz;
1569	>	break;
1570
1571	<	if( globals->haveTauBarostat() )
1572	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1573	<	else{
1574	<	sprintf( painCave.errMsg,
1575	<	"SimSetup error: If you use an NPT\n"
1598	<	"    ensemble, you must set tauBarostat.\n");
1599	<	painCave.isFatal = 1;
1600	<	simError();
1601	<	}
1602	<
1603	<	break;
1604	<
1605	<	case NPTimZCONS_ENS:
1606	<
1607	<	setupZConstraint();
1608	<
1609	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1610	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1611	<
1612	<	if (globals->haveTargetPressure())
1613	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1614	<	else {
1615	<	sprintf( painCave.errMsg,
1616	<	"SimSetup error: If you use a constant pressure\n"
1617	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1618	<	painCave.isFatal = 1;
1619	<	simError();
1571	>	default:
1572	>	sprintf(painCave.errMsg,
1573	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1574	>	painCave.isFatal = 1;
1575	>	simError();
1576		}
1621	–
1622	–	if( globals->haveTauThermostat() )
1623	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624	–	else{
1625	–	sprintf( painCave.errMsg,
1626	–	"SimSetup error: If you use an NPT\n"
1627	–	"    ensemble, you must set tauThermostat.\n");
1628	–	painCave.isFatal = 1;
1629	–	simError();
1630	–	}
1631	–
1632	–	if( globals->haveTauBarostat() )
1633	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634	–	else{
1635	–	sprintf( painCave.errMsg,
1636	–	"SimSetup error: If you use an NPT\n"
1637	–	"    ensemble, you must set tauBarostat.\n");
1638	–	painCave.isFatal = 1;
1639	–	simError();
1640	–	}
1641	–
1642	–	break;
1643	–
1644	–	case NPTfmZCONS_ENS:
1645	–
1646	–	setupZConstraint();
1647	–
1648	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650	–
1651	–	if (globals->haveTargetPressure())
1652	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653	–	else {
1654	–	sprintf( painCave.errMsg,
1655	–	"SimSetup error: If you use a constant pressure\n"
1656	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1657	–	painCave.isFatal = 1;
1658	–	simError();
1659	–	}
1660	–
1661	–	if( globals->haveTauThermostat() )
1662	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663	–	else{
1664	–	sprintf( painCave.errMsg,
1665	–	"SimSetup error: If you use an NPT\n"
1666	–	"    ensemble, you must set tauThermostat.\n");
1667	–	painCave.isFatal = 1;
1668	–	simError();
1669	–	}
1670	–
1671	–	if( globals->haveTauBarostat() )
1672	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673	–	else{
1674	–	sprintf( painCave.errMsg,
1675	–	"SimSetup error: If you use an NPT\n"
1676	–	"    ensemble, you must set tauBarostat.\n");
1677	–	painCave.isFatal = 1;
1678	–	simError();
1679	–	}
1680	–	break;
1681	–
1682	–
1683	–
1684	–	default:
1685	–	sprintf( painCave.errMsg,
1686	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1687	–	painCave.isFatal = 1;
1688	–	simError();
1577		}
1690	–
1578		}
1579
1580	<	void SimSetup::initFortran( void ){
1580	>	void SimSetup::initFortran(void){
1581	>	info[0].refreshSim();
1582
1583	<	info->refreshSim();
1584	<
1697	<	if( !strcmp( info->mixingRule, "standard") ){
1698	<	the_ff->initForceField( LB_MIXING_RULE );
1583	>	if (!strcmp(info[0].mixingRule, "standard")){
1584	>	the_ff->initForceField(LB_MIXING_RULE);
1585		}
1586	<	else if( !strcmp( info->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",
1706	<	info->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,
1714	<	"Successfully intialized the mixingRule for Fortran." );
1598	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1599		MPIcheckPoint();
1600		#endif // is_mpi
1717	–
1601		}
1602
1603	<	void SimSetup::setupZConstraint()
1604	<	{
1605	<	if(globals->haveZConsTime()){
1606	<
1607	<	//add sample time of z-constraint  into SimInfo's property list
1608	<	DoubleData* zconsTimeProp = new DoubleData();
1609	<	zconsTimeProp->setID("zconstime");
1610	<	zconsTimeProp->setData(globals->getZConsTime());
1611	<	info->addProperty(zconsTimeProp);
1603	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1604	>	int nZConstraints;
1605	>	ZconStamp** zconStamp;
1606	>
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);
1611	>	zconsTimeProp->setData(globals->getZconsTime());
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();
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()){
1627	+	zconsTol->setData(globals->getZconsTol());
1628	+	}
1629	+	else{
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	+
1639	+	zconsTol->setData(defaultZConsTol);
1640		}
1641	<
1642	<	if(globals->haveIndexOfAllZConsMols()){
1643	<
1644	<	//add index of z-constraint molecules into SimInfo's property list
1645	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1646	<
1647	<	//sort the index
1648	<	sort(tempIndex.begin(), tempIndex.end());
1745	<
1746	<	IndexData* zconsIndex = new IndexData();
1747	<	zconsIndex->setID("zconsindex");
1748	<	zconsIndex->setIndexData(tempIndex);
1749	<	info->addProperty(zconsIndex);
1641	>	theInfo.addProperty(zconsTol);
1642	>
1643	>	//set Force Subtraction Policy
1644	>	StringData* zconsForcePolicy = new StringData();
1645	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1646	>
1647	>	if (globals->haveZconsForcePolicy()){
1648	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1649		}
1650		else{
1651	<	sprintf( painCave.errMsg,
1652	<	"SimSetup error: If you use an ZConstraint\n"
1653	<	" , you must set index of z-constraint molecules.\n");
1654	<	painCave.isFatal = 1;
1655	<	simError();
1656	<
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	+
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	<
1666	<	string zconsOutput(info->finalName);
1667	<
1665	>
1666	>	string zconsOutput(theInfo.finalName);
1667	>
1668		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1669	<
1669	>
1670		StringData* zconsFilename = new StringData();
1671	<	zconsFilename->setID("zconsfilename");
1671	>	zconsFilename->setID(ZCONSFILENAME_ID);
1672		zconsFilename->setData(zconsOutput);
1673
1674	<	info->addProperty(zconsFilename);
1674	>	theInfo.addProperty(zconsFilename);
1675
1676	+	//setup index, pos and other parameters of z-constraint molecules
1677	+	nZConstraints = globals->getNzConstraints();
1678	+	theInfo.nZconstraints = nZConstraints;
1679	+
1680	+	zconStamp = globals->getZconStamp();
1681	+	ZConsParaItem tempParaItem;
1682	+
1683	+	ZConsParaData* zconsParaData = new ZConsParaData();
1684	+	zconsParaData->setID(ZCONSPARADATA_ID);
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();
1690	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1691	+
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);
1708		}

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