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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 984 by gezelter, Mon Jan 26 21:52:56 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
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
30
31		using namespace std;
32
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58
59	+	initSuspend = false;
60		isInfoArray = 0;
61		nInfo = 1;
62	<
62	>
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
66	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 50 | Line 75 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
75		delete globals;
76		}
77
78	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
79	<	info = the_info;
80	<	nInfo = theNinfo;
81	<	isInfoArray = 1;
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83		}
84
85
86	<	void SimSetup::parseFile( char* fileName ){
61	<
86	>	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120		void SimSetup::createSim(void){
121
97	–	int i, j, k, globalAtomIndex;
98	–
122		// gather all of the information from the Bass file
123
124		gatherInfo();
#	Line 110 | Line 133 | void SimSetup::createSim(void){
133
134		// initialize the system coordinates
135
136	<	if( !isInfoArray ) initSystemCoords();
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	+	if( !(globals->getUseInitTime()) )
140	+	info[0].currentTime = 0.0;
141	+	}
142	+
143		// make the output filenames
144
145		makeOutNames();
146	<
146	>
147		// make the integrator
148	<
148	>
149		makeIntegrator();
150	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 127 | Line 155 | void SimSetup::createSim(void){
155		// initialize the Fortran
156
157		initFortran();
130	–
131	–
132	–
158		}
159
160
161	<	void SimSetup::makeMolecules( void ){
162	<
138	<	int k,l;
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164		molInit molInfo;
165		DirectionalAtom* dAtom;
#	Line 150 | Line 174 | void SimSetup::makeMolecules( void ){
174		bend_set* theBends;
175		torsion_set* theTorsions;
176
153	–
177		//init the forceField paramters
178
179		the_ff->readParams();
180
181	<
181	>
182		// init the atoms
183
184	+	double phi, theta, psi;
185	+	double sux, suy, suz;
186	+	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
187		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
188
189	+	for (k = 0; k < nInfo; k++){
190	+	the_ff->setSimInfo(&(info[k]));
191	+
192		atomOffset = 0;
193		excludeOffset = 0;
194	<	for(i=0; i<info[k].n_mol; i++){
170	<
194	>	for (i = 0; i < info[k].n_mol; i++){
195		stampID = info[k].molecules[i].getStampID();
196
197	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
198	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
199	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
197	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
198	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
199	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
200		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
201		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
202	<
202	>
203		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
204		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
205	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
206	<	molInfo.myBends = new Bend*[molInfo.nBends];
207	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
205	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
206	>	molInfo.myBends = new Bend * [molInfo.nBends];
207	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
208
209		theBonds = new bond_pair[molInfo.nBonds];
210		theBends = new bend_set[molInfo.nBends];
211		theTorsions = new torsion_set[molInfo.nTorsions];
212	<
212	>
213		// make the Atoms
214	<
215	<	for(j=0; j<molInfo.nAtoms; j++){
216	<
217	<	currentAtom = comp_stamps[stampID]->getAtom( j );
218	<	if( currentAtom->haveOrientation() ){
219	<
220	<	dAtom = new DirectionalAtom( (j + atomOffset),
221	<	info[k].getConfiguration() );
222	<	info[k].n_oriented++;
223	<	molInfo.myAtoms[j] = dAtom;
224	<
225	<	ux = currentAtom->getOrntX();
226	<	uy = currentAtom->getOrntY();
227	<	uz = currentAtom->getOrntZ();
228	<
229	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
230	<
231	<	u = sqrt( uSqr );
232	<	ux = ux / u;
233	<	uy = uy / u;
234	<	uz = uz / u;
235	<
236	<	dAtom->setSUx( ux );
237	<	dAtom->setSUy( uy );
238	<	dAtom->setSUz( uz );
239	<	}
240	<	else{
241	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
242	<	info[k].getConfiguration() );
243	<	}
244	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
245	<
214	>
215	>	for (j = 0; j < molInfo.nAtoms; j++){
216	>	currentAtom = comp_stamps[stampID]->getAtom(j);
217	>	if (currentAtom->haveOrientation()){
218	>	dAtom = new DirectionalAtom((j + atomOffset),
219	>	info[k].getConfiguration());
220	>	info[k].n_oriented++;
221	>	molInfo.myAtoms[j] = dAtom;
222	>
223	>	// Directional Atoms have standard unit vectors which are oriented
224	>	// in space using the three Euler angles.  We assume the standard
225	>	// unit vector was originally along the z axis below.
226	>
227	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
228	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
229	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
230	>
231	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
232	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
233	>	Axz = sin(theta) * sin(psi);
234	>
235	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
236	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
237	>	Ayz = sin(theta) * cos(psi);
238	>
239	>	Azx = sin(phi) * sin(theta);
240	>	Azy = -cos(phi) * sin(theta);
241	>	Azz = cos(theta);
242	>
243	>	sux = 0.0;
244	>	suy = 0.0;
245	>	suz = 1.0;
246	>
247	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
248	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
249	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
250	>
251	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
252	>
253	>	u = sqrt(uSqr);
254	>	ux = ux / u;
255	>	uy = uy / u;
256	>	uz = uz / u;
257	>
258	>	dAtom->setSUx(ux);
259	>	dAtom->setSUy(uy);
260	>	dAtom->setSUz(uz);
261	>	}
262	>	else{
263	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	>	info[k].getConfiguration());
265	>	}
266	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
267	>
268		#ifdef IS_MPI
269	<
270	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
271	<
269	>
270	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
271	>
272		#endif // is_mpi
273		}
274	<
275	<	// make the bonds
276	<	for(j=0; j<molInfo.nBonds; j++){
277	<
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;
244	<	}
274	>
275	>	// make the bonds
276	>	for (j = 0; j < molInfo.nBonds; j++){
277	>	currentBond = comp_stamps[stampID]->getBond(j);
278	>	theBonds[j].a = currentBond->getA() + atomOffset;
279	>	theBonds[j].b = currentBond->getB() + atomOffset;
280	>
281	>	exI = theBonds[j].a;
282	>	exJ = theBonds[j].b;
283	>
284	>	// exclude_I must always be the smaller of the pair
285	>	if (exI > exJ){
286	>	tempEx = exI;
287	>	exI = exJ;
288	>	exJ = tempEx;
289	>	}
290		#ifdef IS_MPI
291	<	tempEx = exI;
292	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	<	tempEx = exJ;
294	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295	<
296	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
291	>	tempEx = exI;
292	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	tempEx = exJ;
294	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295	>
296	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
297		#else  // isn't MPI
298	<
299	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
298	>
299	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
300		#endif  //is_mpi
301		}
302		excludeOffset += molInfo.nBonds;
303	<
303	>
304		//make the bends
305	<	for(j=0; j<molInfo.nBends; j++){
306	<
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	<
314	<	extras = currentBend->getExtras();
315	<	current_extra = extras;
316	<
317	<	while( current_extra != NULL ){
318	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
319	<
320	<	switch( current_extra->getType() ){
321	<
322	<	case 0:
323	<	theBends[j].ghost =
324	<	current_extra->getInt() + atomOffset;
325	<	theBends[j].isGhost = 1;
326	<	break;
327	<
328	<	case 1:
329	<	theBends[j].ghost =
330	<	(int)current_extra->getDouble() + atomOffset;
331	<	theBends[j].isGhost = 1;
332	<	break;
333	<
334	<	default:
335	<	sprintf( painCave.errMsg,
336	<	"SimSetup Error: ghostVectorSource was neither a "
337	<	"double nor an int.\n"
338	<	"-->Bend[%d] in %s\n",
339	<	j, comp_stamps[stampID]->getID() );
340	<	painCave.isFatal = 1;
341	<	simError();
305	>	for (j = 0; j < molInfo.nBends; j++){
306	>	currentBend = comp_stamps[stampID]->getBend(j);
307	>	theBends[j].a = currentBend->getA() + atomOffset;
308	>	theBends[j].b = currentBend->getB() + atomOffset;
309	>	theBends[j].c = currentBend->getC() + atomOffset;
310	>
311	>	if (currentBend->haveExtras()){
312	>	extras = currentBend->getExtras();
313	>	current_extra = extras;
314	>
315	>	while (current_extra != NULL){
316	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
317	>	switch (current_extra->getType()){
318	>	case 0:
319	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
320	>	theBends[j].isGhost = 1;
321	>	break;
322	>
323	>	case 1:
324	>	theBends[j].ghost = (int) current_extra->getDouble() +
325	>	atomOffset;
326	>	theBends[j].isGhost = 1;
327	>	break;
328	>
329	>	default:
330	>	sprintf(painCave.errMsg,
331	>	"SimSetup Error: ghostVectorSource was neither a "
332	>	"double nor an int.\n"
333	>	"-->Bend[%d] in %s\n",
334	>	j, comp_stamps[stampID]->getID());
335	>	painCave.isFatal = 1;
336	>	simError();
337	>	}
338	>	}
339	>	else{
340	>	sprintf(painCave.errMsg,
341	>	"SimSetup Error: unhandled bend assignment:\n"
342	>	"    -->%s in Bend[%d] in %s\n",
343	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
344	>	painCave.isFatal = 1;
345	>	simError();
346	>	}
347	>
348	>	current_extra = current_extra->getNext();
349	>	}
350		}
351	<	}
352	<
353	<	else{
354	<
355	<	sprintf( painCave.errMsg,
356	<	"SimSetup Error: unhandled bend assignment:\n"
357	<	"    -->%s in Bend[%d] in %s\n",
358	<	current_extra->getlhs(),
359	<	j, comp_stamps[stampID]->getID() );
360	<	painCave.isFatal = 1;
361	<	simError();
362	<	}
363	<
364	<	current_extra = current_extra->getNext();
365	<	}
366	<	}
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	<	}
351	>
352	>	if (!theBends[j].isGhost){
353	>	exI = theBends[j].a;
354	>	exJ = theBends[j].c;
355	>	}
356	>	else{
357	>	exI = theBends[j].a;
358	>	exJ = theBends[j].b;
359	>	}
360	>
361	>	// exclude_I must always be the smaller of the pair
362	>	if (exI > exJ){
363	>	tempEx = exI;
364	>	exI = exJ;
365	>	exJ = tempEx;
366	>	}
367		#ifdef IS_MPI
368	<	tempEx = exI;
369	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	<	tempEx = exJ;
371	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372	<
373	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372	>
373	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
374		#else  // isn't MPI
375	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
375	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
376		#endif  //is_mpi
377		}
378		excludeOffset += molInfo.nBends;
379	<
380	<	for(j=0; j<molInfo.nTorsions; j++){
381	<
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;
361	<	}
379	>
380	>	for (j = 0; j < molInfo.nTorsions; j++){
381	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
382	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
383	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
384	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
385	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
386	>
387	>	exI = theTorsions[j].a;
388	>	exJ = theTorsions[j].d;
389	>
390	>	// exclude_I must always be the smaller of the pair
391	>	if (exI > exJ){
392	>	tempEx = exI;
393	>	exI = exJ;
394	>	exJ = tempEx;
395	>	}
396		#ifdef IS_MPI
397	<	tempEx = exI;
398	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	<	tempEx = exJ;
400	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
401	<
402	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
397	>	tempEx = exI;
398	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	>	tempEx = exJ;
400	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
401	>
402	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
403		#else  // isn't MPI
404	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
404	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
405		#endif  //is_mpi
406		}
407		excludeOffset += molInfo.nTorsions;
408	<
409	<
408	>
409	>
410		// 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 );
411
412	<
412	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
413	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
414	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
415	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
416	>	theTorsions);
417	>
418	>
419	>	info[k].molecules[i].initialize(molInfo);
420	>
421	>
422		atomOffset += molInfo.nAtoms;
423		delete[] theBonds;
424		delete[] theBends;
425		delete[] theTorsions;
426		}
427		}
428	<
428	>
429		#ifdef IS_MPI
430	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
430	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
431		MPIcheckPoint();
432		#endif // is_mpi
433	<
433	>
434		// clean up the forcefield
435
436		the_ff->calcRcut();
437		the_ff->cleanMe();
403	–
438		}
439
440	<	void SimSetup::initFromBass( void ){
407	<
440	>	void SimSetup::initFromBass(void){
441		int i, j, k;
442		int n_cells;
443		double cellx, celly, cellz;
#	Line 418 | Line 451 | void SimSetup::initFromBass( void ){
451		vel[1] = 0.0;
452		vel[2] = 0.0;
453
454	<	temp1 = (double)tot_nmol / 4.0;
455	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
456	<	temp3 = ceil( temp2 );
454	>	temp1 = (double) tot_nmol / 4.0;
455	>	temp2 = pow(temp1, (1.0 / 3.0));
456	>	temp3 = ceil(temp2);
457
458	<	have_extra =0;
459	<	if( temp2 < temp3 ){ // we have a non-complete lattice
460	<	have_extra =1;
458	>	have_extra = 0;
459	>	if (temp2 < temp3){
460	>	// we have a non-complete lattice
461	>	have_extra = 1;
462
463	<	n_cells = (int)temp3 - 1;
463	>	n_cells = (int) temp3 - 1;
464		cellx = info[0].boxL[0] / temp3;
465		celly = info[0].boxL[1] / temp3;
466		cellz = info[0].boxL[2] / temp3;
467	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
468	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
469	<	n_per_extra = (int)ceil( temp1 );
467	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
468	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
469	>	n_per_extra = (int) ceil(temp1);
470
471	<	if( n_per_extra > 4){
472	<	sprintf( painCave.errMsg,
473	<	"SimSetup error. There has been an error in constructing"
474	<	" the non-complete lattice.\n" );
471	>	if (n_per_extra > 4){
472	>	sprintf(painCave.errMsg,
473	>	"SimSetup error. There has been an error in constructing"
474	>	" the non-complete lattice.\n");
475		painCave.isFatal = 1;
476		simError();
477		}
478		}
479		else{
480	<	n_cells = (int)temp3;
480	>	n_cells = (int) temp3;
481		cellx = info[0].boxL[0] / temp3;
482		celly = info[0].boxL[1] / temp3;
483		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 488 | void SimSetup::initFromBass( void ){
488		current_comp = 0;
489		current_atom_ndx = 0;
490
491	<	for( i=0; i < n_cells ; i++ ){
492	<	for( j=0; j < n_cells; j++ ){
493	<	for( k=0; k < n_cells; k++ ){
494	<
461	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
491	>	for (i = 0; i < n_cells ; i++){
492	>	for (j = 0; j < n_cells; j++){
493	>	for (k = 0; k < n_cells; k++){
494	>	makeElement(i * cellx, j * celly, k * cellz);
495
496	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
496	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
497
498	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
498	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
499
500	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	k * cellz + 0.5 * cellz );
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
501		}
502		}
503		}
504
505	<	if( have_extra ){
505	>	if (have_extra){
506		done = 0;
507
508		int start_ndx;
509	<	for( i=0; i < (n_cells+1) && !done; i++ ){
510	<	for( j=0; j < (n_cells+1) && !done; j++ ){
509	>	for (i = 0; i < (n_cells + 1) && !done; i++){
510	>	for (j = 0; j < (n_cells + 1) && !done; j++){
511	>	if (i < n_cells){
512	>	if (j < n_cells){
513	>	start_ndx = n_cells;
514	>	}
515	>	else
516	>	start_ndx = 0;
517	>	}
518	>	else
519	>	start_ndx = 0;
520
521	<	if( i < n_cells ){
521	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
522	>	makeElement(i * cellx, j * celly, k * cellz);
523	>	done = (current_mol >= tot_nmol);
524
525	<	if( j < n_cells ){
526	<	start_ndx = n_cells;
527	<	}
528	<	else start_ndx = 0;
529	<	}
494	<	else start_ndx = 0;
525	>	if (!done && n_per_extra > 1){
526	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
527	>	k * cellz);
528	>	done = (current_mol >= tot_nmol);
529	>	}
530
531	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
531	>	if (!done && n_per_extra > 2){
532	>	makeElement(i * cellx, j * celly + 0.5 * celly,
533	>	k * cellz + 0.5 * cellz);
534	>	done = (current_mol >= tot_nmol);
535	>	}
536
537	<	makeElement( i * cellx,
538	<	j * celly,
539	<	k * cellz );
540	<	done = ( current_mol >= tot_nmol );
541	<
542	<	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	<	}
537	>	if (!done && n_per_extra > 3){
538	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
539	>	k * cellz + 0.5 * cellz);
540	>	done = (current_mol >= tot_nmol);
541	>	}
542	>	}
543		}
544		}
545		}
546
547	<	for( i=0; i<info[0].n_atoms; i++ ){
548	<	info[0].atoms[i]->setVel( vel );
547	>	for (i = 0; i < info[0].n_atoms; i++){
548	>	info[0].atoms[i]->setVel(vel);
549		}
550		}
551
552	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
552	>	void SimSetup::makeElement(double x, double y, double z){
553		int k;
554		AtomStamp* current_atom;
555		DirectionalAtom* dAtom;
556		double rotMat[3][3];
557		double pos[3];
558
559	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
560	<
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",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
559	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
560	>	current_atom = comp_stamps[current_comp]->getAtom(k);
561	>	if (!current_atom->havePosition()){
562	>	sprintf(painCave.errMsg,
563	>	"SimSetup:initFromBass error.\n"
564	>	"\tComponent %s, atom %s does not have a position specified.\n"
565	>	"\tThe initialization routine is unable to give a start"
566	>	" position.\n",
567	>	comp_stamps[current_comp]->getID(), current_atom->getType());
568		painCave.isFatal = 1;
569		simError();
570		}
571	<
571	>
572		pos[0] = x + current_atom->getPosX();
573		pos[1] = y + current_atom->getPosY();
574		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
575
576	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
576	>	info[0].atoms[current_atom_ndx]->setPos(pos);
577
578	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
578	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
579	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
580
581		rotMat[0][0] = 1.0;
582		rotMat[0][1] = 0.0;
#	Line 575 | Line 590 | void SimSetup::makeElement( double x, double y, double
590		rotMat[2][1] = 0.0;
591		rotMat[2][2] = 1.0;
592
593	<	dAtom->setA( rotMat );
593	>	dAtom->setA(rotMat);
594		}
595
596		current_atom_ndx++;
#	Line 584 | Line 599 | void SimSetup::makeElement( double x, double y, double
599		current_mol++;
600		current_comp_mol++;
601
602	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
602	>	if (current_comp_mol >= components_nmol[current_comp]){
603		current_comp_mol = 0;
604		current_comp++;
605		}
606		}
607
608
609	<	void SimSetup::gatherInfo( void ){
610	<	int i,j,k;
609	>	void SimSetup::gatherInfo(void){
610	>	int i;
611
612		ensembleCase = -1;
613		ffCase = -1;
614
615		// set the easy ones first
616
617	<	for( i=0; i<nInfo; i++){
617	>	for (i = 0; i < nInfo; i++){
618		info[i].target_temp = globals->getTargetTemp();
619		info[i].dt = globals->getDt();
620		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 624 | void SimSetup::gatherInfo( void ){
624
625		// get the forceField
626
627	<	strcpy( force_field, globals->getForceField() );
627	>	strcpy(force_field, globals->getForceField());
628
629	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
630	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
631	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
629	>	if (!strcasecmp(force_field, "DUFF")){
630	>	ffCase = FF_DUFF;
631	>	}
632	>	else if (!strcasecmp(force_field, "LJ")){
633	>	ffCase = FF_LJ;
634	>	}
635	>	else if (!strcasecmp(force_field, "EAM")){
636	>	ffCase = FF_EAM;
637	>	}
638		else{
639	<	sprintf( painCave.errMsg,
640	<	"SimSetup Error. Unrecognized force field -> %s\n",
641	<	force_field );
642	<	painCave.isFatal = 1;
623	<	simError();
639	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
640	>	force_field);
641	>	painCave.isFatal = 1;
642	>	simError();
643		}
644
645	<	// get the ensemble
645	>	// get the ensemble
646
647	<	strcpy( ensemble, globals->getEnsemble() );
647	>	strcpy(ensemble, globals->getEnsemble());
648
649	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
650	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
651	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
649	>	if (!strcasecmp(ensemble, "NVE")){
650	>	ensembleCase = NVE_ENS;
651	>	}
652	>	else if (!strcasecmp(ensemble, "NVT")){
653	>	ensembleCase = NVT_ENS;
654	>	}
655	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
656		ensembleCase = NPTi_ENS;
657	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
658	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
659	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
657	>	}
658	>	else if (!strcasecmp(ensemble, "NPTf")){
659	>	ensembleCase = NPTf_ENS;
660	>	}
661	>	else if (!strcasecmp(ensemble, "NPTxyz")){
662	>	ensembleCase = NPTxyz_ENS;
663	>	}
664		else{
665	<	sprintf( painCave.errMsg,
666	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
667	<	"reverting to NVE for this simulation.\n",
668	<	ensemble );
669	<	painCave.isFatal = 0;
670	<	simError();
671	<	strcpy( ensemble, "NVE" );
672	<	ensembleCase = NVE_ENS;
665	>	sprintf(painCave.errMsg,
666	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
667	>	"\treverting to NVE for this simulation.\n",
668	>	ensemble);
669	>	painCave.isFatal = 0;
670	>	simError();
671	>	strcpy(ensemble, "NVE");
672	>	ensembleCase = NVE_ENS;
673		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
674
675	+	for (i = 0; i < nInfo; i++){
676	+	strcpy(info[i].ensemble, ensemble);
677	+
678		// get the mixing rule
679
680	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
680	>	strcpy(info[i].mixingRule, globals->getMixingRule());
681		info[i].usePBC = globals->getPBC();
682		}
683	<
683	>
684		// get the components and calculate the tot_nMol and indvidual n_mol
685	<
685	>
686		the_components = globals->getComponents();
687		components_nmol = new int[n_components];
688
689
690	<	if( !globals->haveNMol() ){
690	>	if (!globals->haveNMol()){
691		// we don't have the total number of molecules, so we assume it is
692		// given in each component
693
694		tot_nmol = 0;
695	<	for( i=0; i<n_components; i++ ){
696	<
697	<	if( !the_components[i]->haveNMol() ){
698	<	// we have a problem
699	<	sprintf( painCave.errMsg,
700	<	"SimSetup Error. No global NMol or component NMol"
701	<	" given. Cannot calculate the number of atoms.\n" );
702	<	painCave.isFatal = 1;
677	<	simError();
695	>	for (i = 0; i < n_components; i++){
696	>	if (!the_components[i]->haveNMol()){
697	>	// we have a problem
698	>	sprintf(painCave.errMsg,
699	>	"SimSetup Error. No global NMol or component NMol given.\n"
700	>	"\tCannot calculate the number of atoms.\n");
701	>	painCave.isFatal = 1;
702	>	simError();
703		}
704
705		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 707 | void SimSetup::gatherInfo( void ){
707		}
708		}
709		else{
710	<	sprintf( painCave.errMsg,
711	<	"SimSetup error.\n"
712	<	"\tSorry, the ability to specify total"
713	<	" nMols and then give molfractions in the components\n"
714	<	"\tis not currently supported."
715	<	" Please give nMol in the components.\n" );
710	>	sprintf(painCave.errMsg,
711	>	"SimSetup error.\n"
712	>	"\tSorry, the ability to specify total"
713	>	" nMols and then give molfractions in the components\n"
714	>	"\tis not currently supported."
715	>	" Please give nMol in the components.\n");
716		painCave.isFatal = 1;
717		simError();
718		}
719
720	<	// set the status, sample, and thermal kick times
721	<
722	<	for(i=0; i<nInfo; i++){
720	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
721	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
722	>	sprintf(painCave.errMsg,
723	>	"Sample time is not divisible by dt.\n"
724	>	"\tThis will result in samples that are not uniformly\n"
725	>	"\tdistributed in time.  If this is a problem, change\n"
726	>	"\tyour sampleTime variable.\n");
727	>	painCave.isFatal = 0;
728	>	simError();
729	>	}
730
731	<	if( globals->haveSampleTime() ){
731	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
732	>	sprintf(painCave.errMsg,
733	>	"Status time is not divisible by dt.\n"
734	>	"\tThis will result in status reports that are not uniformly\n"
735	>	"\tdistributed in time.  If this is a problem, change \n"
736	>	"\tyour statusTime variable.\n");
737	>	painCave.isFatal = 0;
738	>	simError();
739	>	}
740	>
741	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
742	>	sprintf(painCave.errMsg,
743	>	"Thermal time is not divisible by dt.\n"
744	>	"\tThis will result in thermalizations that are not uniformly\n"
745	>	"\tdistributed in time.  If this is a problem, change \n"
746	>	"\tyour thermalTime variable.\n");
747	>	painCave.isFatal = 0;
748	>	simError();
749	>	}
750	>
751	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
752	>	sprintf(painCave.errMsg,
753	>	"Reset time is not divisible by dt.\n"
754	>	"\tThis will result in integrator resets that are not uniformly\n"
755	>	"\tdistributed in time.  If this is a problem, change\n"
756	>	"\tyour resetTime variable.\n");
757	>	painCave.isFatal = 0;
758	>	simError();
759	>	}
760	>
761	>	// set the status, sample, and thermal kick times
762	>
763	>	for (i = 0; i < nInfo; i++){
764	>	if (globals->haveSampleTime()){
765		info[i].sampleTime = globals->getSampleTime();
766		info[i].statusTime = info[i].sampleTime;
767		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 771 | void SimSetup::gatherInfo( void ){
771		info[i].statusTime = info[i].sampleTime;
772		info[i].thermalTime = info[i].sampleTime;
773		}
774	<
775	<	if( globals->haveStatusTime() ){
774	>
775	>	if (globals->haveStatusTime()){
776		info[i].statusTime = globals->getStatusTime();
777		}
778	<
779	<	if( globals->haveThermalTime() ){
778	>
779	>	if (globals->haveThermalTime()){
780		info[i].thermalTime = globals->getThermalTime();
781		}
782
783	+	info[i].resetIntegrator = 0;
784	+	if( globals->haveResetTime() ){
785	+	info[i].resetTime = globals->getResetTime();
786	+	info[i].resetIntegrator = 1;
787	+	}
788	+
789		// check for the temperature set flag
790	+
791	+	if (globals->haveTempSet())
792	+	info[i].setTemp = globals->getTempSet();
793
794	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
794	>	// check for the extended State init
795	>
796	>	info[i].useInitXSstate = globals->getUseInitXSstate();
797	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
798
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 );
799		}
800	<	else{
801	<	if( !globals->haveBoxX() ){
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup error, no periodic BoxX size given.\n" );
804	<	painCave.isFatal = 1;
805	<	simError();
800	>
801	>	//setup seed for random number generator
802	>	int seedValue;
803	>
804	>	if (globals->haveSeed()){
805	>	seedValue = globals->getSeed();
806	>
807	>	if(seedValue / 1E9 == 0){
808	>	sprintf(painCave.errMsg,
809	>	"Seed for sprng library should contain at least 9 digits\n"
810	>	"OOPSE will generate a seed for user\n");
811	>	painCave.isFatal = 0;
812	>	simError();
813	>
814	>	//using seed generated by system instead of invalid seed set by user
815	>	#ifndef IS_MPI
816	>	seedValue = make_sprng_seed();
817	>	#else
818	>	if (worldRank == 0){
819	>	seedValue = make_sprng_seed();
820		}
821	<	boxVector[0] = globals->getBoxX();
822	<
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 );
821	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
822	>	#endif
823		}
824	+	}//end of if branch of globals->haveSeed()
825	+	else{
826	+
827	+	#ifndef IS_MPI
828	+	seedValue = make_sprng_seed();
829	+	#else
830	+	if (worldRank == 0){
831	+	seedValue = make_sprng_seed();
832	+	}
833	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
834	+	#endif
835	+	}//end of globals->haveSeed()
836
837	+	for (int i = 0; i < nInfo; i++){
838	+	info[i].setSeed(seedValue);
839		}
840	<
840	>
841		#ifdef IS_MPI
842	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
842	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
843		MPIcheckPoint();
844		#endif // is_mpi
776	–
845		}
846
847
848	<	void SimSetup::finalInfoCheck( void ){
848	>	void SimSetup::finalInfoCheck(void){
849		int index;
850		int usesDipoles;
851		int i;
852
853	<	for(i=0; i<nInfo; i++){
853	>	for (i = 0; i < nInfo; i++){
854		// check electrostatic parameters
855	<
855	>
856		index = 0;
857		usesDipoles = 0;
858	<	while( (index < info[i].n_atoms) && !usesDipoles ){
858	>	while ((index < info[i].n_atoms) && !usesDipoles){
859		usesDipoles = (info[i].atoms[index])->hasDipole();
860		index++;
861		}
862	<
862	>
863		#ifdef IS_MPI
864		int myUse = usesDipoles;
865	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
865	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866		#endif //is_mpi
867	<
867	>
868		double theEcr, theEst;
869	<
870	<	if (globals->getUseRF() ) {
869	>
870	>	if (globals->getUseRF()){
871		info[i].useReactionField = 1;
872	<
873	<	if( !globals->haveECR() ){
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Warning: using default value of 1/2 the smallest "
876	<	"box length for the electrostaticCutoffRadius.\n"
877	<	"I hope you have a very fast processor!\n");
878	<	painCave.isFatal = 0;
879	<	simError();
880	<	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();
872	>
873	>	if (!globals->haveECR()){
874	>	sprintf(painCave.errMsg,
875	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
876	>	"\tOOPSE will use a default value of 15.0 angstroms"
877	>	"\tfor the electrostaticCutoffRadius.\n");
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEcr = 15.0;
881		}
882	<
883	<	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();
882	>	else{
883	>	theEcr = globals->getECR();
884		}
885	<
886	<	info[i].setEcr( theEcr, theEst );
887	<
888	<	if(!globals->haveDielectric() ){
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Error: You are trying to use Reaction Field without"
891	<	"setting a dielectric constant!\n"
892	<	);
893	<	painCave.isFatal = 1;
894	<	simError();
885	>
886	>	if (!globals->haveEST()){
887	>	sprintf(painCave.errMsg,
888	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
889	>	"\tOOPSE will use a default value of\n"
890	>	"\t0.05 * electrostaticCutoffRadius\n"
891	>	"\tfor the electrostaticSkinThickness\n");
892	>	painCave.isFatal = 0;
893	>	simError();
894	>	theEst = 0.05 * theEcr;
895		}
896	<	info[i].dielectric = globals->getDielectric();
897	<	}
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 );
896	>	else{
897	>	theEst = globals->getEST();
898		}
879	–	}
880	–	}
899
900	+	info[i].setDefaultEcr(theEcr, theEst);
901	+
902	+	if (!globals->haveDielectric()){
903	+	sprintf(painCave.errMsg,
904	+	"SimSetup Error: No Dielectric constant was set.\n"
905	+	"\tYou are trying to use Reaction Field without"
906	+	"\tsetting a dielectric constant!\n");
907	+	painCave.isFatal = 1;
908	+	simError();
909	+	}
910	+	info[i].dielectric = globals->getDielectric();
911	+	}
912	+	else{
913	+	if (usesDipoles){
914	+	if (!globals->haveECR()){
915	+	sprintf(painCave.errMsg,
916	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
917	+	"\tOOPSE will use a default value of 15.0 angstroms"
918	+	"\tfor the electrostaticCutoffRadius.\n");
919	+	painCave.isFatal = 0;
920	+	simError();
921	+	theEcr = 15.0;
922	+	}
923	+	else{
924	+	theEcr = globals->getECR();
925	+	}
926	+
927	+	if (!globals->haveEST()){
928	+	sprintf(painCave.errMsg,
929	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
930	+	"\tOOPSE will use a default value of\n"
931	+	"\t0.05 * electrostaticCutoffRadius\n"
932	+	"\tfor the electrostaticSkinThickness\n");
933	+	painCave.isFatal = 0;
934	+	simError();
935	+	theEst = 0.05 * theEcr;
936	+	}
937	+	else{
938	+	theEst = globals->getEST();
939	+	}
940	+
941	+	info[i].setDefaultEcr(theEcr, theEst);
942	+	}
943	+	}
944	+	}
945		#ifdef IS_MPI
946	<	strcpy( checkPointMsg, "post processing checks out" );
946	>	strcpy(checkPointMsg, "post processing checks out");
947		MPIcheckPoint();
948		#endif // is_mpi
886	–
949		}
888	–
889	–	void SimSetup::initSystemCoords( void ){
890	–	int i;
950
951	+	void SimSetup::initSystemCoords(void){
952	+	int i;
953	+
954		char* inName;
955
956	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
956	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
957
958	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
959	<
960	<	if( globals->haveInitialConfig() ){
961	<
958	>	for (i = 0; i < info[0].n_atoms; i++)
959	>	info[0].atoms[i]->setCoords();
960	>
961	>	if (globals->haveInitialConfig()){
962		InitializeFromFile* fileInit;
963		#ifdef IS_MPI // is_mpi
964	<	if( worldRank == 0 ){
964	>	if (worldRank == 0){
965		#endif //is_mpi
966		inName = globals->getInitialConfig();
967	<	double* tempDouble = new double[1000000];
906	<	fileInit = new InitializeFromFile( inName );
967	>	fileInit = new InitializeFromFile(inName);
968		#ifdef IS_MPI
969	<	}else fileInit = new InitializeFromFile( NULL );
969	>	}
970	>	else
971	>	fileInit = new InitializeFromFile(NULL);
972		#endif
973	<	fileInit->readInit( info ); // default velocities on
974	<
973	>	fileInit->readInit(info); // default velocities on
974	>
975		delete fileInit;
976		}
977		else{
978
916	–	#ifdef IS_MPI
917	–
979		// no init from bass
980
981	<	sprintf( painCave.errMsg,
982	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
983	<	painCave.isFatal;
981	>	sprintf(painCave.errMsg,
982	>	"Cannot intialize a simulation without an initial configuration file.\n");
983	>	painCave.isFatal = 1;;
984		simError();
985
925	–	#else
926	–
927	–	initFromBass();
928	–
929	–
930	–	#endif
986		}
987	<
987	>
988		#ifdef IS_MPI
989	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
989	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
990		MPIcheckPoint();
991		#endif // is_mpi
937	–
992		}
993
994
995	<	void SimSetup::makeOutNames( void ){
942	<
995	>	void SimSetup::makeOutNames(void){
996		int k;
997
945	–
946	–	for(k=0; k<nInfo; k++){
998
999	+	for (k = 0; k < nInfo; k++){
1000		#ifdef IS_MPI
1001	<	if( worldRank == 0 ){
1001	>	if (worldRank == 0){
1002		#endif // is_mpi
1003	<
1004	<	if( globals->haveFinalConfig() ){
1005	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1003	>
1004	>	if (globals->haveFinalConfig()){
1005	>	strcpy(info[k].finalName, globals->getFinalConfig());
1006		}
1007		else{
1008	<	strcpy( info[k].finalName, inFileName );
1009	<	char* endTest;
1010	<	int nameLength = strlen( info[k].finalName );
1011	<	endTest = &(info[k].finalName[nameLength - 5]);
1012	<	if( !strcmp( endTest, ".bass" ) ){
1013	<	strcpy( endTest, ".eor" );
1014	<	}
1015	<	else if( !strcmp( endTest, ".BASS" ) ){
1016	<	strcpy( endTest, ".eor" );
1017	<	}
1018	<	else{
1019	<	endTest = &(info[k].finalName[nameLength - 4]);
1020	<	if( !strcmp( endTest, ".bss" ) ){
1021	<	strcpy( endTest, ".eor" );
1022	<	}
1023	<	else if( !strcmp( endTest, ".mdl" ) ){
1024	<	strcpy( endTest, ".eor" );
1025	<	}
1026	<	else{
1027	<	strcat( info[k].finalName, ".eor" );
1028	<	}
1029	<	}
1008	>	strcpy(info[k].finalName, inFileName);
1009	>	char* endTest;
1010	>	int nameLength = strlen(info[k].finalName);
1011	>	endTest = &(info[k].finalName[nameLength - 5]);
1012	>	if (!strcmp(endTest, ".bass")){
1013	>	strcpy(endTest, ".eor");
1014	>	}
1015	>	else if (!strcmp(endTest, ".BASS")){
1016	>	strcpy(endTest, ".eor");
1017	>	}
1018	>	else{
1019	>	endTest = &(info[k].finalName[nameLength - 4]);
1020	>	if (!strcmp(endTest, ".bss")){
1021	>	strcpy(endTest, ".eor");
1022	>	}
1023	>	else if (!strcmp(endTest, ".mdl")){
1024	>	strcpy(endTest, ".eor");
1025	>	}
1026	>	else{
1027	>	strcat(info[k].finalName, ".eor");
1028	>	}
1029	>	}
1030		}
1031	<
1031	>
1032		// make the sample and status out names
1033	<
1034	<	strcpy( info[k].sampleName, inFileName );
1033	>
1034	>	strcpy(info[k].sampleName, inFileName);
1035		char* endTest;
1036	<	int nameLength = strlen( info[k].sampleName );
1036	>	int nameLength = strlen(info[k].sampleName);
1037		endTest = &(info[k].sampleName[nameLength - 5]);
1038	<	if( !strcmp( endTest, ".bass" ) ){
1039	<	strcpy( endTest, ".dump" );
1038	>	if (!strcmp(endTest, ".bass")){
1039	>	strcpy(endTest, ".dump");
1040		}
1041	<	else if( !strcmp( endTest, ".BASS" ) ){
1042	<	strcpy( endTest, ".dump" );
1041	>	else if (!strcmp(endTest, ".BASS")){
1042	>	strcpy(endTest, ".dump");
1043		}
1044		else{
1045	<	endTest = &(info[k].sampleName[nameLength - 4]);
1046	<	if( !strcmp( endTest, ".bss" ) ){
1047	<	strcpy( endTest, ".dump" );
1048	<	}
1049	<	else if( !strcmp( endTest, ".mdl" ) ){
1050	<	strcpy( endTest, ".dump" );
1051	<	}
1052	<	else{
1053	<	strcat( info[k].sampleName, ".dump" );
1054	<	}
1045	>	endTest = &(info[k].sampleName[nameLength - 4]);
1046	>	if (!strcmp(endTest, ".bss")){
1047	>	strcpy(endTest, ".dump");
1048	>	}
1049	>	else if (!strcmp(endTest, ".mdl")){
1050	>	strcpy(endTest, ".dump");
1051	>	}
1052	>	else{
1053	>	strcat(info[k].sampleName, ".dump");
1054	>	}
1055		}
1056	<
1057	<	strcpy( info[k].statusName, inFileName );
1058	<	nameLength = strlen( info[k].statusName );
1056	>
1057	>	strcpy(info[k].statusName, inFileName);
1058	>	nameLength = strlen(info[k].statusName);
1059		endTest = &(info[k].statusName[nameLength - 5]);
1060	<	if( !strcmp( endTest, ".bass" ) ){
1061	<	strcpy( endTest, ".stat" );
1060	>	if (!strcmp(endTest, ".bass")){
1061	>	strcpy(endTest, ".stat");
1062		}
1063	<	else if( !strcmp( endTest, ".BASS" ) ){
1064	<	strcpy( endTest, ".stat" );
1063	>	else if (!strcmp(endTest, ".BASS")){
1064	>	strcpy(endTest, ".stat");
1065		}
1066		else{
1067	<	endTest = &(info[k].statusName[nameLength - 4]);
1068	<	if( !strcmp( endTest, ".bss" ) ){
1069	<	strcpy( endTest, ".stat" );
1070	<	}
1071	<	else if( !strcmp( endTest, ".mdl" ) ){
1072	<	strcpy( endTest, ".stat" );
1073	<	}
1074	<	else{
1075	<	strcat( info[k].statusName, ".stat" );
1076	<	}
1067	>	endTest = &(info[k].statusName[nameLength - 4]);
1068	>	if (!strcmp(endTest, ".bss")){
1069	>	strcpy(endTest, ".stat");
1070	>	}
1071	>	else if (!strcmp(endTest, ".mdl")){
1072	>	strcpy(endTest, ".stat");
1073	>	}
1074	>	else{
1075	>	strcat(info[k].statusName, ".stat");
1076	>	}
1077		}
1078	<
1078	>
1079		#ifdef IS_MPI
1080	+
1081		}
1082		#endif // is_mpi
1083		}
1084		}
1085
1086
1087	<	void SimSetup::sysObjectsCreation( void ){
1088	<
1089	<	int i,k;
1037	<
1087	>	void SimSetup::sysObjectsCreation(void){
1088	>	int i, k;
1089	>
1090		// create the forceField
1091
1092		createFF();
#	Line 1049 | Line 1101 | void SimSetup::sysObjectsCreation( void ){
1101
1102		#ifdef IS_MPI
1103		// divide the molecules among the processors
1104	<
1104	>
1105		mpiMolDivide();
1106		#endif //is_mpi
1107	<
1107	>
1108		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1109	<
1109	>
1110		makeSysArrays();
1111
1112		// make and initialize the molecules (all but atomic coordinates)
1113	<
1113	>
1114		makeMolecules();
1115	<
1116	<	for(k=0; k<nInfo; k++){
1115	>
1116	>	for (k = 0; k < nInfo; k++){
1117		info[k].identArray = new int[info[k].n_atoms];
1118	<	for(i=0; i<info[k].n_atoms; i++){
1118	>	for (i = 0; i < info[k].n_atoms; i++){
1119		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1120		}
1121		}
1122		}
1123
1124
1125	<	void SimSetup::createFF( void ){
1125	>	void SimSetup::createFF(void){
1126	>	switch (ffCase){
1127	>	case FF_DUFF:
1128	>	the_ff = new DUFF();
1129	>	break;
1130
1131	<	switch( ffCase ){
1131	>	case FF_LJ:
1132	>	the_ff = new LJFF();
1133	>	break;
1134
1135	<	case FF_DUFF:
1136	<	the_ff = new DUFF();
1137	<	break;
1135	>	case FF_EAM:
1136	>	the_ff = new EAM_FF();
1137	>	break;
1138
1139	<	case FF_LJ:
1140	<	the_ff = new LJFF();
1141	<	break;
1142	<
1143	<	case FF_EAM:
1086	<	the_ff = new EAM_FF();
1087	<	break;
1088	<
1089	<	default:
1090	<	sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	<	painCave.isFatal = 1;
1093	<	simError();
1139	>	default:
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144		}
1145
1146		#ifdef IS_MPI
1147	<	strcpy( checkPointMsg, "ForceField creation successful" );
1147	>	strcpy(checkPointMsg, "ForceField creation successful");
1148		MPIcheckPoint();
1149		#endif // is_mpi
1100	–
1150		}
1151
1152
1153	<	void SimSetup::compList( void ){
1105	<
1153	>	void SimSetup::compList(void){
1154		int i;
1155		char* id;
1156		LinkedMolStamp* headStamp = new LinkedMolStamp();
1157		LinkedMolStamp* currentStamp = NULL;
1158	<	comp_stamps = new MoleculeStamp*[n_components];
1159	<
1158	>	comp_stamps = new MoleculeStamp * [n_components];
1159	>
1160		// make an array of molecule stamps that match the components used.
1161		// also extract the used stamps out into a separate linked list
1162	<
1163	<	for(i=0; i<nInfo; i++){
1162	>
1163	>	for (i = 0; i < nInfo; i++){
1164		info[i].nComponents = n_components;
1165		info[i].componentsNmol = components_nmol;
1166		info[i].compStamps = comp_stamps;
1167		info[i].headStamp = headStamp;
1168		}
1121	–
1169
1123	–	for( i=0; i<n_components; i++ ){
1170
1171	+	for (i = 0; i < n_components; i++){
1172		id = the_components[i]->getType();
1173		comp_stamps[i] = NULL;
1174	<
1174	>
1175		// check to make sure the component isn't already in the list
1176
1177	<	comp_stamps[i] = headStamp->match( id );
1178	<	if( comp_stamps[i] == NULL ){
1132	<
1177	>	comp_stamps[i] = headStamp->match(id);
1178	>	if (comp_stamps[i] == NULL){
1179		// extract the component from the list;
1180	<
1181	<	currentStamp = stamps->extractMolStamp( id );
1182	<	if( currentStamp == NULL ){
1183	<	sprintf( painCave.errMsg,
1184	<	"SimSetup error: Component \"%s\" was not found in the "
1185	<	"list of declared molecules\n",
1186	<	id );
1187	<	painCave.isFatal = 1;
1188	<	simError();
1180	>
1181	>	currentStamp = stamps->extractMolStamp(id);
1182	>	if (currentStamp == NULL){
1183	>	sprintf(painCave.errMsg,
1184	>	"SimSetup error: Component \"%s\" was not found in the "
1185	>	"list of declared molecules\n",
1186	>	id);
1187	>	painCave.isFatal = 1;
1188	>	simError();
1189		}
1190	<
1191	<	headStamp->add( currentStamp );
1192	<	comp_stamps[i] = headStamp->match( id );
1190	>
1191	>	headStamp->add(currentStamp);
1192	>	comp_stamps[i] = headStamp->match(id);
1193		}
1194		}
1195
1196		#ifdef IS_MPI
1197	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1197	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1198		MPIcheckPoint();
1199		#endif // is_mpi
1200	+	}
1201
1202	+	void SimSetup::calcSysValues(void){
1203	+	int i;
1204
1205	<	}
1205	>	int* molMembershipArray;
1206
1158	–	void SimSetup::calcSysValues( void ){
1159	–	int i, j, k;
1160	–
1161	–	int *molMembershipArray;
1162	–
1207		tot_atoms = 0;
1208		tot_bonds = 0;
1209		tot_bends = 0;
1210		tot_torsions = 0;
1211	<	for( i=0; i<n_components; i++ ){
1212	<
1213	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1214	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1211	>	for (i = 0; i < n_components; i++){
1212	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1213	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1214	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1215		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1216		}
1217	<
1217	>
1218		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1219		molMembershipArray = new int[tot_atoms];
1220	<
1221	<	for(i=0; i<nInfo; i++){
1220	>
1221	>	for (i = 0; i < nInfo; i++){
1222		info[i].n_atoms = tot_atoms;
1223		info[i].n_bonds = tot_bonds;
1224		info[i].n_bends = tot_bends;
1225		info[i].n_torsions = tot_torsions;
1226		info[i].n_SRI = tot_SRI;
1227		info[i].n_mol = tot_nmol;
1228	<
1228	>
1229		info[i].molMembershipArray = molMembershipArray;
1230	<	}
1230	>	}
1231		}
1232
1233		#ifdef IS_MPI
1234
1235	<	void SimSetup::mpiMolDivide( void ){
1193	<
1235	>	void SimSetup::mpiMolDivide(void){
1236		int i, j, k;
1237		int localMol, allMol;
1238		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1239
1240	<	mpiSim = new mpiSimulation( info );
1241	<
1240	>	mpiSim = new mpiSimulation(info);
1241	>
1242		globalIndex = mpiSim->divideLabor();
1243
1244		// set up the local variables
1245	<
1245	>
1246		mol2proc = mpiSim->getMolToProcMap();
1247		molCompType = mpiSim->getMolComponentType();
1248	<
1248	>
1249		allMol = 0;
1250		localMol = 0;
1251		local_atoms = 0;
#	Line 1213 | Line 1255 | void SimSetup::mpiMolDivide( void ){
1255		globalAtomIndex = 0;
1256
1257
1258	<	for( i=0; i<n_components; i++ ){
1259	<
1260	<	for( j=0; j<components_nmol[i]; j++ ){
1261	<
1262	<	if( mol2proc[allMol] == worldRank ){
1263	<
1264	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1265	<	local_bonds +=    comp_stamps[i]->getNBonds();
1224	<	local_bends +=    comp_stamps[i]->getNBends();
1225	<	local_torsions += comp_stamps[i]->getNTorsions();
1226	<	localMol++;
1258	>	for (i = 0; i < n_components; i++){
1259	>	for (j = 0; j < components_nmol[i]; j++){
1260	>	if (mol2proc[allMol] == worldRank){
1261	>	local_atoms += comp_stamps[i]->getNAtoms();
1262	>	local_bonds += comp_stamps[i]->getNBonds();
1263	>	local_bends += comp_stamps[i]->getNBends();
1264	>	local_torsions += comp_stamps[i]->getNTorsions();
1265	>	localMol++;
1266		}
1267	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1267	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1268		info[0].molMembershipArray[globalAtomIndex] = allMol;
1269		globalAtomIndex++;
1270		}
1271
1272	<	allMol++;
1272	>	allMol++;
1273		}
1274		}
1275		local_SRI = local_bonds + local_bends + local_torsions;
1276	<
1276	>
1277		info[0].n_atoms = mpiSim->getMyNlocal();
1278	<
1279	<	if( local_atoms != info[0].n_atoms ){
1280	<	sprintf( painCave.errMsg,
1281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1282	<	" localAtom (%d) are not equal.\n",
1283	<	info[0].n_atoms,
1245	<	local_atoms );
1278	>
1279	>	if (local_atoms != info[0].n_atoms){
1280	>	sprintf(painCave.errMsg,
1281	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1282	>	"\tlocalAtom (%d) are not equal.\n",
1283	>	info[0].n_atoms, local_atoms);
1284		painCave.isFatal = 1;
1285		simError();
1286		}
#	Line 1253 | Line 1291 | void SimSetup::mpiMolDivide( void ){
1291		info[0].n_SRI = local_SRI;
1292		info[0].n_mol = localMol;
1293
1294	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1294	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1295		MPIcheckPoint();
1296		}
1297	<
1297	>
1298		#endif // is_mpi
1299
1300
1301	<	void SimSetup::makeSysArrays( void ){
1302	<	int i, j, k, l;
1301	>	void SimSetup::makeSysArrays(void){
1302	>
1303	>	#ifndef IS_MPI
1304	>	int k, j;
1305	>	#endif // is_mpi
1306	>	int i, l;
1307
1308		Atom** the_atoms;
1309		Molecule* the_molecules;
1310		Exclude** the_excludes;
1311
1312	<
1313	<	for(l=0; l<nInfo; l++){
1272	<
1312	>
1313	>	for (l = 0; l < nInfo; l++){
1314		// create the atom and short range interaction arrays
1315	<
1316	<	the_atoms = new Atom*[info[l].n_atoms];
1315	>
1316	>	the_atoms = new Atom * [info[l].n_atoms];
1317		the_molecules = new Molecule[info[l].n_mol];
1318		int molIndex;
1319
1320		// initialize the molecule's stampID's
1321	<
1321	>
1322		#ifdef IS_MPI
1323	<
1324	<
1323	>
1324	>
1325		molIndex = 0;
1326	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1327	<
1328	<	if(mol2proc[i] == worldRank ){
1329	<	the_molecules[molIndex].setStampID( molCompType[i] );
1330	<	the_molecules[molIndex].setMyIndex( molIndex );
1331	<	the_molecules[molIndex].setGlobalIndex( i );
1291	<	molIndex++;
1326	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1327	>	if (mol2proc[i] == worldRank){
1328	>	the_molecules[molIndex].setStampID(molCompType[i]);
1329	>	the_molecules[molIndex].setMyIndex(molIndex);
1330	>	the_molecules[molIndex].setGlobalIndex(i);
1331	>	molIndex++;
1332		}
1333		}
1334	<
1334	>
1335		#else // is_mpi
1336	<
1336	>
1337		molIndex = 0;
1338		globalAtomIndex = 0;
1339	<	for(i=0; i<n_components; i++){
1340	<	for(j=0; j<components_nmol[i]; j++ ){
1341	<	the_molecules[molIndex].setStampID( i );
1342	<	the_molecules[molIndex].setMyIndex( molIndex );
1343	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1344	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1345	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1346	<	globalAtomIndex++;
1347	<	}
1348	<	molIndex++;
1339	>	for (i = 0; i < n_components; i++){
1340	>	for (j = 0; j < components_nmol[i]; j++){
1341	>	the_molecules[molIndex].setStampID(i);
1342	>	the_molecules[molIndex].setMyIndex(molIndex);
1343	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1344	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1345	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1346	>	globalAtomIndex++;
1347	>	}
1348	>	molIndex++;
1349		}
1350		}
1351	<
1352	<
1351	>
1352	>
1353		#endif // is_mpi
1354
1355
1356	<	if( info[l].n_SRI ){
1317	<
1356	>	if (info[l].n_SRI){
1357		Exclude::createArray(info[l].n_SRI);
1358	<	the_excludes = new Exclude*[info[l].n_SRI];
1359	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1360	<	the_excludes[ex] = new Exclude(ex);
1358	>	the_excludes = new Exclude * [info[l].n_SRI];
1359	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1360	>	the_excludes[ex] = new Exclude(ex);
1361		}
1362		info[l].globalExcludes = new int;
1363		info[l].n_exclude = info[l].n_SRI;
1364		}
1365		else{
1366	<
1367	<	Exclude::createArray( 1 );
1329	<	the_excludes = new Exclude*;
1366	>	Exclude::createArray(1);
1367	>	the_excludes = new Exclude * ;
1368		the_excludes[0] = new Exclude(0);
1369	<	the_excludes[0]->setPair( 0,0 );
1369	>	the_excludes[0]->setPair(0, 0);
1370		info[l].globalExcludes = new int;
1371		info[l].globalExcludes[0] = 0;
1372		info[l].n_exclude = 0;
#	Line 1341 | Line 1379 | void SimSetup::makeSysArrays( void ){
1379		info[l].nGlobalExcludes = 0;
1380		info[l].excludes = the_excludes;
1381
1382	<	the_ff->setSimInfo( info );
1345	<
1382	>	the_ff->setSimInfo(info);
1383		}
1384		}
1385
1386	<	void SimSetup::makeIntegrator( void ){
1350	<
1386	>	void SimSetup::makeIntegrator(void){
1387		int k;
1388
1389	<	NVT<RealIntegrator>*  myNVT = NULL;
1390	<	NPTi<RealIntegrator>* myNPTi = NULL;
1391	<	NPTf<RealIntegrator>* myNPTf = NULL;
1392	<	NPTim<RealIntegrator>* myNPTim = NULL;
1393	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1394	<
1395	<	for(k=0; k<nInfo; k++){
1396	<
1397	<	switch( ensembleCase ){
1398	<
1399	<	case NVE_ENS:
1400	<	if (globals->haveZconstraints()){
1401	<	setupZConstraint(info[k]);
1402	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1403	<	}
1389	>	NVE<RealIntegrator>* myNVE = NULL;
1390	>	NVT<RealIntegrator>* myNVT = NULL;
1391	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1392	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1393	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1394	>
1395	>	for (k = 0; k < nInfo; k++){
1396	>	switch (ensembleCase){
1397	>	case NVE_ENS:
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1401	>	}
1402	>	else{
1403	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1404	>	}
1405	>
1406	>	info->the_integrator = myNVE;
1407	>	break;
1408
1409	<	else
1410	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1411	<	break;
1412	<
1413	<	case NVT_ENS:
1414	<	if (globals->haveZconstraints()){
1415	<	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 );
1409	>	case NVT_ENS:
1410	>	if (globals->haveZconstraints()){
1411	>	setupZConstraint(info[k]);
1412	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1413	>	}
1414	>	else
1415	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1416
1417		myNVT->setTargetTemp(globals->getTargetTemp());
1418	<
1419	<	if (globals->haveTauThermostat())
1418	>
1419	>	if (globals->haveTauThermostat())
1420		myNVT->setTauThermostat(globals->getTauThermostat());
1421	<
1422	<	else {
1423	<	sprintf( painCave.errMsg,
1424	<	"SimSetup error: If you use the NVT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1421	>	else{
1422	>	sprintf(painCave.errMsg,
1423	>	"SimSetup error: If you use the NVT\n"
1424	>	"\tensemble, you must set tauThermostat.\n");
1425		painCave.isFatal = 1;
1426		simError();
1427		}
1428	+
1429	+	info->the_integrator = myNVT;
1430		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 );
1431
1432	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1433	<
1434	<	if (globals->haveTargetPressure())
1435	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1436	<	else {
1437	<	sprintf( painCave.errMsg,
1438	<	"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 );
1432	>	case NPTi_ENS:
1433	>	if (globals->haveZconstraints()){
1434	>	setupZConstraint(info[k]);
1435	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1436	>	}
1437	>	else
1438	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1439
1440	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1441	<
1442	<	if (globals->haveTargetPressure())
1443	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1444	<	else {
1445	<	sprintf( painCave.errMsg,
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"
1447	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1448	<	painCave.isFatal = 1;
1449	<	simError();
1450	<	}
1451	<
1452	<	if( globals->haveTauThermostat() )
1453	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1454	<	else{
1455	<	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,
1447	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1448	>	painCave.isFatal = 1;
1449	>	simError();
1450	>	}
1451	>
1452	>	if (globals->haveTauThermostat())
1453	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1454	>	else{
1455	>	sprintf(painCave.errMsg,
1456		"SimSetup error: If you use an NPT\n"
1457	<	"    ensemble, you must set tauBarostat.\n");
1458	<	painCave.isFatal = 1;
1459	<	simError();
1460	<	}
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 );
1457	>	"\tensemble, you must set tauThermostat.\n");
1458	>	painCave.isFatal = 1;
1459	>	simError();
1460	>	}
1461
1462	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1463	<
1464	<	if (globals->haveTargetPressure())
1465	<	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,
1462	>	if (globals->haveTauBarostat())
1463	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1464	>	else{
1465	>	sprintf(painCave.errMsg,
1466		"SimSetup error: If you use an NPT\n"
1467	<	"    ensemble, you must set tauThermostat.\n");
1468	<	painCave.isFatal = 1;
1469	<	simError();
1470	<	}
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 );
1467	>	"\tensemble, you must set tauBarostat.\n");
1468	>	painCave.isFatal = 1;
1469	>	simError();
1470	>	}
1471
1472	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1473	<
1474	<	if (globals->haveTargetPressure())
1475	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1476	<	else {
1477	<	sprintf( painCave.errMsg,
1472	>	info->the_integrator = myNPTi;
1473	>	break;
1474	>
1475	>	case NPTf_ENS:
1476	>	if (globals->haveZconstraints()){
1477	>	setupZConstraint(info[k]);
1478	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1479	>	}
1480	>	else
1481	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1482	>
1483	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1484	>
1485	>	if (globals->haveTargetPressure())
1486	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1487	>	else{
1488	>	sprintf(painCave.errMsg,
1489		"SimSetup error: If you use a constant pressure\n"
1490	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1491	<	painCave.isFatal = 1;
1492	<	simError();
1493	<	}
1490	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494
1495	<	if( globals->haveTauThermostat() )
1496	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1497	<	else{
1498	<	sprintf( painCave.errMsg,
1495	>	if (globals->haveTauThermostat())
1496	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1497	>
1498	>	else{
1499	>	sprintf(painCave.errMsg,
1500		"SimSetup error: If you use an NPT\n"
1501	<	"    ensemble, you must set tauThermostat.\n");
1502	<	painCave.isFatal = 1;
1503	<	simError();
1504	<	}
1501	>	"\tensemble, you must set tauThermostat.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505
1506	<	if( globals->haveTauBarostat() )
1507	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1508	<	else{
1509	<	sprintf( painCave.errMsg,
1506	>	if (globals->haveTauBarostat())
1507	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1508	>
1509	>	else{
1510	>	sprintf(painCave.errMsg,
1511		"SimSetup error: If you use an NPT\n"
1512	<	"    ensemble, you must set tauBarostat.\n");
1512	>	"\tensemble, you must set tauBarostat.\n");
1513	>	painCave.isFatal = 1;
1514	>	simError();
1515	>	}
1516	>
1517	>	info->the_integrator = myNPTf;
1518	>	break;
1519	>
1520	>	case NPTxyz_ENS:
1521	>	if (globals->haveZconstraints()){
1522	>	setupZConstraint(info[k]);
1523	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1524	>	}
1525	>	else
1526	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1527	>
1528	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1529	>
1530	>	if (globals->haveTargetPressure())
1531	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1532	>	else{
1533	>	sprintf(painCave.errMsg,
1534	>	"SimSetup error: If you use a constant pressure\n"
1535	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1536	>	painCave.isFatal = 1;
1537	>	simError();
1538	>	}
1539	>
1540	>	if (globals->haveTauThermostat())
1541	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1542	>	else{
1543	>	sprintf(painCave.errMsg,
1544	>	"SimSetup error: If you use an NPT\n"
1545	>	"\tensemble, you must set tauThermostat.\n");
1546	>	painCave.isFatal = 1;
1547	>	simError();
1548	>	}
1549	>
1550	>	if (globals->haveTauBarostat())
1551	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1552	>	else{
1553	>	sprintf(painCave.errMsg,
1554	>	"SimSetup error: If you use an NPT\n"
1555	>	"\tensemble, you must set tauBarostat.\n");
1556	>	painCave.isFatal = 1;
1557	>	simError();
1558	>	}
1559	>
1560	>	info->the_integrator = myNPTxyz;
1561	>	break;
1562	>
1563	>	default:
1564	>	sprintf(painCave.errMsg,
1565	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1566		painCave.isFatal = 1;
1567		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();
1568		}
1569		}
1570		}
1571
1572	<	void SimSetup::initFortran( void ){
1569	<
1572	>	void SimSetup::initFortran(void){
1573		info[0].refreshSim();
1574	<
1575	<	if( !strcmp( info[0].mixingRule, "standard") ){
1576	<	the_ff->initForceField( LB_MIXING_RULE );
1574	>
1575	>	if (!strcmp(info[0].mixingRule, "standard")){
1576	>	the_ff->initForceField(LB_MIXING_RULE);
1577		}
1578	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1579	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1579	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1580		}
1581		else{
1582	<	sprintf( painCave.errMsg,
1583	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info[0].mixingRule );
1582	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1583	>	info[0].mixingRule);
1584		painCave.isFatal = 1;
1585		simError();
1586		}
1587
1588
1589		#ifdef IS_MPI
1590	<	strcpy( checkPointMsg,
1589	<	"Successfully intialized the mixingRule for Fortran." );
1590	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1591		MPIcheckPoint();
1592		#endif // is_mpi
1592	–
1593		}
1594
1595	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	<	{
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1596		int nZConstraints;
1597		ZconStamp** zconStamp;
1598
1599	<	if(globals->haveZconstraintTime()){
1601	<
1599	>	if (globals->haveZconstraintTime()){
1600		//add sample time of z-constraint  into SimInfo's property list
1601		DoubleData* zconsTimeProp = new DoubleData();
1602		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1606 | Line 1604 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1604		theInfo.addProperty(zconsTimeProp);
1605		}
1606		else{
1607	<	sprintf( painCave.errMsg,
1608	<	"ZConstraint error: If you use an ZConstraint\n"
1609	<	" , you must set sample time.\n");
1607	>	sprintf(painCave.errMsg,
1608	>	"ZConstraint error: If you use a ZConstraint,\n"
1609	>	"\tyou must set zconsTime.\n");
1610		painCave.isFatal = 1;
1611	<	simError();
1611	>	simError();
1612		}
1613
1614		//push zconsTol into siminfo, if user does not specify
1615		//value for zconsTol, a default value will be used
1616		DoubleData* zconsTol = new DoubleData();
1617		zconsTol->setID(ZCONSTOL_ID);
1618	<	if(globals->haveZconsTol()){
1618	>	if (globals->haveZconsTol()){
1619		zconsTol->setData(globals->getZconsTol());
1620		}
1621		else{
1622	<	double defaultZConsTol = 0.01;
1623	<	sprintf( painCave.errMsg,
1624	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1625	<	" , default value %f is used.\n", defaultZConsTol);
1622	>	double defaultZConsTol = 0.01;
1623	>	sprintf(painCave.errMsg,
1624	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1625	>	"\tOOPSE will use a default value of %f.\n"
1626	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1627	>	defaultZConsTol);
1628		painCave.isFatal = 0;
1629		simError();
1630
#	Line 1632 | Line 1632 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1632		}
1633		theInfo.addProperty(zconsTol);
1634
1635	<	//set Force Substraction Policy
1636	<	StringData* zconsForcePolicy =  new StringData();
1635	>	//set Force Subtraction Policy
1636	>	StringData* zconsForcePolicy = new StringData();
1637		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	<
1639	<	if(globals->haveZconsForcePolicy()){
1638	>
1639	>	if (globals->haveZconsForcePolicy()){
1640		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	<	}
1641	>	}
1642		else{
1643	<	sprintf( painCave.errMsg,
1644	<	"ZConstraint Warning: User does not set force substraction policy, "
1645	<	"average force substraction policy is used\n");
1646	<	painCave.isFatal = 0;
1647	<	simError();
1648	<	zconsForcePolicy->setData("BYNUMBER");
1643	>	sprintf(painCave.errMsg,
1644	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1645	>	"\tOOPSE will use PolicyByMass.\n"
1646	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1647	>	painCave.isFatal = 0;
1648	>	simError();
1649	>	zconsForcePolicy->setData("BYMASS");
1650		}
1651	<
1652	<	theInfo.addProperty(zconsForcePolicy);
1653	<
1651	>
1652	>	theInfo.addProperty(zconsForcePolicy);
1653	>
1654		//Determine the name of ouput file and add it into SimInfo's property list
1655		//Be careful, do not use inFileName, since it is a pointer which
1656		//point to a string at master node, and slave nodes do not contain that string
1657	<
1657	>
1658		string zconsOutput(theInfo.finalName);
1659	<
1659	>
1660		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	<
1661	>
1662		StringData* zconsFilename = new StringData();
1663		zconsFilename->setID(ZCONSFILENAME_ID);
1664		zconsFilename->setData(zconsOutput);
1665	<
1665	>
1666		theInfo.addProperty(zconsFilename);
1667	<
1667	>
1668		//setup index, pos and other parameters of z-constraint molecules
1669		nZConstraints = globals->getNzConstraints();
1670		theInfo.nZconstraints = nZConstraints;
#	Line 1673 | Line 1674 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1674
1675		ZConsParaData* zconsParaData = new ZConsParaData();
1676		zconsParaData->setID(ZCONSPARADATA_ID);
1677	<
1678	<	for(int i = 0; i < nZConstraints; i++){
1677	>
1678	>	for (int i = 0; i < nZConstraints; i++){
1679		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680		tempParaItem.zPos = zconStamp[i]->getZpos();
1681		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1683 | Line 1684 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1684		zconsParaData->addItem(tempParaItem);
1685		}
1686
1687	+	//check the uniqueness of index
1688	+	if(!zconsParaData->isIndexUnique()){
1689	+	sprintf(painCave.errMsg,
1690	+	"ZConstraint Error: molIndex is not unique!\n");
1691	+	painCave.isFatal = 1;
1692	+	simError();
1693	+	}
1694	+
1695		//sort the parameters by index of molecules
1696		zconsParaData->sortByIndex();
1697
1698		//push data into siminfo, therefore, we can retrieve later
1699		theInfo.addProperty(zconsParaData);
1691	–
1700		}

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