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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 661 by tim, Fri Aug 1 16:18:13 2003 UTC vs.
Revision 983 by gezelter, Mon Jan 26 21:45:03 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
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 55 | Line 75 | SimSetup::~SimSetup(){
75		delete globals;
76		}
77
78	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
79	<	info = the_info;
80	<	nInfo = theNinfo;
81	<	isInfoArray = 1;
82	<	}
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 ){
66	<
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();
94	<	mpiEventLoop();
95	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
102	–	int i, j, k, globalAtomIndex;
103	–
122		// gather all of the information from the Bass file
123	<
123	>
124		gatherInfo();
125
126		// creation of complex system objects
#	Line 110 | Line 128 | void SimSetup::createSim( void ){
128		sysObjectsCreation();
129
130		// check on the post processing info
131	<
131	>
132		finalInfoCheck();
133
134		// initialize the system coordinates
135
136	<	initSystemCoords();
137	<
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 133 | Line 155 | void SimSetup::createSim( void ){
155		// initialize the Fortran
156
157		initFortran();
136	–
137	–
138	–
158		}
159
160
161	<	void SimSetup::makeMolecules( void ){
162	<
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 155 | Line 174 | void SimSetup::makeMolecules( void ){
174		bend_set* theBends;
175		torsion_set* theTorsions;
176
158	–
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;
167	–
168	–	atomOffset = 0;
169	–	excludeOffset = 0;
170	–	for(i=0; i<info->n_mol; i++){
171	–
172	–	stampID = the_molecules[i].getStampID();
188
189	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
190	<	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;
189	>	for (k = 0; k < nInfo; k++){
190	>	the_ff->setSimInfo(&(info[k]));
191
192	<	molInfo.myAtoms = &the_atoms[atomOffset];
193	<	molInfo.myExcludes = &the_excludes[excludeOffset];
194	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
195	<	molInfo.myBends = new Bend*[molInfo.nBends];
196	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192	>	atomOffset = 0;
193	>	excludeOffset = 0;
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();
200	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
201	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
202
203	<	theBonds = new bond_pair[molInfo.nBonds];
204	<	theBends = new bend_set[molInfo.nBends];
205	<	theTorsions = new torsion_set[molInfo.nTorsions];
206	<
207	<	// make the Atoms
208	<
209	<	for(j=0; j<molInfo.nAtoms; j++){
210	<
211	<	currentAtom = comp_stamps[stampID]->getAtom( j );
212	<	if( currentAtom->haveOrientation() ){
213	<
214	<	dAtom = new DirectionalAtom(j + atomOffset);
215	<	info->n_oriented++;
216	<	molInfo.myAtoms[j] = dAtom;
217	<
218	<	ux = currentAtom->getOrntX();
219	<	uy = currentAtom->getOrntY();
220	<	uz = currentAtom->getOrntZ();
221	<
222	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
223	<
224	<	u = sqrt( uSqr );
225	<	ux = ux / u;
226	<	uy = uy / u;
227	<	uz = uz / u;
228	<
229	<	dAtom->setSUx( ux );
230	<	dAtom->setSUy( uy );
231	<	dAtom->setSUz( uz );
232	<	}
233	<	else{
234	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
235	<	}
236	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
237	<
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];
208	>
209	>	theBonds = new bond_pair[molInfo.nBonds];
210	>	theBends = new bend_set[molInfo.nBends];
211	>	theTorsions = new torsion_set[molInfo.nTorsions];
212	>
213	>	// make the Atoms
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();
228	>	theta = currentAtom->getEulerTheta();
229	>	psi = currentAtom->getEulerPsi();
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	<	}
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;
273	>	}
274
275	<	exI = theBonds[j].a;
276	<	exJ = theBonds[j].b;
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	<	// exclude_I must always be the smaller of the pair
282	<	if( exI > exJ ){
283	<	tempEx = exI;
284	<	exI = exJ;
285	<	exJ = tempEx;
286	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
293	<	tempEx = exJ;
294	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
295	<
296	<	the_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	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
299	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
300		#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	–	}
301		}
302	<
303	<	if( !theBends[j].isGhost ){
304	<
305	<	exI = theBends[j].a;
306	<	exJ = theBends[j].c;
307	<	}
308	<	else{
309	<
310	<	exI = theBends[j].a;
311	<	exJ = theBends[j].b;
312	<	}
313	<
314	<	// exclude_I must always be the smaller of the pair
315	<	if( exI > exJ ){
316	<	tempEx = exI;
317	<	exI = exJ;
318	<	exJ = tempEx;
319	<	}
302	>	excludeOffset += molInfo.nBonds;
303	>
304	>	//make the bends
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	>	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 = the_atoms[tempEx]->getGlobalIndex() + 1;
370	<	tempEx = exJ;
371	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
372	<
373	<	the_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	<	the_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;
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;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
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	<	// exclude_I must always be the smaller of the pair
388	<	if( exI > exJ ){
389	<	tempEx = exI;
390	<	exI = exJ;
391	<	exJ = tempEx;
392	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
399	<	tempEx = exJ;
400	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
401	<
402	<	the_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	<	the_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;
406	>	}
407	>	excludeOffset += molInfo.nTorsions;
408
374	–
375	–	// send the arrays off to the forceField for init.
409
410	<	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 );
410	>	// send the arrays off to the forceField for init.
411
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
383	–	the_molecules[i].initialize( molInfo );
418
419	+	info[k].molecules[i].initialize(molInfo);
420
421	<	atomOffset += molInfo.nAtoms;
422	<	delete[] theBonds;
423	<	delete[] theBends;
424	<	delete[] theTorsions;
421	>
422	>	atomOffset += molInfo.nAtoms;
423	>	delete[] theBonds;
424	>	delete[] theBends;
425	>	delete[] theTorsions;
426	>	}
427		}
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
434		// clean up the forcefield
435	+
436		the_ff->calcRcut();
437		the_ff->cleanMe();
400	–
438		}
439
440	<	void SimSetup::initFromBass( void ){
404	<
440	>	void SimSetup::initFromBass(void){
441		int i, j, k;
442		int n_cells;
443		double cellx, celly, cellz;
#	Line 410 | Line 446 | void SimSetup::initFromBass( void ){
446		int n_extra;
447		int have_extra, done;
448
449	<	temp1 = (double)tot_nmol / 4.0;
450	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
451	<	temp3 = ceil( temp2 );
449	>	double vel[3];
450	>	vel[0] = 0.0;
451	>	vel[1] = 0.0;
452	>	vel[2] = 0.0;
453
454	<	have_extra =0;
455	<	if( temp2 < temp3 ){ // we have a non-complete lattice
456	<	have_extra =1;
454	>	temp1 = (double) tot_nmol / 4.0;
455	>	temp2 = pow(temp1, (1.0 / 3.0));
456	>	temp3 = ceil(temp2);
457
458	<	n_cells = (int)temp3 - 1;
459	<	cellx = info->boxL[0] / temp3;
460	<	celly = info->boxL[1] / temp3;
461	<	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 );
458	>	have_extra = 0;
459	>	if (temp2 < temp3){
460	>	// we have a non-complete lattice
461	>	have_extra = 1;
462
463	<	if( n_per_extra > 4){
464	<	sprintf( painCave.errMsg,
465	<	"SimSetup error. There has been an error in constructing"
466	<	" the non-complete lattice.\n" );
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);
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");
475		painCave.isFatal = 1;
476		simError();
477		}
478		}
479		else{
480	<	n_cells = (int)temp3;
481	<	cellx = info->boxL[0] / temp3;
482	<	celly = info->boxL[1] / temp3;
483	<	cellz = info->boxL[2] / 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;
484		}
485
486		current_mol = 0;
#	Line 446 | 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++ ){
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,
454	<	j * celly,
455	<	k * cellz );
496	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
497
498	<	makeElement( i * cellx + 0.5 * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz );
498	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
499
500	<	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 );
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	<	}
486	<	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 ){
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	<	}
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	<
548	<	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 );
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 ){
529	<
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",
544	<	comp_stamps[current_comp]->getID(),
545	<	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
572	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
573	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
574	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
572	>	pos[0] = x + current_atom->getPosX();
573	>	pos[1] = y + current_atom->getPosY();
574	>	pos[2] = z + current_atom->getPosZ();
575
576	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
576	>	info[0].atoms[current_atom_ndx]->setPos(pos);
577
578	<	dAtom = (DirectionalAtom *)the_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 567 | 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 576 | 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] ){
580	<
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
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
615		// set the easy ones first
616	<	info->target_temp = globals->getTargetTemp();
617	<	info->dt = globals->getDt();
618	<	info->run_time = globals->getRunTime();
616	>
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();
621	>	}
622		n_components = globals->getNComponents();
623
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;
616	<	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;
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, "NPTZCONS"))
634	<	ensembleCase = NPTiZCONS_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	<	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  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" );
649	>	if (!strcasecmp(ensemble, "NVE")){
650		ensembleCase = NVE_ENS;
651	<	}
652	<	strcpy( info->ensemble, ensemble );
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	>	}
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 \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	>	}
674
675	<	// get the mixing rule
675	>	for (i = 0; i < nInfo; i++){
676	>	strcpy(info[i].ensemble, ensemble);
677
678	<	strcpy( info->mixingRule, globals->getMixingRule() );
679	<	info->usePBC = globals->getPBC();
680	<
681	<
678	>	// get the mixing rule
679	>
680	>	strcpy(info[i].mixingRule, globals->getMixingRule());
681	>	info[i].usePBC = globals->getPBC();
682	>	}
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;
676	<	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 681 | 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	<	if( globals->haveSampleTime() ){
723	<	info->sampleTime = globals->getSampleTime();
724	<	info->statusTime = info->sampleTime;
725	<	info->thermalTime = info->sampleTime;
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		}
701	–	else{
702	–	info->sampleTime = globals->getRunTime();
703	–	info->statusTime = info->sampleTime;
704	–	info->thermalTime = info->sampleTime;
705	–	}
730
731	<	if( globals->haveStatusTime() ){
732	<	info->statusTime = globals->getStatusTime();
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() ){
742	<	info->thermalTime = globals->getThermalTime();
743	<	}
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	<	// check for the temperature set flag
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	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
761	>	// set the status, sample, and thermal kick times
762
763	<	// get some of the tricky things that may still be in the globals
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;
768	>	}
769	>	else{
770	>	info[i].sampleTime = globals->getRunTime();
771	>	info[i].statusTime = info[i].sampleTime;
772	>	info[i].thermalTime = info[i].sampleTime;
773	>	}
774
775	<	double boxVector[3];
776	<	if( globals->haveBox() ){
777	<	boxVector[0] = globals->getBox();
778	<	boxVector[1] = globals->getBox();
779	<	boxVector[2] = globals->getBox();
775	>	if (globals->haveStatusTime()){
776	>	info[i].statusTime = globals->getStatusTime();
777	>	}
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	<	info->setBox( boxVector );
792	<	}
729	<	else if( globals->haveDensity() ){
791	>	if (globals->haveTempSet())
792	>	info[i].setTemp = globals->getTempSet();
793
794	<	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];
794	>	// check for the extended State init
795
796	<	info->setBox( boxVector );
796	>	info[i].useInitXSstate = globals->getUseInitXSstate();
797	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
798	>
799		}
800	<	else{
801	<	if( !globals->haveBoxX() ){
802	<	sprintf( painCave.errMsg,
742	<	"SimSetup error, no periodic BoxX size given.\n" );
743	<	painCave.isFatal = 1;
744	<	simError();
745	<	}
746	<	boxVector[0] = globals->getBoxX();
800	>
801	>	//setup seed for random number generator
802	>	int seedValue;
803
804	<	if( !globals->haveBoxY() ){
805	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
753	<	}
754	<	boxVector[1] = globals->getBoxY();
804	>	if (globals->haveSeed()){
805	>	seedValue = globals->getSeed();
806
807	<	if( !globals->haveBoxZ() ){
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup error, no periodic BoxZ size given.\n" );
810	<	painCave.isFatal = 1;
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	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
822	+	#endif
823		}
824	<	boxVector[2] = globals->getBoxZ();
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	<	info->setBox( boxVector );
837	>	for (int i = 0; i < nInfo; i++){
838	>	info[i].setSeed(seedValue);
839		}
840
767	–
768	–
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
773	–
845		}
846
847
848	<	void SimSetup::finalInfoCheck( void ){
848	>	void SimSetup::finalInfoCheck(void){
849		int index;
850		int usesDipoles;
851	<
851	>	int i;
852
853	<	// check electrostatic parameters
854	<
855	<	index = 0;
856	<	usesDipoles = 0;
857	<	while( (index < info->n_atoms) && !usesDipoles ){
858	<	usesDipoles = ((info->atoms)[index])->hasDipole();
859	<	index++;
860	<	}
861	<
853	>	for (i = 0; i < nInfo; i++){
854	>	// check electrostatic parameters
855	>
856	>	index = 0;
857	>	usesDipoles = 0;
858	>	while ((index < info[i].n_atoms) && !usesDipoles){
859	>	usesDipoles = (info[i].atoms[index])->hasDipole();
860	>	index++;
861	>	}
862	>
863		#ifdef IS_MPI
864	<	int myUse = usesDipoles;
865	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
864	>	int myUse = usesDipoles;
865	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866		#endif //is_mpi
867
868	<	double theEcr, theEst;
868	>	double theEcr, theEst;
869
870	<	if (globals->getUseRF() ) {
871	<	info->useReactionField = 1;
800	<
801	<	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");
806	<	painCave.isFatal = 0;
807	<	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	<	}
870	>	if (globals->getUseRF()){
871	>	info[i].useReactionField = 1;
872
873	<	if( !globals->haveEST() ){
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Warning: using default value of 0.05 * the "
876	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
877	<	);
878	<	painCave.isFatal = 0;
879	<	simError();
880	<	theEst = 0.05 * theEcr;
881	<	} else {
882	<	theEst= globals->getEST();
883	<	}
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	>	else{
883	>	theEcr = globals->getECR();
884	>	}
885
886	<	info->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();
838	<	}
839	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	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();
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	<
897	<	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();
896	>	else{
897	>	theEst = globals->getEST();
898		}
899
900	<	info->setEcr( theEcr, theEst );
874	<	}
875	<	}
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
881	–
949		}
950	+
951	+	void SimSetup::initSystemCoords(void){
952	+	int i;
953
954	<	void SimSetup::initSystemCoords( void ){
954	>	char* inName;
955
956	<	if( globals->haveInitialConfig() ){
957	<
958	<	InitializeFromFile* fileInit;
956	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
957	>
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	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
966	>	inName = globals->getInitialConfig();
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
973	>	fileInit->readInit(info); // default velocities on
974
975	<	delete fileInit;
976	<	}
977	<	else{
978	<
979	<	#ifdef IS_MPI
975	>	delete fileInit;
976	>	}
977	>	else{
978	>
979	>	// no init from bass
980	>
981	>	sprintf(painCave.errMsg,
982	>	"Cannot intialize a simulation without an initial configuration file.\n");
983	>	painCave.isFatal = 1;;
984	>	simError();
985	>
986	>	}
987
904	–	// no init from bass
905	–
906	–	sprintf( painCave.errMsg,
907	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
908	–	painCave.isFatal;
909	–	simError();
910	–
911	–	#else
912	–
913	–	initFromBass();
914	–
915	–
916	–	#endif
917	–	}
918	–
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
923	–
992		}
993
994
995	<	void SimSetup::makeOutNames( void ){
995	>	void SimSetup::makeOutNames(void){
996	>	int k;
997
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->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" );
1003	>
1004	>	if (globals->haveFinalConfig()){
1005	>	strcpy(info[k].finalName, globals->getFinalConfig());
1006		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
1007		else{
1008	<	endTest = &(info->finalName[nameLength - 4]);
1009	<	if( !strcmp( endTest, ".bss" ) ){
1010	<	strcpy( endTest, ".eor" );
1011	<	}
1012	<	else if( !strcmp( endTest, ".mdl" ) ){
1013	<	strcpy( endTest, ".eor" );
1014	<	}
1015	<	else{
1016	<	strcat( info->finalName, ".eor" );
1017	<	}
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	<	}
1032	<
1033	<	// make the sample and status out names
1034	<
1035	<	strcpy( info->sampleName, inFileName );
1036	<	char* endTest;
1037	<	int nameLength = strlen( info->sampleName );
1038	<	endTest = &(info->sampleName[nameLength - 5]);
1039	<	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" );
1031	>
1032	>	// make the sample and status out names
1033	>
1034	>	strcpy(info[k].sampleName, inFileName);
1035	>	char* endTest;
1036	>	int nameLength = strlen(info[k].sampleName);
1037	>	endTest = &(info[k].sampleName[nameLength - 5]);
1038	>	if (!strcmp(endTest, ".bass")){
1039	>	strcpy(endTest, ".dump");
1040		}
1041	<	else if( !strcmp( endTest, ".mdl" ) ){
1042	<	strcpy( endTest, ".dump" );
1041	>	else if (!strcmp(endTest, ".BASS")){
1042	>	strcpy(endTest, ".dump");
1043		}
1044		else{
1045	<	strcat( info->sampleName, ".dump" );
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	<
1058	<	strcpy( info->statusName, inFileName );
1059	<	nameLength = strlen( info->statusName );
1060	<	endTest = &(info->statusName[nameLength - 5]);
1061	<	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" );
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");
1062		}
1063	<	else if( !strcmp( endTest, ".mdl" ) ){
1064	<	strcpy( endTest, ".stat" );
1063	>	else if (!strcmp(endTest, ".BASS")){
1064	>	strcpy(endTest, ".stat");
1065		}
1066		else{
1067	<	strcat( info->statusName, ".stat" );
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	<	}
1007	<
1078	>
1079		#ifdef IS_MPI
1009	–	}
1010	–	#endif // is_mpi
1080
1081	+	}
1082	+	#endif // is_mpi
1083	+	}
1084		}
1085
1086
1087	<	void SimSetup::sysObjectsCreation( void ){
1087	>	void SimSetup::sysObjectsCreation(void){
1088	>	int i, k;
1089
1017	–	int i;
1018	–
1090		// create the forceField
1091
1092		createFF();
#	Line 1030 | 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();
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	–
1115
1116	<
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++){
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:
1067	<	the_ff = new EAM_FF();
1068	<	break;
1069	<
1070	<	default:
1071	<	sprintf( painCave.errMsg,
1072	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1073	<	painCave.isFatal = 1;
1074	<	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
1081	–
1150		}
1151
1152
1153	<	void SimSetup::compList( void ){
1086	<
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
1089	–	comp_stamps = new MoleculeStamp*[n_components];
1090	–
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	<	info->nComponents = n_components;
1164	<	info->componentsNmol = components_nmol;
1165	<	info->compStamps = comp_stamps;
1166	<	info->headStamp = new LinkedMolStamp();
1167	<
1168	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1102	<	for( i=0; i<n_components; i++ ){
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	>	}
1169
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 ){
1111	<
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
1133	–
1134	–
1200		}
1201
1202	<	void SimSetup::calcSysValues( void ){
1203	<	int i, j, k;
1202	>	void SimSetup::calcSysValues(void){
1203	>	int i;
1204
1205	+	int* molMembershipArray;
1206
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();
1149	<	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
1218		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1219	+	molMembershipArray = new int[tot_atoms];
1220
1221	<	info->n_atoms = tot_atoms;
1222	<	info->n_bonds = tot_bonds;
1223	<	info->n_bends = tot_bends;
1224	<	info->n_torsions = tot_torsions;
1225	<	info->n_SRI = tot_SRI;
1226	<	info->n_mol = tot_nmol;
1227	<
1228	<	info->molMembershipArray = new int[tot_atoms];
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	>
1229	>	info[i].molMembershipArray = molMembershipArray;
1230	>	}
1231		}
1232
1165	–
1233		#ifdef IS_MPI
1234
1235	<	void SimSetup::mpiMolDivide( void ){
1169	<
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 1189 | 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();
1200	<	local_bends +=    comp_stamps[i]->getNBends();
1201	<	local_torsions += comp_stamps[i]->getNTorsions();
1202	<	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++) {
1268	<	info->molMembershipArray[globalAtomIndex] = allMol;
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	<
1277	<	info->n_atoms = mpiSim->getMyNlocal();
1278	<
1279	<	if( local_atoms != info->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->n_atoms,
1221	<	local_atoms );
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\n"
1282	>	"\tlocalAtom (%d) are not equal.\n",
1283	>	info[0].n_atoms, local_atoms);
1284		painCave.isFatal = 1;
1285		simError();
1286		}
1287
1288	<	info->n_bonds = local_bonds;
1289	<	info->n_bends = local_bends;
1290	<	info->n_torsions = local_torsions;
1291	<	info->n_SRI = local_SRI;
1292	<	info->n_mol = localMol;
1288	>	info[0].n_bonds = local_bonds;
1289	>	info[0].n_bends = local_bends;
1290	>	info[0].n_torsions = local_torsions;
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;
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
1243	–	// create the atom and short range interaction arrays
1312
1313	<	Atom::createArrays(info->n_atoms);
1314	<	the_atoms = new Atom*[info->n_atoms];
1247	<	the_molecules = new Molecule[info->n_mol];
1248	<	int molIndex;
1313	>	for (l = 0; l < nInfo; l++){
1314	>	// create the atom and short range interaction arrays
1315
1316	<	// initialize the molecule's stampID's
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	+
1322		#ifdef IS_MPI
1253	–
1323
1324	<	molIndex = 0;
1325	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1326	<
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++;
1324	>
1325	>	molIndex = 0;
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		}
1264	–	}
1334
1335		#else // is_mpi
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->molMembershipArray[globalAtomIndex] = molIndex;
1346	<	globalAtomIndex++;
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++;
1349		}
1279	–	molIndex++;
1350		}
1281	–	}
1282	–
1351
1352	+
1353		#endif // is_mpi
1354
1355
1356	<	if( info->n_SRI ){
1357	<
1358	<	Exclude::createArray(info->n_SRI);
1359	<	the_excludes = new Exclude*[info->n_SRI];
1360	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1361	<	info->globalExcludes = new int;
1362	<	info->n_exclude = info->n_SRI;
1363	<	}
1364	<	else{
1365	<
1366	<	Exclude::createArray( 1 );
1367	<	the_excludes = new Exclude*;
1368	<	the_excludes[0] = new Exclude(0);
1369	<	the_excludes[0]->setPair( 0,0 );
1370	<	info->globalExcludes = new int;
1371	<	info->globalExcludes[0] = 0;
1372	<	info->n_exclude = 0;
1373	<	}
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);
1361	>	}
1362	>	info[l].globalExcludes = new int;
1363	>	info[l].n_exclude = info[l].n_SRI;
1364	>	}
1365	>	else{
1366	>	Exclude::createArray(1);
1367	>	the_excludes = new Exclude * ;
1368	>	the_excludes[0] = new Exclude(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;
1373	>	}
1374
1375	<	// set the arrays into the SimInfo object
1375	>	// set the arrays into the SimInfo object
1376
1377	<	info->atoms = the_atoms;
1378	<	info->molecules = the_molecules;
1379	<	info->nGlobalExcludes = 0;
1380	<	info->excludes = the_excludes;
1377	>	info[l].atoms = the_atoms;
1378	>	info[l].molecules = the_molecules;
1379	>	info[l].nGlobalExcludes = 0;
1380	>	info[l].excludes = the_excludes;
1381
1382	<	the_ff->setSimInfo( info );
1383	<
1382	>	the_ff->setSimInfo(info);
1383	>	}
1384		}
1385
1386	<	void SimSetup::makeIntegrator( void ){
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	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1395	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1396	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1397	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1398	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1399	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1400	<
1401	<	switch( ensembleCase ){
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	<	case NVE_ENS:
1410	<	new NVE<RealIntegrator>( info, the_ff );
1411	<	break;
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	<	case NVT_ENS:
1338	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1339	<	myNVT->setTargetTemp(globals->getTargetTemp());
1417	>	myNVT->setTargetTemp(globals->getTargetTemp());
1418
1419	<	if (globals->haveTauThermostat())
1420	<	myNVT->setTauThermostat(globals->getTauThermostat());
1419	>	if (globals->haveTauThermostat())
1420	>	myNVT->setTauThermostat(globals->getTauThermostat());
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	<	else {
1430	<	sprintf( painCave.errMsg,
1346	<	"SimSetup error: If you use the NVT\n"
1347	<	"    ensemble, you must set tauThermostat.\n");
1348	<	painCave.isFatal = 1;
1349	<	simError();
1350	<	}
1351	<	break;
1429	>	info->the_integrator = myNVT;
1430	>	break;
1431
1432	<	case NPTi_ENS:
1433	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1434	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
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	<	if (globals->haveTargetPressure())
1358	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1359	<	else {
1360	<	sprintf( painCave.errMsg,
1361	<	"SimSetup error: If you use a constant pressure\n"
1362	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1363	<	painCave.isFatal = 1;
1364	<	simError();
1365	<	}
1366	<
1367	<	if( globals->haveTauThermostat() )
1368	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1369	<	else{
1370	<	sprintf( painCave.errMsg,
1371	<	"SimSetup error: If you use an NPT\n"
1372	<	"    ensemble, you must set tauThermostat.\n");
1373	<	painCave.isFatal = 1;
1374	<	simError();
1375	<	}
1440	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1441
1442	<	if( globals->haveTauBarostat() )
1443	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1444	<	else{
1445	<	sprintf( painCave.errMsg,
1446	<	"SimSetup error: If you use an NPT\n"
1447	<	"    ensemble, you must set tauBarostat.\n");
1448	<	painCave.isFatal = 1;
1449	<	simError();
1450	<	}
1386	<	break;
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	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1448	>	painCave.isFatal = 1;
1449	>	simError();
1450	>	}
1451
1452	<	case NPTf_ENS:
1453	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1454	<	myNPTf->setTargetTemp( globals->getTargetTemp());
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	>	"\tensemble, you must set tauThermostat.\n");
1458	>	painCave.isFatal = 1;
1459	>	simError();
1460	>	}
1461
1462	<	if (globals->haveTargetPressure())
1463	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1464	<	else {
1465	<	sprintf( painCave.errMsg,
1466	<	"SimSetup error: If you use a constant pressure\n"
1467	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1468	<	painCave.isFatal = 1;
1469	<	simError();
1470	<	}
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	>	"\tensemble, you must set tauBarostat.\n");
1468	>	painCave.isFatal = 1;
1469	>	simError();
1470	>	}
1471
1472	<	if( globals->haveTauThermostat() )
1473	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1404	<	else{
1405	<	sprintf( painCave.errMsg,
1406	<	"SimSetup error: If you use an NPT\n"
1407	<	"    ensemble, you must set tauThermostat.\n");
1408	<	painCave.isFatal = 1;
1409	<	simError();
1410	<	}
1472	>	info->the_integrator = myNPTi;
1473	>	break;
1474
1475	<	if( globals->haveTauBarostat() )
1476	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	<	else{
1478	<	sprintf( painCave.errMsg,
1479	<	"SimSetup error: If you use an NPT\n"
1480	<	"    ensemble, you must set tauBarostat.\n");
1481	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<	break;
1422	<
1423	<	case NPTim_ENS:
1424	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1425	<	myNPTim->setTargetTemp( globals->getTargetTemp());
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	<	if (globals->haveTargetPressure())
1428	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1429	<	else {
1430	<	sprintf( painCave.errMsg,
1431	<	"SimSetup error: If you use a constant pressure\n"
1432	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1433	<	painCave.isFatal = 1;
1434	<	simError();
1435	<	}
1436	<
1437	<	if( globals->haveTauThermostat() )
1438	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1439	<	else{
1440	<	sprintf( painCave.errMsg,
1441	<	"SimSetup error: If you use an NPT\n"
1442	<	"    ensemble, you must set tauThermostat.\n");
1443	<	painCave.isFatal = 1;
1444	<	simError();
1445	<	}
1483	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1484
1485	<	if( globals->haveTauBarostat() )
1486	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1487	<	else{
1488	<	sprintf( painCave.errMsg,
1489	<	"SimSetup error: If you use an NPT\n"
1490	<	"    ensemble, you must set tauBarostat.\n");
1491	<	painCave.isFatal = 1;
1492	<	simError();
1493	<	}
1456	<	break;
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	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494
1495	<	case NPTfm_ENS:
1496	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1460	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1495	>	if (globals->haveTauThermostat())
1496	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1497
1498	<	if (globals->haveTargetPressure())
1499	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1500	<	else {
1501	<	sprintf( painCave.errMsg,
1502	<	"SimSetup error: If you use a constant pressure\n"
1503	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1504	<	painCave.isFatal = 1;
1469	<	simError();
1470	<	}
1471	<
1472	<	if( globals->haveTauThermostat() )
1473	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1474	<	else{
1475	<	sprintf( painCave.errMsg,
1476	<	"SimSetup error: If you use an NPT\n"
1477	<	"    ensemble, you must set tauThermostat.\n");
1478	<	painCave.isFatal = 1;
1479	<	simError();
1480	<	}
1498	>	else{
1499	>	sprintf(painCave.errMsg,
1500	>	"SimSetup error: If you use an NPT\n"
1501	>	"\tensemble, you must set tauThermostat.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505
1506	<	if( globals->haveTauBarostat() )
1507	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1484	<	else{
1485	<	sprintf( painCave.errMsg,
1486	<	"SimSetup error: If you use an NPT\n"
1487	<	"    ensemble, you must set tauBarostat.\n");
1488	<	painCave.isFatal = 1;
1489	<	simError();
1490	<	}
1491	<	break;
1492	<
1493	<	case NVEZCONS_ENS:
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	+	"\tensemble, you must set tauBarostat.\n");
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516
1517	<	//setup index of z-constraint molecules, z-constraint sampel time
1518	<	//and z-constraint force output name. These parameter should be known
1498	<	//before constructing the z-constraint integrator
1499	<	setupZConstraint();
1500	<
1501	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1502	<
1503	<	break;
1504	<
1505	<
1506	<	case NVTZCONS_ENS:
1507	<
1508	<	setupZConstraint();
1509	<
1510	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1511	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1517	>	info->the_integrator = myNPTf;
1518	>	break;
1519
1520	<	if (globals->haveTauThermostat())
1521	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
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	<	else {
1517	<	sprintf( painCave.errMsg,
1518	<	"SimSetup error: If you use the NVT\n"
1519	<	"    ensemble, you must set tauThermostat.\n");
1520	<	painCave.isFatal = 1;
1521	<	simError();
1522	<	}
1523	<	break;
1524	<
1525	<	case NPTiZCONS_ENS:
1526	<
1527	<	setupZConstraint();
1528	<
1529	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1530	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1528	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1529
1530	<	if (globals->haveTargetPressure())
1531	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1532	<	else {
1533	<	sprintf( painCave.errMsg,
1534	<	"SimSetup error: If you use a constant pressure\n"
1535	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1536	<	painCave.isFatal = 1;
1537	<	simError();
1538	<	}
1541	<
1542	<	if( globals->haveTauThermostat() )
1543	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1544	<	else{
1545	<	sprintf( painCave.errMsg,
1546	<	"SimSetup error: If you use an NPT\n"
1547	<	"    ensemble, you must set tauThermostat.\n");
1548	<	painCave.isFatal = 1;
1549	<	simError();
1550	<	}
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->haveTauBarostat() )
1541	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1542	<	else{
1543	<	sprintf( painCave.errMsg,
1544	<	"SimSetup error: If you use an NPT\n"
1545	<	"    ensemble, you must set tauBarostat.\n");
1546	<	painCave.isFatal = 1;
1547	<	simError();
1548	<	}
1561	<
1562	<	break;
1563	<
1564	<	case NPTfZCONS_ENS:
1565	<
1566	<	setupZConstraint();
1567	<
1568	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1569	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
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->haveTargetPressure())
1551	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1552	<	else {
1553	<	sprintf( painCave.errMsg,
1554	<	"SimSetup error: If you use a constant pressure\n"
1555	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1556	<	painCave.isFatal = 1;
1557	<	simError();
1558	<	}
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	<	if( globals->haveTauThermostat() )
1561	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1583	<	else{
1584	<	sprintf( painCave.errMsg,
1585	<	"SimSetup error: If you use an NPT\n"
1586	<	"    ensemble, you must set tauThermostat.\n");
1587	<	painCave.isFatal = 1;
1588	<	simError();
1589	<	}
1560	>	info->the_integrator = myNPTxyz;
1561	>	break;
1562
1563	<	if( globals->haveTauBarostat() )
1564	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1565	<	else{
1566	<	sprintf( painCave.errMsg,
1567	<	"SimSetup error: If you use an NPT\n"
1596	<	"    ensemble, you must set tauBarostat.\n");
1597	<	painCave.isFatal = 1;
1598	<	simError();
1599	<	}
1600	<
1601	<	break;
1602	<
1603	<	case NPTimZCONS_ENS:
1604	<
1605	<	setupZConstraint();
1606	<
1607	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1608	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1609	<
1610	<	if (globals->haveTargetPressure())
1611	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1612	<	else {
1613	<	sprintf( painCave.errMsg,
1614	<	"SimSetup error: If you use a constant pressure\n"
1615	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1616	<	painCave.isFatal = 1;
1617	<	simError();
1563	>	default:
1564	>	sprintf(painCave.errMsg,
1565	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1566	>	painCave.isFatal = 1;
1567	>	simError();
1568		}
1619	–
1620	–	if( globals->haveTauThermostat() )
1621	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1622	–	else{
1623	–	sprintf( painCave.errMsg,
1624	–	"SimSetup error: If you use an NPT\n"
1625	–	"    ensemble, you must set tauThermostat.\n");
1626	–	painCave.isFatal = 1;
1627	–	simError();
1628	–	}
1629	–
1630	–	if( globals->haveTauBarostat() )
1631	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1632	–	else{
1633	–	sprintf( painCave.errMsg,
1634	–	"SimSetup error: If you use an NPT\n"
1635	–	"    ensemble, you must set tauBarostat.\n");
1636	–	painCave.isFatal = 1;
1637	–	simError();
1638	–	}
1639	–
1640	–	break;
1641	–
1642	–	case NPTfmZCONS_ENS:
1643	–
1644	–	setupZConstraint();
1645	–
1646	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1647	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1648	–
1649	–	if (globals->haveTargetPressure())
1650	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1651	–	else {
1652	–	sprintf( painCave.errMsg,
1653	–	"SimSetup error: If you use a constant pressure\n"
1654	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1655	–	painCave.isFatal = 1;
1656	–	simError();
1657	–	}
1658	–
1659	–	if( globals->haveTauThermostat() )
1660	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1661	–	else{
1662	–	sprintf( painCave.errMsg,
1663	–	"SimSetup error: If you use an NPT\n"
1664	–	"    ensemble, you must set tauThermostat.\n");
1665	–	painCave.isFatal = 1;
1666	–	simError();
1667	–	}
1668	–
1669	–	if( globals->haveTauBarostat() )
1670	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1671	–	else{
1672	–	sprintf( painCave.errMsg,
1673	–	"SimSetup error: If you use an NPT\n"
1674	–	"    ensemble, you must set tauBarostat.\n");
1675	–	painCave.isFatal = 1;
1676	–	simError();
1677	–	}
1678	–	break;
1679	–
1680	–
1681	–
1682	–	default:
1683	–	sprintf( painCave.errMsg,
1684	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1685	–	painCave.isFatal = 1;
1686	–	simError();
1569		}
1688	–
1570		}
1571
1572	<	void SimSetup::initFortran( void ){
1572	>	void SimSetup::initFortran(void){
1573	>	info[0].refreshSim();
1574
1575	<	info->refreshSim();
1576	<
1695	<	if( !strcmp( info->mixingRule, "standard") ){
1696	<	the_ff->initForceField( LB_MIXING_RULE );
1575	>	if (!strcmp(info[0].mixingRule, "standard")){
1576	>	the_ff->initForceField(LB_MIXING_RULE);
1577		}
1578	<	else if( !strcmp( info->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",
1704	<	info->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,
1712	<	"Successfully intialized the mixingRule for Fortran." );
1590	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1591		MPIcheckPoint();
1592		#endif // is_mpi
1715	–
1593		}
1594
1595	<	void SimSetup::setupZConstraint()
1596	<	{
1597	<	if(globals->haveZConsTime()){
1598	<
1599	<	//add sample time of z-constraint  into SimInfo's property list
1600	<	DoubleData* zconsTimeProp = new DoubleData();
1601	<	zconsTimeProp->setID("zconstime");
1602	<	zconsTimeProp->setData(globals->getZConsTime());
1603	<	info->addProperty(zconsTimeProp);
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1596	>	int nZConstraints;
1597	>	ZconStamp** zconStamp;
1598	>
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);
1603	>	zconsTimeProp->setData(globals->getZconsTime());
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();
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()){
1619	+	zconsTol->setData(globals->getZconsTol());
1620	+	}
1621	+	else{
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	+
1631	+	zconsTol->setData(defaultZConsTol);
1632		}
1633	<
1634	<	if(globals->haveIndexOfAllZConsMols()){
1635	<
1636	<	//add index of z-constraint molecules into SimInfo's property list
1637	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1638	<
1639	<	//sort the index
1640	<	sort(tempIndex.begin(), tempIndex.end());
1743	<
1744	<	IndexData* zconsIndex = new IndexData();
1745	<	zconsIndex->setID("zconsindex");
1746	<	zconsIndex->setIndexData(tempIndex);
1747	<	info->addProperty(zconsIndex);
1633	>	theInfo.addProperty(zconsTol);
1634	>
1635	>	//set Force Subtraction Policy
1636	>	StringData* zconsForcePolicy = new StringData();
1637	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	>
1639	>	if (globals->haveZconsForcePolicy()){
1640	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641		}
1642		else{
1643	<	sprintf( painCave.errMsg,
1644	<	"SimSetup error: If you use an ZConstraint\n"
1645	<	" , you must set index of z-constraint molecules.\n");
1646	<	painCave.isFatal = 1;
1647	<	simError();
1648	<
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	+
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	<
1658	<	string zconsOutput(info->finalName);
1659	<
1657	>
1658	>	string zconsOutput(theInfo.finalName);
1659	>
1660		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	<
1661	>
1662		StringData* zconsFilename = new StringData();
1663	<	zconsFilename->setID("zconsfilename");
1663	>	zconsFilename->setID(ZCONSFILENAME_ID);
1664		zconsFilename->setData(zconsOutput);
1665
1666	<	info->addProperty(zconsFilename);
1666	>	theInfo.addProperty(zconsFilename);
1667
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
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();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
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);
1700		}

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