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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 20 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
24	<	#define NPTfm_ENS      5
25	<	#define NVEZCONS_ENS   6
26	<	#define NVTZCONS_ENS   7
27	<	#define NPTiZCONS_ENS  8
28	<	#define NPTfZCONS_ENS  9
29	<	#define NPTimZCONS_ENS 10
30	<	#define NPTfmZCONS_ENS 11
27	>	#define NPTxyz_ENS     4
28
32	–	#define FF_DUFF 0
33	–	#define FF_LJ   1
34	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 55 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87		}
88
89
90	<	void SimSetup::parseFile( char* fileName ){
66	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
94	<	mpiEventLoop();
95	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
102	–	int i, j, k, globalAtomIndex;
103	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
#	Line 110 | Line 132 | void SimSetup::createSim(void){
132		sysObjectsCreation();
133
134		// check on the post processing info
135	<
135	>
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	if( !isInfoArray ) initSystemCoords();
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
123	–
124	–	// make the integrator
150
126	–	makeIntegrator();
127	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 133 | Line 156 | void SimSetup::createSim(void){
156
157		initFortran();
158
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165
137	–
166		}
167
168
169	<	void SimSetup::makeMolecules( void ){
170	<
171	<	int k,l;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186
187		bond_pair* theBonds;
188		bend_set* theBends;
189		torsion_set* theTorsions;
190
191	<
191	>	set<int> skipList;
192	>
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196	>
197		//init the forceField paramters
198
199		the_ff->readParams();
200
163	–
201		// init the atoms
202
203	<	double ux, uy, uz, u, uSqr;
167	<
168	<	for(k=0; k<nInfo; k++){
169	<
170	<	the_ff->setSimInfo( &(info[k]) );
203	>	int nMembers, nNew, rb1, rb2;
204
205	+	for (k = 0; k < nInfo; k++){
206	+	the_ff->setSimInfo(&(info[k]));
207	+
208		atomOffset = 0;
209	<	excludeOffset = 0;
210	<	for(i=0; i<info[k].n_mol; i++){
175	<
209	>
210	>	for (i = 0; i < info[k].n_mol; i++){
211		stampID = info[k].molecules[i].getStampID();
212	+	molName = comp_stamps[stampID]->getID();
213
214	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
215	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
216	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219
220		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
185	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
186	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
187	–	molInfo.myBends = new Bend*[molInfo.nBends];
188	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
221
222	+	if (molInfo.nBonds > 0)
223	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	+	else
225	+	molInfo.myBonds = NULL;
226	+
227	+	if (molInfo.nBends > 0)
228	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	+	else
230	+	molInfo.myBends = NULL;
231	+
232	+	if (molInfo.nTorsions > 0)
233	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	+	else
235	+	molInfo.myTorsions = NULL;
236	+
237		theBonds = new bond_pair[molInfo.nBonds];
238		theBends = new bend_set[molInfo.nBends];
239		theTorsions = new torsion_set[molInfo.nTorsions];
240	<
240	>
241		// make the Atoms
242	<
243	<	for(j=0; j<molInfo.nAtoms; j++){
244	<
245	<	currentAtom = comp_stamps[stampID]->getAtom( j );
246	<	if( currentAtom->haveOrientation() ){
247	<
248	<	dAtom = new DirectionalAtom( (j + atomOffset),
249	<	info[k].getConfiguration() );
250	<	info[k].n_oriented++;
251	<	molInfo.myAtoms[j] = dAtom;
252	<
253	<	ux = currentAtom->getOrntX();
254	<	uy = currentAtom->getOrntY();
255	<	uz = currentAtom->getOrntZ();
256	<
257	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258	<
259	<	u = sqrt( uSqr );
260	<	ux = ux / u;
261	<	uy = uy / u;
262	<	uz = uz / u;
263	<
264	<	dAtom->setSUx( ux );
265	<	dAtom->setSUy( uy );
266	<	dAtom->setSUz( uz );
267	<	}
268	<	else{
269	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
223	<	info[k].getConfiguration() );
224	<	}
225	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
226	<
242	>
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245	>
246	>	if (currentAtom->haveOrientation()){
247	>	dAtom = new DirectionalAtom((j + atomOffset),
248	>	info[k].getConfiguration());
249	>	info[k].n_oriented++;
250	>	molInfo.myAtoms[j] = dAtom;
251	>
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255	>
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259	>
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264	>
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266	>
267	>	}
268	>
269	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271	<
272	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
273	<
271	>
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273	>
274		#endif // is_mpi
275		}
276	<
277	<	// make the bonds
278	<	for(j=0; j<molInfo.nBonds; j++){
279	<
280	<	currentBond = comp_stamps[stampID]->getBond( j );
281	<	theBonds[j].a = currentBond->getA() + atomOffset;
282	<	theBonds[j].b = currentBond->getB() + atomOffset;
283	<
284	<	exI = theBonds[j].a;
285	<	exJ = theBonds[j].b;
286	<
287	<	// exclude_I must always be the smaller of the pair
288	<	if( exI > exJ ){
289	<	tempEx = exI;
290	<	exI = exJ;
291	<	exJ = tempEx;
292	<	}
293	<	#ifdef IS_MPI
294	<	tempEx = exI;
295	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
296	<	tempEx = exJ;
254	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
255	<
256	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
257	<	#else  // isn't MPI
258	<
259	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
260	<	#endif  //is_mpi
261	<	}
262	<	excludeOffset += molInfo.nBonds;
263	<
276	>
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282	>
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285	>
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293	>
294	>	info[k].excludes->addPair(exI, exJ);
295	>	}
296	>
297		//make the bends
298	<	for(j=0; j<molInfo.nBends; j++){
299	<
300	<	currentBend = comp_stamps[stampID]->getBend( j );
301	<	theBends[j].a = currentBend->getA() + atomOffset;
302	<	theBends[j].b = currentBend->getB() + atomOffset;
303	<	theBends[j].c = currentBend->getC() + atomOffset;
304	<
305	<	if( currentBend->haveExtras() ){
306	<
307	<	extras = currentBend->getExtras();
308	<	current_extra = extras;
309	<
310	<	while( current_extra != NULL ){
311	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
312	<
313	<	switch( current_extra->getType() ){
314	<
315	<	case 0:
316	<	theBends[j].ghost =
317	<	current_extra->getInt() + atomOffset;
318	<	theBends[j].isGhost = 1;
319	<	break;
320	<
321	<	case 1:
322	<	theBends[j].ghost =
323	<	(int)current_extra->getDouble() + atomOffset;
324	<	theBends[j].isGhost = 1;
325	<	break;
326	<
327	<	default:
328	<	sprintf( painCave.errMsg,
329	<	"SimSetup Error: ghostVectorSource was neither a "
330	<	"double nor an int.\n"
331	<	"-->Bend[%d] in %s\n",
332	<	j, comp_stamps[stampID]->getID() );
333	<	painCave.isFatal = 1;
334	<	simError();
335	<	}
336	<	}
337	<
338	<	else{
339	<
340	<	sprintf( painCave.errMsg,
341	<	"SimSetup Error: unhandled bend assignment:\n"
342	<	"    -->%s in Bend[%d] in %s\n",
343	<	current_extra->getlhs(),
344	<	j, comp_stamps[stampID]->getID() );
345	<	painCave.isFatal = 1;
346	<	simError();
347	<	}
348	<
349	<	current_extra = current_extra->getNext();
317	<	}
318	<	}
319	<
320	<	if( !theBends[j].isGhost ){
321	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].c;
324	<	}
325	<	else{
326	<
327	<	exI = theBends[j].a;
328	<	exJ = theBends[j].b;
329	<	}
330	<
331	<	// exclude_I must always be the smaller of the pair
332	<	if( exI > exJ ){
333	<	tempEx = exI;
334	<	exI = exJ;
335	<	exJ = tempEx;
336	<	}
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303	>
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307	>
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315	>
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321	>
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>
341	>	current_extra = current_extra->getNext();
342	>	}
343	>	}
344	>
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350		#ifdef IS_MPI
351	<	tempEx = exI;
352	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
353	<	tempEx = exJ;
354	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
355	<
356	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
357	<	#else  // isn't MPI
358	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
359	<	#endif  //is_mpi
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358	>
359	>	} else {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
380	<	excludeOffset += molInfo.nBends;
381	<
382	<	for(j=0; j<molInfo.nTorsions; j++){
383	<
384	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
385	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
386	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
387	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
388	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
389	<
390	<	exI = theTorsions[j].a;
391	<	exJ = theTorsions[j].d;
392	<
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	<	}
380	>
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387	>
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392	>
393		#ifdef IS_MPI
394	<	tempEx = exI;
395	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
396	<	tempEx = exJ;
397	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
398	<
399	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
400	<	#else  // isn't MPI
401	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
402	<	#endif  //is_mpi
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404	>
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411		}
412	<	excludeOffset += molInfo.nTorsions;
412	>
413
414	+	molInfo.myRigidBodies.clear();
415
416	<	// send the arrays off to the forceField for init.
417	<
418	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
419	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
420	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
421	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417	>
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420	>
421	>	// Create the Rigid Body:
422	>
423	>	myRB = new RigidBody();
424	>
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	>
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432	>
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435	>
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	>
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478	>
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481	>	}
482
483	+
484	+	// After this is all set up, scan through the atoms to
485	+	// see if they can be added to the integrableObjects:
486	+
487	+	molInfo.myIntegrableObjects.clear();
488
389	–	info[k].molecules[i].initialize( molInfo );
489
490	+	for (j = 0; j < molInfo.nAtoms; j++){
491	+
492	+	#ifdef IS_MPI
493	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	+	#else
495	+	slJ = j+atomOffset;
496	+	#endif
497	+
498	+	// if they aren't on the skip list, then they can be integrated
499	+
500	+	if (skipList.find(slJ) == skipList.end()) {
501	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	+	info[k].integrableObjects.push_back(mySD);
503	+	molInfo.myIntegrableObjects.push_back(mySD);
504	+	}
505	+	}
506	+
507	+	// all rigid bodies are integrated:
508	+
509	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	+	info[k].integrableObjects.push_back(mySD);
512	+	molInfo.myIntegrableObjects.push_back(mySD);
513	+	}
514	+
515
516	+	// send the arrays off to the forceField for init.
517	+
518	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	+	theTorsions);
523	+
524	+	info[k].molecules[i].initialize(molInfo);
525	+
526	+
527		atomOffset += molInfo.nAtoms;
528		delete[] theBonds;
529		delete[] theBends;
530		delete[] theTorsions;
531	<	}
531	>	}
532		}
533	<
533	>
534		#ifdef IS_MPI
535	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
538	<
538	>
539		// clean up the forcefield
540
541	<	the_ff->calcRcut();
541	>	if (!globals->haveLJrcut()){
542	>
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getLJrcut() );
548	>	}
549	>
550		the_ff->cleanMe();
408	–
551		}
552
553	<	void SimSetup::initFromBass( void ){
412	<
553	>	void SimSetup::initFromBass(void){
554		int i, j, k;
555		int n_cells;
556		double cellx, celly, cellz;
#	Line 423 | Line 564 | void SimSetup::initFromBass( void ){
564		vel[1] = 0.0;
565		vel[2] = 0.0;
566
567	<	temp1 = (double)tot_nmol / 4.0;
568	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
569	<	temp3 = ceil( temp2 );
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	<	have_extra =0;
572	<	if( temp2 < temp3 ){ // we have a non-complete lattice
573	<	have_extra =1;
571	>	have_extra = 0;
572	>	if (temp2 < temp3){
573	>	// we have a non-complete lattice
574	>	have_extra = 1;
575
576	<	n_cells = (int)temp3 - 1;
576	>	n_cells = (int) temp3 - 1;
577		cellx = info[0].boxL[0] / temp3;
578		celly = info[0].boxL[1] / temp3;
579		cellz = info[0].boxL[2] / temp3;
580	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
581	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
582	<	n_per_extra = (int)ceil( temp1 );
580	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	>	n_per_extra = (int) ceil(temp1);
583
584	<	if( n_per_extra > 4){
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup error. There has been an error in constructing"
587	<	" the non-complete lattice.\n" );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588		painCave.isFatal = 1;
589		simError();
590		}
591		}
592		else{
593	<	n_cells = (int)temp3;
593	>	n_cells = (int) temp3;
594		cellx = info[0].boxL[0] / temp3;
595		celly = info[0].boxL[1] / temp3;
596		cellz = info[0].boxL[2] / temp3;
#	Line 459 | Line 601 | void SimSetup::initFromBass( void ){
601		current_comp = 0;
602		current_atom_ndx = 0;
603
604	<	for( i=0; i < n_cells ; i++ ){
605	<	for( j=0; j < n_cells; j++ ){
606	<	for( k=0; k < n_cells; k++ ){
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	makeElement( i * cellx,
467	<	j * celly,
468	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	makeElement( i * cellx,
475	<	j * celly + 0.5 * celly,
476	<	k * cellz + 0.5 * cellz );
477	<
478	<	makeElement( i * cellx + 0.5 * cellx,
479	<	j * celly,
480	<	k * cellz + 0.5 * cellz );
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
615		}
616		}
617
618	<	if( have_extra ){
618	>	if (have_extra){
619		done = 0;
620
621		int start_ndx;
622	<	for( i=0; i < (n_cells+1) && !done; i++ ){
623	<	for( j=0; j < (n_cells+1) && !done; j++ ){
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	if( i < n_cells ){
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( j < n_cells ){
639	<	start_ndx = n_cells;
640	<	}
641	<	else start_ndx = 0;
642	<	}
499	<	else start_ndx = 0;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	makeElement( i * cellx,
651	<	j * celly,
652	<	k * cellz );
653	<	done = ( current_mol >= tot_nmol );
654	<
655	<	if( !done && n_per_extra > 1 ){
509	<	makeElement( i * cellx + 0.5 * cellx,
510	<	j * celly + 0.5 * celly,
511	<	k * cellz );
512	<	done = ( current_mol >= tot_nmol );
513	<	}
514	<
515	<	if( !done && n_per_extra > 2){
516	<	makeElement( i * cellx,
517	<	j * celly + 0.5 * celly,
518	<	k * cellz + 0.5 * cellz );
519	<	done = ( current_mol >= tot_nmol );
520	<	}
521	<
522	<	if( !done && n_per_extra > 3){
523	<	makeElement( i * cellx + 0.5 * cellx,
524	<	j * celly,
525	<	k * cellz + 0.5 * cellz );
526	<	done = ( current_mol >= tot_nmol );
527	<	}
528	<	}
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657		}
658		}
659
660	<	for( i=0; i<info[0].n_atoms; i++ ){
661	<	info[0].atoms[i]->setVel( vel );
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662		}
663		}
664
665	<	void SimSetup::makeElement( double x, double y, double z ){
539	<
665	>	void SimSetup::makeElement(double x, double y, double z){
666		int k;
667		AtomStamp* current_atom;
668		DirectionalAtom* dAtom;
669		double rotMat[3][3];
670		double pos[3];
671
672	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
673	<
674	<	current_atom = comp_stamps[current_comp]->getAtom( k );
675	<	if( !current_atom->havePosition() ){
676	<	sprintf( painCave.errMsg,
677	<	"SimSetup:initFromBass error.\n"
678	<	"\tComponent %s, atom %s does not have a position specified.\n"
679	<	"\tThe initialization routine is unable to give a start"
680	<	" position.\n",
555	<	comp_stamps[current_comp]->getID(),
556	<	current_atom->getType() );
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
684	<
684	>
685		pos[0] = x + current_atom->getPosX();
686		pos[1] = y + current_atom->getPosY();
687		pos[2] = z + current_atom->getPosZ();
564	–
565	–	info[0].atoms[current_atom_ndx]->setPos( pos );
688
689	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694		rotMat[0][0] = 1.0;
695		rotMat[0][1] = 0.0;
#	Line 580 | Line 703 | void SimSetup::makeElement( double x, double y, double
703		rotMat[2][1] = 0.0;
704		rotMat[2][2] = 1.0;
705
706	<	dAtom->setA( rotMat );
706	>	dAtom->setA(rotMat);
707		}
708
709		current_atom_ndx++;
#	Line 589 | Line 712 | void SimSetup::makeElement( double x, double y, double
712		current_mol++;
713		current_comp_mol++;
714
715	<	if( current_comp_mol >= components_nmol[current_comp] ){
593	<
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716		current_comp_mol = 0;
717		current_comp++;
718		}
719		}
720
721
722	<	void SimSetup::gatherInfo( void ){
723	<	int i,j,k;
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725		ensembleCase = -1;
726		ffCase = -1;
727
728		// set the easy ones first
729
730	<	for( i=0; i<nInfo; i++){
730	>	for (i = 0; i < nInfo; i++){
731		info[i].target_temp = globals->getTargetTemp();
732		info[i].dt = globals->getDt();
733		info[i].run_time = globals->getRunTime();
#	Line 615 | Line 737 | void SimSetup::gatherInfo( void ){
737
738		// get the forceField
739
740	<	strcpy( force_field, globals->getForceField() );
740	>	strcpy(force_field, globals->getForceField());
741
742	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
743	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
744	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
742	>	if (!strcasecmp(force_field, "DUFF")){
743	>	ffCase = FF_DUFF;
744	>	}
745	>	else if (!strcasecmp(force_field, "LJ")){
746	>	ffCase = FF_LJ;
747	>	}
748	>	else if (!strcasecmp(force_field, "EAM")){
749	>	ffCase = FF_EAM;
750	>	}
751	>	else if (!strcasecmp(force_field, "WATER")){
752	>	ffCase = FF_H2O;
753	>	}
754		else{
755	<	sprintf( painCave.errMsg,
756	<	"SimSetup Error. Unrecognized force field -> %s\n",
757	<	force_field );
758	<	painCave.isFatal = 1;
628	<	simError();
755	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	>	force_field);
757	>	painCave.isFatal = 1;
758	>	simError();
759		}
760
761	<	// get the ensemble
761	>	// get the ensemble
762
763	<	strcpy( ensemble, globals->getEnsemble() );
763	>	strcpy(ensemble, globals->getEnsemble());
764
765	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
766	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
767	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
765	>	if (!strcasecmp(ensemble, "NVE")){
766	>	ensembleCase = NVE_ENS;
767	>	}
768	>	else if (!strcasecmp(ensemble, "NVT")){
769	>	ensembleCase = NVT_ENS;
770	>	}
771	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772		ensembleCase = NPTi_ENS;
773	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
774	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
775	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
776	<
777	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
778	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
779	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	<	ensembleCase = NPTiZCONS_ENS;
647	<	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	<	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	<
773	>	}
774	>	else if (!strcasecmp(ensemble, "NPTf")){
775	>	ensembleCase = NPTf_ENS;
776	>	}
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779	>	}
780		else{
781	<	sprintf( painCave.errMsg,
782	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
783	<	"reverting to NVE for this simulation.\n",
784	<	ensemble );
785	<	painCave.isFatal = 0;
786	<	simError();
787	<	strcpy( ensemble, "NVE" );
788	<	ensembleCase = NVE_ENS;
781	>	sprintf(painCave.errMsg,
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784	>	ensemble);
785	>	painCave.isFatal = 0;
786	>	simError();
787	>	strcpy(ensemble, "NVE");
788	>	ensembleCase = NVE_ENS;
789		}
661	–
662	–	for(i=0; i<nInfo; i++){
663	–
664	–	strcpy( info[i].ensemble, ensemble );
790
791	+	for (i = 0; i < nInfo; i++){
792	+	strcpy(info[i].ensemble, ensemble);
793	+
794		// get the mixing rule
795
796	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797		info[i].usePBC = globals->getPBC();
798		}
799	<
799	>
800		// get the components and calculate the tot_nMol and indvidual n_mol
801	<
801	>
802		the_components = globals->getComponents();
803		components_nmol = new int[n_components];
804
805
806	<	if( !globals->haveNMol() ){
806	>	if (!globals->haveNMol()){
807		// we don't have the total number of molecules, so we assume it is
808		// given in each component
809
810		tot_nmol = 0;
811	<	for( i=0; i<n_components; i++ ){
812	<
813	<	if( !the_components[i]->haveNMol() ){
814	<	// we have a problem
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup Error. No global NMol or component NMol"
817	<	" given. Cannot calculate the number of atoms.\n" );
818	<	painCave.isFatal = 1;
691	<	simError();
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819		}
820
821		tot_nmol += the_components[i]->getNMol();
#	Line 696 | Line 823 | void SimSetup::gatherInfo( void ){
823		}
824		}
825		else{
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup error.\n"
828	<	"\tSorry, the ability to specify total"
829	<	" nMols and then give molfractions in the components\n"
830	<	"\tis not currently supported."
831	<	" Please give nMol in the components.\n" );
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup error.\n"
828	>	"\tSorry, the ability to specify total"
829	>	" nMols and then give molfractions in the components\n"
830	>	"\tis not currently supported."
831	>	" Please give nMol in the components.\n");
832		painCave.isFatal = 1;
833		simError();
834		}
835
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time.  If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time.  If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time.  If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time.  If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876	+
877		// set the status, sample, and thermal kick times
710	–
711	–	for(i=0; i<nInfo; i++){
878
879	<	if( globals->haveSampleTime() ){
879	>	for (i = 0; i < nInfo; i++){
880	>	if (globals->haveSampleTime()){
881		info[i].sampleTime = globals->getSampleTime();
882		info[i].statusTime = info[i].sampleTime;
716	–	info[i].thermalTime = info[i].sampleTime;
883		}
884		else{
885		info[i].sampleTime = globals->getRunTime();
886		info[i].statusTime = info[i].sampleTime;
721	–	info[i].thermalTime = info[i].sampleTime;
887		}
888	<
889	<	if( globals->haveStatusTime() ){
888	>
889	>	if (globals->haveStatusTime()){
890		info[i].statusTime = globals->getStatusTime();
891		}
892	<
893	<	if( globals->haveThermalTime() ){
892	>
893	>	if (globals->haveThermalTime()){
894		info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897		}
898
899	+	info[i].resetIntegrator = 0;
900	+	if( globals->haveResetTime() ){
901	+	info[i].resetTime = globals->getResetTime();
902	+	info[i].resetIntegrator = 1;
903	+	}
904	+
905		// check for the temperature set flag
906	+
907	+	if (globals->haveTempSet())
908	+	info[i].setTemp = globals->getTempSet();
909
910	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
910	>	// check for the extended State init
911	>
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	>	info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915	>
916
736	–	// get some of the tricky things that may still be in the globals
737	–
738	–	double boxVector[3];
739	–	if( globals->haveBox() ){
740	–	boxVector[0] = globals->getBox();
741	–	boxVector[1] = globals->getBox();
742	–	boxVector[2] = globals->getBox();
743	–
744	–	info[i].setBox( boxVector );
745	–	}
746	–	else if( globals->haveDensity() ){
747	–
748	–	double vol;
749	–	vol = (double)tot_nmol / globals->getDensity();
750	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	–	boxVector[1] = boxVector[0];
752	–	boxVector[2] = boxVector[0];
753	–
754	–	info[i].setBox( boxVector );
917		}
918	<	else{
919	<	if( !globals->haveBoxX() ){
920	<	sprintf( painCave.errMsg,
921	<	"SimSetup error, no periodic BoxX size given.\n" );
922	<	painCave.isFatal = 1;
923	<	simError();
918	>
919	>	//setup seed for random number generator
920	>	int seedValue;
921	>
922	>	if (globals->haveSeed()){
923	>	seedValue = globals->getSeed();
924	>
925	>	if(seedValue / 1E9 == 0){
926	>	sprintf(painCave.errMsg,
927	>	"Seed for sprng library should contain at least 9 digits\n"
928	>	"OOPSE will generate a seed for user\n");
929	>	painCave.isFatal = 0;
930	>	simError();
931	>
932	>	//using seed generated by system instead of invalid seed set by user
933	>	#ifndef IS_MPI
934	>	seedValue = make_sprng_seed();
935	>	#else
936	>	if (worldRank == 0){
937	>	seedValue = make_sprng_seed();
938		}
939	<	boxVector[0] = globals->getBoxX();
940	<
765	<	if( !globals->haveBoxY() ){
766	<	sprintf( painCave.errMsg,
767	<	"SimSetup error, no periodic BoxY size given.\n" );
768	<	painCave.isFatal = 1;
769	<	simError();
770	<	}
771	<	boxVector[1] = globals->getBoxY();
772	<
773	<	if( !globals->haveBoxZ() ){
774	<	sprintf( painCave.errMsg,
775	<	"SimSetup error, no periodic BoxZ size given.\n" );
776	<	painCave.isFatal = 1;
777	<	simError();
778	<	}
779	<	boxVector[2] = globals->getBoxZ();
780	<
781	<	info[i].setBox( boxVector );
939	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
940	>	#endif
941		}
942	+	}//end of if branch of globals->haveSeed()
943	+	else{
944	+
945	+	#ifndef IS_MPI
946	+	seedValue = make_sprng_seed();
947	+	#else
948	+	if (worldRank == 0){
949	+	seedValue = make_sprng_seed();
950	+	}
951	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
952	+	#endif
953	+	}//end of globals->haveSeed()
954
955	+	for (int i = 0; i < nInfo; i++){
956	+	info[i].setSeed(seedValue);
957		}
958	<
958	>
959		#ifdef IS_MPI
960	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
960	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
961		MPIcheckPoint();
962		#endif // is_mpi
790	–
963		}
964
965
966	<	void SimSetup::finalInfoCheck( void ){
966	>	void SimSetup::finalInfoCheck(void){
967		int index;
968		int usesDipoles;
969	+	int usesCharges;
970		int i;
971
972	<	for(i=0; i<nInfo; i++){
972	>	for (i = 0; i < nInfo; i++){
973		// check electrostatic parameters
974	<
974	>
975		index = 0;
976		usesDipoles = 0;
977	<	while( (index < info[i].n_atoms) && !usesDipoles ){
977	>	while ((index < info[i].n_atoms) && !usesDipoles){
978		usesDipoles = (info[i].atoms[index])->hasDipole();
979		index++;
980		}
981	<
981	>	index = 0;
982	>	usesCharges = 0;
983	>	while ((index < info[i].n_atoms) && !usesCharges){
984	>	usesCharges= (info[i].atoms[index])->hasCharge();
985	>	index++;
986	>	}
987		#ifdef IS_MPI
988		int myUse = usesDipoles;
989	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
989	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
990		#endif //is_mpi
991	<
991	>
992		double theEcr, theEst;
993	<
994	<	if (globals->getUseRF() ) {
993	>
994	>	if (globals->getUseRF()){
995		info[i].useReactionField = 1;
996	<
997	<	if( !globals->haveECR() ){
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Warning: using default value of 1/2 the smallest "
1000	<	"box length for the electrostaticCutoffRadius.\n"
1001	<	"I hope you have a very fast processor!\n");
1002	<	painCave.isFatal = 0;
1003	<	simError();
1004	<	double smallest;
827	<	smallest = info[i].boxL[0];
828	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830	<	theEcr = 0.5 * smallest;
831	<	} else {
832	<	theEcr = globals->getECR();
996	>
997	>	if (!globals->haveECR()){
998	>	sprintf(painCave.errMsg,
999	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1000	>	"\tOOPSE will use a default value of 15.0 angstroms"
1001	>	"\tfor the electrostaticCutoffRadius.\n");
1002	>	painCave.isFatal = 0;
1003	>	simError();
1004	>	theEcr = 15.0;
1005		}
1006	<
1007	<	if( !globals->haveEST() ){
836	<	sprintf( painCave.errMsg,
837	<	"SimSetup Warning: using default value of 0.05 * the "
838	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	<	);
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	theEst = 0.05 * theEcr;
843	<	} else {
844	<	theEst= globals->getEST();
1006	>	else{
1007	>	theEcr = globals->getECR();
1008		}
1009	<
1010	<	info[i].setEcr( theEcr, theEst );
1011	<
1012	<	if(!globals->haveDielectric() ){
1013	<	sprintf( painCave.errMsg,
1014	<	"SimSetup Error: You are trying to use Reaction Field without"
1015	<	"setting a dielectric constant!\n"
1016	<	);
1017	<	painCave.isFatal = 1;
1018	<	simError();
1009	>
1010	>	if (!globals->haveEST()){
1011	>	sprintf(painCave.errMsg,
1012	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1013	>	"\tOOPSE will use a default value of\n"
1014	>	"\t0.05 * electrostaticCutoffRadius\n"
1015	>	"\tfor the electrostaticSkinThickness\n");
1016	>	painCave.isFatal = 0;
1017	>	simError();
1018	>	theEst = 0.05 * theEcr;
1019		}
1020	<	info[i].dielectric = globals->getDielectric();
1021	<	}
1022	<	else {
1023	<	if (usesDipoles) {
1024	<
1025	<	if( !globals->haveECR() ){
1026	<	sprintf( painCave.errMsg,
1027	<	"SimSetup Warning: using default value of 1/2 the smallest "
1028	<	"box length for the electrostaticCutoffRadius.\n"
1029	<	"I hope you have a very fast processor!\n");
1020	>	else{
1021	>	theEst = globals->getEST();
1022	>	}
1023	>
1024	>	info[i].setDefaultEcr(theEcr, theEst);
1025	>
1026	>	if (!globals->haveDielectric()){
1027	>	sprintf(painCave.errMsg,
1028	>	"SimSetup Error: No Dielectric constant was set.\n"
1029	>	"\tYou are trying to use Reaction Field without"
1030	>	"\tsetting a dielectric constant!\n");
1031	>	painCave.isFatal = 1;
1032	>	simError();
1033	>	}
1034	>	info[i].dielectric = globals->getDielectric();
1035	>	}
1036	>	else{
1037	>	if (usesDipoles || usesCharges){
1038	>	if (!globals->haveECR()){
1039	>	sprintf(painCave.errMsg,
1040	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1041	>	"\tOOPSE will use a default value of 15.0 angstroms"
1042	>	"\tfor the electrostaticCutoffRadius.\n");
1043		painCave.isFatal = 0;
1044		simError();
1045	<	double smallest;
1046	<	smallest = info[i].boxL[0];
1047	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
1048	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
1049	<	theEcr = 0.5 * smallest;
874	<	} else {
875	<	theEcr = globals->getECR();
876	<	}
1045	>	theEcr = 15.0;
1046	>	}
1047	>	else{
1048	>	theEcr = globals->getECR();
1049	>	}
1050
1051	<	if( !globals->haveEST() ){
1052	<	sprintf( painCave.errMsg,
1053	<	"SimSetup Warning: using default value of 0.05 * the "
1054	<	"electrostaticCutoffRadius for the "
1055	<	"electrostaticSkinThickness\n"
1056	<	);
1057	<	painCave.isFatal = 0;
1058	<	simError();
1059	<	theEst = 0.05 * theEcr;
1060	<	} else {
1061	<	theEst= globals->getEST();
1062	<	}
1051	>	if (!globals->haveEST()){
1052	>	sprintf(painCave.errMsg,
1053	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1054	>	"\tOOPSE will use a default value of\n"
1055	>	"\t0.05 * electrostaticCutoffRadius\n"
1056	>	"\tfor the electrostaticSkinThickness\n");
1057	>	painCave.isFatal = 0;
1058	>	simError();
1059	>	theEst = 0.05 * theEcr;
1060	>	}
1061	>	else{
1062	>	theEst = globals->getEST();
1063	>	}
1064
1065	<	info[i].setEcr( theEcr, theEst );
1065	>	info[i].setDefaultEcr(theEcr, theEst);
1066		}
1067	<	}
1067	>	}
1068		}
895	–
1069		#ifdef IS_MPI
1070	<	strcpy( checkPointMsg, "post processing checks out" );
1070	>	strcpy(checkPointMsg, "post processing checks out");
1071		MPIcheckPoint();
1072		#endif // is_mpi
900	–
1073		}
902	–
903	–	void SimSetup::initSystemCoords( void ){
904	–	int i;
1074
1075	<	std::cerr << "Setting atom Coords\n";
1075	>	void SimSetup::initSystemCoords(void){
1076	>	int i;
1077
1078	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1079	<
1080	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1081	<
1082	<	if( globals->haveInitialConfig() ){
1083	<
1078	>	char* inName;
1079	>
1080	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1081	>
1082	>	for (i = 0; i < info[0].n_atoms; i++)
1083	>	info[0].atoms[i]->setCoords();
1084	>
1085	>	if (globals->haveInitialConfig()){
1086		InitializeFromFile* fileInit;
1087		#ifdef IS_MPI // is_mpi
1088	<	if( worldRank == 0 ){
1088	>	if (worldRank == 0){
1089		#endif //is_mpi
1090	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
1090	>	inName = globals->getInitialConfig();
1091	>	fileInit = new InitializeFromFile(inName);
1092		#ifdef IS_MPI
1093	<	}else fileInit = new InitializeFromFile( NULL );
1093	>	}
1094	>	else
1095	>	fileInit = new InitializeFromFile(NULL);
1096		#endif
1097	<	fileInit->readInit( info ); // default velocities on
1098	<
1097	>	fileInit->readInit(info); // default velocities on
1098	>
1099		delete fileInit;
1100		}
1101		else{
1102
928	–	#ifdef IS_MPI
929	–
1103		// no init from bass
1104
1105	<	sprintf( painCave.errMsg,
1106	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1107	<	painCave.isFatal;
1105	>	sprintf(painCave.errMsg,
1106	>	"Cannot intialize a simulation without an initial configuration file.\n");
1107	>	painCave.isFatal = 1;;
1108		simError();
1109
937	–	#else
938	–
939	–	initFromBass();
940	–
941	–
942	–	#endif
1110		}
1111	<
1111	>
1112		#ifdef IS_MPI
1113	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1113	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1114		MPIcheckPoint();
1115		#endif // is_mpi
949	–
1116		}
1117
1118
1119	<	void SimSetup::makeOutNames( void ){
954	<
1119	>	void SimSetup::makeOutNames(void){
1120		int k;
1121
957	–
958	–	for(k=0; k<nInfo; k++){
1122
1123	+	for (k = 0; k < nInfo; k++){
1124		#ifdef IS_MPI
1125	<	if( worldRank == 0 ){
1125	>	if (worldRank == 0){
1126		#endif // is_mpi
1127	<
1128	<	if( globals->haveFinalConfig() ){
1129	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1127	>
1128	>	if (globals->haveFinalConfig()){
1129	>	strcpy(info[k].finalName, globals->getFinalConfig());
1130		}
1131		else{
1132	<	strcpy( info[k].finalName, inFileName );
1133	<	char* endTest;
1134	<	int nameLength = strlen( info[k].finalName );
1135	<	endTest = &(info[k].finalName[nameLength - 5]);
1136	<	if( !strcmp( endTest, ".bass" ) ){
1137	<	strcpy( endTest, ".eor" );
1138	<	}
1139	<	else if( !strcmp( endTest, ".BASS" ) ){
1140	<	strcpy( endTest, ".eor" );
1141	<	}
1142	<	else{
1143	<	endTest = &(info[k].finalName[nameLength - 4]);
1144	<	if( !strcmp( endTest, ".bss" ) ){
1145	<	strcpy( endTest, ".eor" );
1146	<	}
1147	<	else if( !strcmp( endTest, ".mdl" ) ){
1148	<	strcpy( endTest, ".eor" );
1149	<	}
1150	<	else{
1151	<	strcat( info[k].finalName, ".eor" );
1152	<	}
1153	<	}
1132	>	strcpy(info[k].finalName, inFileName);
1133	>	char* endTest;
1134	>	int nameLength = strlen(info[k].finalName);
1135	>	endTest = &(info[k].finalName[nameLength - 5]);
1136	>	if (!strcmp(endTest, ".bass")){
1137	>	strcpy(endTest, ".eor");
1138	>	}
1139	>	else if (!strcmp(endTest, ".BASS")){
1140	>	strcpy(endTest, ".eor");
1141	>	}
1142	>	else{
1143	>	endTest = &(info[k].finalName[nameLength - 4]);
1144	>	if (!strcmp(endTest, ".bss")){
1145	>	strcpy(endTest, ".eor");
1146	>	}
1147	>	else if (!strcmp(endTest, ".mdl")){
1148	>	strcpy(endTest, ".eor");
1149	>	}
1150	>	else{
1151	>	strcat(info[k].finalName, ".eor");
1152	>	}
1153	>	}
1154		}
1155	<
1155	>
1156		// make the sample and status out names
1157	<
1158	<	strcpy( info[k].sampleName, inFileName );
1157	>
1158	>	strcpy(info[k].sampleName, inFileName);
1159		char* endTest;
1160	<	int nameLength = strlen( info[k].sampleName );
1160	>	int nameLength = strlen(info[k].sampleName);
1161		endTest = &(info[k].sampleName[nameLength - 5]);
1162	<	if( !strcmp( endTest, ".bass" ) ){
1163	<	strcpy( endTest, ".dump" );
1162	>	if (!strcmp(endTest, ".bass")){
1163	>	strcpy(endTest, ".dump");
1164		}
1165	<	else if( !strcmp( endTest, ".BASS" ) ){
1166	<	strcpy( endTest, ".dump" );
1165	>	else if (!strcmp(endTest, ".BASS")){
1166	>	strcpy(endTest, ".dump");
1167		}
1168		else{
1169	<	endTest = &(info[k].sampleName[nameLength - 4]);
1170	<	if( !strcmp( endTest, ".bss" ) ){
1171	<	strcpy( endTest, ".dump" );
1172	<	}
1173	<	else if( !strcmp( endTest, ".mdl" ) ){
1174	<	strcpy( endTest, ".dump" );
1175	<	}
1176	<	else{
1177	<	strcat( info[k].sampleName, ".dump" );
1178	<	}
1169	>	endTest = &(info[k].sampleName[nameLength - 4]);
1170	>	if (!strcmp(endTest, ".bss")){
1171	>	strcpy(endTest, ".dump");
1172	>	}
1173	>	else if (!strcmp(endTest, ".mdl")){
1174	>	strcpy(endTest, ".dump");
1175	>	}
1176	>	else{
1177	>	strcat(info[k].sampleName, ".dump");
1178	>	}
1179		}
1180	<
1181	<	strcpy( info[k].statusName, inFileName );
1182	<	nameLength = strlen( info[k].statusName );
1180	>
1181	>	strcpy(info[k].statusName, inFileName);
1182	>	nameLength = strlen(info[k].statusName);
1183		endTest = &(info[k].statusName[nameLength - 5]);
1184	<	if( !strcmp( endTest, ".bass" ) ){
1185	<	strcpy( endTest, ".stat" );
1184	>	if (!strcmp(endTest, ".bass")){
1185	>	strcpy(endTest, ".stat");
1186		}
1187	<	else if( !strcmp( endTest, ".BASS" ) ){
1188	<	strcpy( endTest, ".stat" );
1187	>	else if (!strcmp(endTest, ".BASS")){
1188	>	strcpy(endTest, ".stat");
1189		}
1190		else{
1191	<	endTest = &(info[k].statusName[nameLength - 4]);
1192	<	if( !strcmp( endTest, ".bss" ) ){
1193	<	strcpy( endTest, ".stat" );
1194	<	}
1195	<	else if( !strcmp( endTest, ".mdl" ) ){
1196	<	strcpy( endTest, ".stat" );
1197	<	}
1198	<	else{
1199	<	strcat( info[k].statusName, ".stat" );
1200	<	}
1201	<	}
1202	<
1191	>	endTest = &(info[k].statusName[nameLength - 4]);
1192	>	if (!strcmp(endTest, ".bss")){
1193	>	strcpy(endTest, ".stat");
1194	>	}
1195	>	else if (!strcmp(endTest, ".mdl")){
1196	>	strcpy(endTest, ".stat");
1197	>	}
1198	>	else{
1199	>	strcat(info[k].statusName, ".stat");
1200	>	}
1201	>	}
1202	>
1203		#ifdef IS_MPI
1204	+
1205		}
1206		#endif // is_mpi
1207		}
1208		}
1209
1210
1211	<	void SimSetup::sysObjectsCreation( void ){
1212	<
1213	<	int i,k;
1049	<
1211	>	void SimSetup::sysObjectsCreation(void){
1212	>	int i, k;
1213	>
1214		// create the forceField
1215	<
1215	>
1216		createFF();
1217
1218		// extract componentList
#	Line 1061 | Line 1225 | void SimSetup::sysObjectsCreation( void ){
1225
1226		#ifdef IS_MPI
1227		// divide the molecules among the processors
1228	<
1228	>
1229		mpiMolDivide();
1230		#endif //is_mpi
1231	<
1231	>
1232		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1233	<
1233	>
1234		makeSysArrays();
1235
1236		// make and initialize the molecules (all but atomic coordinates)
1237	<
1237	>
1238		makeMolecules();
1239	<
1240	<	for(k=0; k<nInfo; k++){
1239	>
1240	>	for (k = 0; k < nInfo; k++){
1241		info[k].identArray = new int[info[k].n_atoms];
1242	<	for(i=0; i<info[k].n_atoms; i++){
1242	>	for (i = 0; i < info[k].n_atoms; i++){
1243		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1244		}
1245		}
1246		}
1247
1248
1249	<	void SimSetup::createFF( void ){
1249	>	void SimSetup::createFF(void){
1250	>	switch (ffCase){
1251	>	case FF_DUFF:
1252	>	the_ff = new DUFF();
1253	>	break;
1254
1255	<	switch( ffCase ){
1255	>	case FF_LJ:
1256	>	the_ff = new LJFF();
1257	>	break;
1258
1259	<	case FF_DUFF:
1260	<	the_ff = new DUFF();
1261	<	break;
1259	>	case FF_EAM:
1260	>	the_ff = new EAM_FF();
1261	>	break;
1262
1263	<	case FF_LJ:
1264	<	the_ff = new LJFF();
1265	<	break;
1263	>	case FF_H2O:
1264	>	the_ff = new WATER();
1265	>	break;
1266
1267	<	case FF_EAM:
1268	<	the_ff = new EAM_FF();
1269	<	break;
1270	<
1271	<	default:
1102	<	sprintf( painCave.errMsg,
1103	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1104	<	painCave.isFatal = 1;
1105	<	simError();
1267	>	default:
1268	>	sprintf(painCave.errMsg,
1269	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1270	>	painCave.isFatal = 1;
1271	>	simError();
1272		}
1273
1274		#ifdef IS_MPI
1275	<	strcpy( checkPointMsg, "ForceField creation successful" );
1275	>	strcpy(checkPointMsg, "ForceField creation successful");
1276		MPIcheckPoint();
1277		#endif // is_mpi
1112	–
1278		}
1279
1280
1281	<	void SimSetup::compList( void ){
1117	<
1281	>	void SimSetup::compList(void){
1282		int i;
1283		char* id;
1284		LinkedMolStamp* headStamp = new LinkedMolStamp();
1285		LinkedMolStamp* currentStamp = NULL;
1286	<	comp_stamps = new MoleculeStamp*[n_components];
1287	<
1286	>	comp_stamps = new MoleculeStamp * [n_components];
1287	>
1288		// make an array of molecule stamps that match the components used.
1289		// also extract the used stamps out into a separate linked list
1290	<
1291	<	for(i=0; i<nInfo; i++){
1290	>
1291	>	for (i = 0; i < nInfo; i++){
1292		info[i].nComponents = n_components;
1293		info[i].componentsNmol = components_nmol;
1294		info[i].compStamps = comp_stamps;
1295		info[i].headStamp = headStamp;
1296		}
1133	–
1297
1135	–	for( i=0; i<n_components; i++ ){
1298
1299	+	for (i = 0; i < n_components; i++){
1300		id = the_components[i]->getType();
1301		comp_stamps[i] = NULL;
1302	<
1302	>
1303		// check to make sure the component isn't already in the list
1304
1305	<	comp_stamps[i] = headStamp->match( id );
1306	<	if( comp_stamps[i] == NULL ){
1144	<
1305	>	comp_stamps[i] = headStamp->match(id);
1306	>	if (comp_stamps[i] == NULL){
1307		// extract the component from the list;
1308	<
1309	<	currentStamp = stamps->extractMolStamp( id );
1310	<	if( currentStamp == NULL ){
1311	<	sprintf( painCave.errMsg,
1312	<	"SimSetup error: Component \"%s\" was not found in the "
1313	<	"list of declared molecules\n",
1314	<	id );
1315	<	painCave.isFatal = 1;
1316	<	simError();
1308	>
1309	>	currentStamp = stamps->extractMolStamp(id);
1310	>	if (currentStamp == NULL){
1311	>	sprintf(painCave.errMsg,
1312	>	"SimSetup error: Component \"%s\" was not found in the "
1313	>	"list of declared molecules\n",
1314	>	id);
1315	>	painCave.isFatal = 1;
1316	>	simError();
1317		}
1318	<
1319	<	headStamp->add( currentStamp );
1320	<	comp_stamps[i] = headStamp->match( id );
1318	>
1319	>	headStamp->add(currentStamp);
1320	>	comp_stamps[i] = headStamp->match(id);
1321		}
1322		}
1323
1324		#ifdef IS_MPI
1325	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1325	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1326		MPIcheckPoint();
1327		#endif // is_mpi
1328	+	}
1329
1330	+	void SimSetup::calcSysValues(void){
1331	+	int i;
1332
1333	<	}
1333	>	int* molMembershipArray;
1334
1170	–	void SimSetup::calcSysValues( void ){
1171	–	int i, j, k;
1172	–
1173	–	int *molMembershipArray;
1174	–
1335		tot_atoms = 0;
1336		tot_bonds = 0;
1337		tot_bends = 0;
1338		tot_torsions = 0;
1339	<	for( i=0; i<n_components; i++ ){
1340	<
1341	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1342	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1343	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1339	>	tot_rigid = 0;
1340	>	for (i = 0; i < n_components; i++){
1341	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1342	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1343	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1344		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1345	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1346		}
1347
1348		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1349		molMembershipArray = new int[tot_atoms];
1350	<
1351	<	for(i=0; i<nInfo; i++){
1350	>
1351	>	for (i = 0; i < nInfo; i++){
1352		info[i].n_atoms = tot_atoms;
1353		info[i].n_bonds = tot_bonds;
1354		info[i].n_bends = tot_bends;
1355		info[i].n_torsions = tot_torsions;
1356		info[i].n_SRI = tot_SRI;
1357		info[i].n_mol = tot_nmol;
1358	<
1358	>
1359		info[i].molMembershipArray = molMembershipArray;
1360	<	}
1360	>	}
1361		}
1362
1363		#ifdef IS_MPI
1364
1365	<	void SimSetup::mpiMolDivide( void ){
1205	<
1365	>	void SimSetup::mpiMolDivide(void){
1366		int i, j, k;
1367		int localMol, allMol;
1368		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369	+	int local_rigid;
1370	+	vector<int> globalMolIndex;
1371
1372	<	mpiSim = new mpiSimulation( info );
1211	<
1212	<	globalIndex = mpiSim->divideLabor();
1372	>	mpiSim = new mpiSimulation(info);
1373
1374	+	mpiSim->divideLabor();
1375	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1377	+
1378		// set up the local variables
1379	<
1379	>
1380		mol2proc = mpiSim->getMolToProcMap();
1381		molCompType = mpiSim->getMolComponentType();
1382	<
1382	>
1383		allMol = 0;
1384		localMol = 0;
1385		local_atoms = 0;
1386		local_bonds = 0;
1387		local_bends = 0;
1388		local_torsions = 0;
1389	<	globalAtomIndex = 0;
1389	>	local_rigid = 0;
1390	>	globalAtomCounter = 0;
1391
1392	<
1393	<	for( i=0; i<n_components; i++ ){
1394	<
1395	<	for( j=0; j<components_nmol[i]; j++ ){
1396	<
1397	<	if( mol2proc[allMol] == worldRank ){
1398	<
1399	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1400	<	local_bonds +=    comp_stamps[i]->getNBonds();
1236	<	local_bends +=    comp_stamps[i]->getNBends();
1237	<	local_torsions += comp_stamps[i]->getNTorsions();
1238	<	localMol++;
1392	>	for (i = 0; i < n_components; i++){
1393	>	for (j = 0; j < components_nmol[i]; j++){
1394	>	if (mol2proc[allMol] == worldRank){
1395	>	local_atoms += comp_stamps[i]->getNAtoms();
1396	>	local_bonds += comp_stamps[i]->getNBonds();
1397	>	local_bends += comp_stamps[i]->getNBends();
1398	>	local_torsions += comp_stamps[i]->getNTorsions();
1399	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1400	>	localMol++;
1401		}
1402	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1403	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1404	<	globalAtomIndex++;
1402	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1403	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1404	>	globalAtomCounter++;
1405		}
1406
1407	<	allMol++;
1407	>	allMol++;
1408		}
1409		}
1410		local_SRI = local_bonds + local_bends + local_torsions;
1411	<
1411	>
1412		info[0].n_atoms = mpiSim->getMyNlocal();
1413
1414	<	if( local_atoms != info[0].n_atoms ){
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1417	<	" localAtom (%d) are not equal.\n",
1418	<	info[0].n_atoms,
1419	<	local_atoms );
1414	>
1415	>	if (local_atoms != info[0].n_atoms){
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1418	>	"\tlocalAtom (%d) are not equal.\n",
1419	>	info[0].n_atoms, local_atoms);
1420		painCave.isFatal = 1;
1421		simError();
1422		}
#	Line 1265 | Line 1427 | void SimSetup::mpiMolDivide( void ){
1427		info[0].n_SRI = local_SRI;
1428		info[0].n_mol = localMol;
1429
1430	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1430	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1431		MPIcheckPoint();
1432		}
1433	<
1433	>
1434		#endif // is_mpi
1435
1436
1437	<	void SimSetup::makeSysArrays( void ){
1438	<	int i, j, k, l;
1437	>	void SimSetup::makeSysArrays(void){
1438	>
1439	>	#ifndef IS_MPI
1440	>	int k, j;
1441	>	#endif // is_mpi
1442	>	int i, l;
1443
1444		Atom** the_atoms;
1445		Molecule* the_molecules;
1280	–	Exclude** the_excludes;
1446
1447	<
1283	<	for(l=0; l<nInfo; l++){
1284	<
1447	>	for (l = 0; l < nInfo; l++){
1448		// create the atom and short range interaction arrays
1449	<
1450	<	the_atoms = new Atom*[info[l].n_atoms];
1449	>
1450	>	the_atoms = new Atom * [info[l].n_atoms];
1451		the_molecules = new Molecule[info[l].n_mol];
1452		int molIndex;
1453
1454		// initialize the molecule's stampID's
1455	<
1455	>
1456		#ifdef IS_MPI
1457	<
1458	<
1457	>
1458	>
1459		molIndex = 0;
1460	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1461	<
1462	<	if(mol2proc[i] == worldRank ){
1463	<	the_molecules[molIndex].setStampID( molCompType[i] );
1464	<	the_molecules[molIndex].setMyIndex( molIndex );
1465	<	the_molecules[molIndex].setGlobalIndex( i );
1303	<	molIndex++;
1460	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1461	>	if (mol2proc[i] == worldRank){
1462	>	the_molecules[molIndex].setStampID(molCompType[i]);
1463	>	the_molecules[molIndex].setMyIndex(molIndex);
1464	>	the_molecules[molIndex].setGlobalIndex(i);
1465	>	molIndex++;
1466		}
1467		}
1468	<
1468	>
1469		#else // is_mpi
1470	<
1470	>
1471		molIndex = 0;
1472	<	globalAtomIndex = 0;
1473	<	for(i=0; i<n_components; i++){
1474	<	for(j=0; j<components_nmol[i]; j++ ){
1475	<	the_molecules[molIndex].setStampID( i );
1476	<	the_molecules[molIndex].setMyIndex( molIndex );
1477	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1478	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1479	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1480	<	globalAtomIndex++;
1481	<	}
1482	<	molIndex++;
1472	>	globalAtomCounter = 0;
1473	>	for (i = 0; i < n_components; i++){
1474	>	for (j = 0; j < components_nmol[i]; j++){
1475	>	the_molecules[molIndex].setStampID(i);
1476	>	the_molecules[molIndex].setMyIndex(molIndex);
1477	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1478	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1479	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1480	>	globalAtomCounter++;
1481	>	}
1482	>	molIndex++;
1483		}
1484		}
1323	–
1324	–
1325	–	#endif // is_mpi
1485
1486
1487	<	if( info[l].n_SRI ){
1329	<
1330	<	Exclude::createArray(info[l].n_SRI);
1331	<	the_excludes = new Exclude*[info[l].n_SRI];
1332	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1333	<	the_excludes[ex] = new Exclude(ex);
1334	<	}
1335	<	info[l].globalExcludes = new int;
1336	<	info[l].n_exclude = info[l].n_SRI;
1337	<	}
1338	<	else{
1339	<
1340	<	Exclude::createArray( 1 );
1341	<	the_excludes = new Exclude*;
1342	<	the_excludes[0] = new Exclude(0);
1343	<	the_excludes[0]->setPair( 0,0 );
1344	<	info[l].globalExcludes = new int;
1345	<	info[l].globalExcludes[0] = 0;
1346	<	info[l].n_exclude = 0;
1347	<	}
1487	>	#endif // is_mpi
1488
1489	+	info[l].globalExcludes = new int;
1490	+	info[l].globalExcludes[0] = 0;
1491	+
1492		// set the arrays into the SimInfo object
1493
1494		info[l].atoms = the_atoms;
1495		info[l].molecules = the_molecules;
1496		info[l].nGlobalExcludes = 0;
1354	–	info[l].excludes = the_excludes;
1497
1498	<	the_ff->setSimInfo( info );
1357	<
1498	>	the_ff->setSimInfo(info);
1499		}
1500		}
1501
1502	<	void SimSetup::makeIntegrator( void ){
1362	<
1502	>	void SimSetup::makeIntegrator(void){
1503		int k;
1504
1505	<	NVT<RealIntegrator>*  myNVT = NULL;
1506	<	NPTi<RealIntegrator>* myNPTi = NULL;
1507	<	NPTf<RealIntegrator>* myNPTf = NULL;
1508	<	NPTim<RealIntegrator>* myNPTim = NULL;
1509	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1510	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1511	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1512	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1513	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1514	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1515	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1516	<
1517	<	for(k=0; k<nInfo; k++){
1518	<
1519	<	switch( ensembleCase ){
1520	<
1521	<	case NVE_ENS:
1522	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1523	<	break;
1524	<
1525	<	case NVT_ENS:
1526	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1527	<	myNVT->setTargetTemp(globals->getTargetTemp());
1528	<
1529	<	if (globals->haveTauThermostat())
1530	<	myNVT->setTauThermostat(globals->getTauThermostat());
1531	<
1532	<	else {
1533	<	sprintf( painCave.errMsg,
1534	<	"SimSetup error: If you use the NVT\n"
1535	<	"    ensemble, you must set tauThermostat.\n");
1536	<	painCave.isFatal = 1;
1537	<	simError();
1538	<	}
1539	<	break;
1540	<
1541	<	case NPTi_ENS:
1542	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1543	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1544	<
1545	<	if (globals->haveTargetPressure())
1546	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1547	<	else {
1548	<	sprintf( painCave.errMsg,
1549	<	"SimSetup error: If you use a constant pressure\n"
1550	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1551	<	painCave.isFatal = 1;
1552	<	simError();
1553	<	}
1554	<
1555	<	if( globals->haveTauThermostat() )
1556	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1557	<	else{
1558	<	sprintf( painCave.errMsg,
1559	<	"SimSetup error: If you use an NPT\n"
1560	<	"    ensemble, you must set tauThermostat.\n");
1561	<	painCave.isFatal = 1;
1562	<	simError();
1563	<	}
1564	<
1565	<	if( globals->haveTauBarostat() )
1566	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1567	<	else{
1568	<	sprintf( painCave.errMsg,
1569	<	"SimSetup error: If you use an NPT\n"
1570	<	"    ensemble, you must set tauBarostat.\n");
1571	<	painCave.isFatal = 1;
1572	<	simError();
1573	<	}
1574	<	break;
1575	<
1576	<	case NPTf_ENS:
1577	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1578	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1579	<
1580	<	if (globals->haveTargetPressure())
1581	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1582	<	else {
1583	<	sprintf( painCave.errMsg,
1584	<	"SimSetup error: If you use a constant pressure\n"
1585	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	<	painCave.isFatal = 1;
1587	<	simError();
1588	<	}
1589	<
1590	<	if( globals->haveTauThermostat() )
1591	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1592	<	else{
1593	<	sprintf( painCave.errMsg,
1594	<	"SimSetup error: If you use an NPT\n"
1595	<	"    ensemble, you must set tauThermostat.\n");
1596	<	painCave.isFatal = 1;
1597	<	simError();
1598	<	}
1599	<
1600	<	if( globals->haveTauBarostat() )
1601	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1602	<	else{
1603	<	sprintf( painCave.errMsg,
1604	<	"SimSetup error: If you use an NPT\n"
1605	<	"    ensemble, you must set tauBarostat.\n");
1606	<	painCave.isFatal = 1;
1607	<	simError();
1608	<	}
1609	<	break;
1610	<
1611	<	case NPTim_ENS:
1612	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1613	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1614	<
1615	<	if (globals->haveTargetPressure())
1616	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1617	<	else {
1618	<	sprintf( painCave.errMsg,
1619	<	"SimSetup error: If you use a constant pressure\n"
1620	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1621	<	painCave.isFatal = 1;
1622	<	simError();
1623	<	}
1624	<
1625	<	if( globals->haveTauThermostat() )
1626	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1627	<	else{
1628	<	sprintf( painCave.errMsg,
1629	<	"SimSetup error: If you use an NPT\n"
1630	<	"    ensemble, you must set tauThermostat.\n");
1631	<	painCave.isFatal = 1;
1632	<	simError();
1633	<	}
1634	<
1635	<	if( globals->haveTauBarostat() )
1636	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1637	<	else{
1638	<	sprintf( painCave.errMsg,
1639	<	"SimSetup error: If you use an NPT\n"
1640	<	"    ensemble, you must set tauBarostat.\n");
1641	<	painCave.isFatal = 1;
1642	<	simError();
1643	<	}
1644	<	break;
1645	<
1646	<	case NPTfm_ENS:
1647	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1648	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1649	<
1650	<	if (globals->haveTargetPressure())
1651	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1652	<	else {
1653	<	sprintf( painCave.errMsg,
1654	<	"SimSetup error: If you use a constant pressure\n"
1655	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1656	<	painCave.isFatal = 1;
1657	<	simError();
1658	<	}
1659	<
1660	<	if( globals->haveTauThermostat() )
1661	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1662	<	else{
1663	<	sprintf( painCave.errMsg,
1664	<	"SimSetup error: If you use an NPT\n"
1665	<	"    ensemble, you must set tauThermostat.\n");
1666	<	painCave.isFatal = 1;
1667	<	simError();
1668	<	}
1669	<
1670	<	if( globals->haveTauBarostat() )
1671	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1672	<	else{
1673	<	sprintf( painCave.errMsg,
1674	<	"SimSetup error: If you use an NPT\n"
1675	<	"    ensemble, you must set tauBarostat.\n");
1676	<	painCave.isFatal = 1;
1677	<	simError();
1678	<	}
1679	<	break;
1680	<
1681	<	case NVEZCONS_ENS:
1682	<
1683	<
1544	<	//setup index of z-constraint molecules, z-constraint sampel time
1545	<	//and z-constraint force output name. These parameter should be known
1546	<	//before constructing the z-constraint integrator
1547	<	setupZConstraint();
1548	<
1549	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	<
1551	<	break;
1552	<
1553	<
1554	<	case NVTZCONS_ENS:
1555	<
1556	<	setupZConstraint();
1557	<
1558	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	<
1561	<	if (globals->haveTauThermostat())
1562	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	<
1564	<	else {
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use the NVT\n"
1567	<	"    ensemble, you must set tauThermostat.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1570	<	}
1571	<	break;
1572	<
1573	<	case NPTiZCONS_ENS:
1574	<
1575	<	setupZConstraint();
1576	<
1577	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	<
1580	<	if (globals->haveTargetPressure())
1581	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	<	else {
1583	<	sprintf( painCave.errMsg,
1584	<	"SimSetup error: If you use a constant pressure\n"
1585	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	<	painCave.isFatal = 1;
1587	<	simError();
1588	<	}
1589	<
1590	<	if( globals->haveTauThermostat() )
1591	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	<	else{
1593	<	sprintf( painCave.errMsg,
1594	<	"SimSetup error: If you use an NPT\n"
1595	<	"    ensemble, you must set tauThermostat.\n");
1596	<	painCave.isFatal = 1;
1597	<	simError();
1598	<	}
1599	<
1600	<	if( globals->haveTauBarostat() )
1601	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	<	else{
1603	<	sprintf( painCave.errMsg,
1604	<	"SimSetup error: If you use an NPT\n"
1605	<	"    ensemble, you must set tauBarostat.\n");
1606	<	painCave.isFatal = 1;
1607	<	simError();
1608	<	}
1609	<
1610	<	break;
1611	<
1612	<	case NPTfZCONS_ENS:
1613	<
1614	<	setupZConstraint();
1615	<
1616	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	<
1619	<	if (globals->haveTargetPressure())
1620	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	<	else {
1622	<	sprintf( painCave.errMsg,
1623	<	"SimSetup error: If you use a constant pressure\n"
1624	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	<	painCave.isFatal = 1;
1626	<	simError();
1627	<	}
1628	<
1629	<	if( globals->haveTauThermostat() )
1630	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	<	else{
1632	<	sprintf( painCave.errMsg,
1633	<	"SimSetup error: If you use an NPT\n"
1634	<	"    ensemble, you must set tauThermostat.\n");
1635	<	painCave.isFatal = 1;
1636	<	simError();
1637	<	}
1638	<
1639	<	if( globals->haveTauBarostat() )
1640	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	<	else{
1642	<	sprintf( painCave.errMsg,
1643	<	"SimSetup error: If you use an NPT\n"
1644	<	"    ensemble, you must set tauBarostat.\n");
1645	<	painCave.isFatal = 1;
1646	<	simError();
1647	<	}
1648	<
1649	<	break;
1650	<
1651	<	case NPTimZCONS_ENS:
1652	<
1653	<	setupZConstraint();
1654	<
1655	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	<
1658	<	if (globals->haveTargetPressure())
1659	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	<	else {
1661	<	sprintf( painCave.errMsg,
1662	<	"SimSetup error: If you use a constant pressure\n"
1663	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	<	painCave.isFatal = 1;
1665	<	simError();
1666	<	}
1667	<
1668	<	if( globals->haveTauThermostat() )
1669	<	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	<	else{
1671	<	sprintf( painCave.errMsg,
1672	<	"SimSetup error: If you use an NPT\n"
1673	<	"    ensemble, you must set tauThermostat.\n");
1674	<	painCave.isFatal = 1;
1675	<	simError();
1676	<	}
1677	<
1678	<	if( globals->haveTauBarostat() )
1679	<	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	<	else{
1681	<	sprintf( painCave.errMsg,
1682	<	"SimSetup error: If you use an NPT\n"
1683	<	"    ensemble, you must set tauBarostat.\n");
1684	<	painCave.isFatal = 1;
1685	<	simError();
1686	<	}
1687	<
1688	<	break;
1689	<
1690	<	case NPTfmZCONS_ENS:
1691	<
1692	<	setupZConstraint();
1693	<
1694	<	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	<	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	<
1697	<	if (globals->haveTargetPressure())
1698	<	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	<	else {
1700	<	sprintf( painCave.errMsg,
1701	<	"SimSetup error: If you use a constant pressure\n"
1702	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	<	painCave.isFatal = 1;
1704	<	simError();
1705	<	}
1706	<
1707	<	if( globals->haveTauThermostat() )
1708	<	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	<	else{
1710	<	sprintf( painCave.errMsg,
1711	<	"SimSetup error: If you use an NPT\n"
1712	<	"    ensemble, you must set tauThermostat.\n");
1713	<	painCave.isFatal = 1;
1714	<	simError();
1715	<	}
1716	<
1717	<	if( globals->haveTauBarostat() )
1718	<	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	<	else{
1720	<	sprintf( painCave.errMsg,
1721	<	"SimSetup error: If you use an NPT\n"
1722	<	"    ensemble, you must set tauBarostat.\n");
1723	<	painCave.isFatal = 1;
1724	<	simError();
1725	<	}
1726	<	break;
1727	<
1728	<
1729	<
1730	<	default:
1731	<	sprintf( painCave.errMsg,
1732	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733	<	painCave.isFatal = 1;
1734	<	simError();
1505	>	NVE<RealIntegrator>* myNVE = NULL;
1506	>	NVT<RealIntegrator>* myNVT = NULL;
1507	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1508	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1509	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1510	>
1511	>	for (k = 0; k < nInfo; k++){
1512	>	switch (ensembleCase){
1513	>	case NVE_ENS:
1514	>	if (globals->haveZconstraints()){
1515	>	setupZConstraint(info[k]);
1516	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1517	>	}
1518	>	else{
1519	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1520	>	}
1521	>
1522	>	info->the_integrator = myNVE;
1523	>	break;
1524	>
1525	>	case NVT_ENS:
1526	>	if (globals->haveZconstraints()){
1527	>	setupZConstraint(info[k]);
1528	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1529	>	}
1530	>	else
1531	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1532	>
1533	>	myNVT->setTargetTemp(globals->getTargetTemp());
1534	>
1535	>	if (globals->haveTauThermostat())
1536	>	myNVT->setTauThermostat(globals->getTauThermostat());
1537	>	else{
1538	>	sprintf(painCave.errMsg,
1539	>	"SimSetup error: If you use the NVT\n"
1540	>	"\tensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544	>
1545	>	info->the_integrator = myNVT;
1546	>	break;
1547	>
1548	>	case NPTi_ENS:
1549	>	if (globals->haveZconstraints()){
1550	>	setupZConstraint(info[k]);
1551	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1552	>	}
1553	>	else
1554	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1555	>
1556	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1557	>
1558	>	if (globals->haveTargetPressure())
1559	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1560	>	else{
1561	>	sprintf(painCave.errMsg,
1562	>	"SimSetup error: If you use a constant pressure\n"
1563	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1564	>	painCave.isFatal = 1;
1565	>	simError();
1566	>	}
1567	>
1568	>	if (globals->haveTauThermostat())
1569	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1570	>	else{
1571	>	sprintf(painCave.errMsg,
1572	>	"SimSetup error: If you use an NPT\n"
1573	>	"\tensemble, you must set tauThermostat.\n");
1574	>	painCave.isFatal = 1;
1575	>	simError();
1576	>	}
1577	>
1578	>	if (globals->haveTauBarostat())
1579	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1580	>	else{
1581	>	sprintf(painCave.errMsg,
1582	>	"SimSetup error: If you use an NPT\n"
1583	>	"\tensemble, you must set tauBarostat.\n");
1584	>	painCave.isFatal = 1;
1585	>	simError();
1586	>	}
1587	>
1588	>	info->the_integrator = myNPTi;
1589	>	break;
1590	>
1591	>	case NPTf_ENS:
1592	>	if (globals->haveZconstraints()){
1593	>	setupZConstraint(info[k]);
1594	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1595	>	}
1596	>	else
1597	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1598	>
1599	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1600	>
1601	>	if (globals->haveTargetPressure())
1602	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1603	>	else{
1604	>	sprintf(painCave.errMsg,
1605	>	"SimSetup error: If you use a constant pressure\n"
1606	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1607	>	painCave.isFatal = 1;
1608	>	simError();
1609	>	}
1610	>
1611	>	if (globals->haveTauThermostat())
1612	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1613	>
1614	>	else{
1615	>	sprintf(painCave.errMsg,
1616	>	"SimSetup error: If you use an NPT\n"
1617	>	"\tensemble, you must set tauThermostat.\n");
1618	>	painCave.isFatal = 1;
1619	>	simError();
1620	>	}
1621	>
1622	>	if (globals->haveTauBarostat())
1623	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1624	>
1625	>	else{
1626	>	sprintf(painCave.errMsg,
1627	>	"SimSetup error: If you use an NPT\n"
1628	>	"\tensemble, you must set tauBarostat.\n");
1629	>	painCave.isFatal = 1;
1630	>	simError();
1631	>	}
1632	>
1633	>	info->the_integrator = myNPTf;
1634	>	break;
1635	>
1636	>	case NPTxyz_ENS:
1637	>	if (globals->haveZconstraints()){
1638	>	setupZConstraint(info[k]);
1639	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1640	>	}
1641	>	else
1642	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1643	>
1644	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1645	>
1646	>	if (globals->haveTargetPressure())
1647	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1648	>	else{
1649	>	sprintf(painCave.errMsg,
1650	>	"SimSetup error: If you use a constant pressure\n"
1651	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1652	>	painCave.isFatal = 1;
1653	>	simError();
1654	>	}
1655	>
1656	>	if (globals->haveTauThermostat())
1657	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1658	>	else{
1659	>	sprintf(painCave.errMsg,
1660	>	"SimSetup error: If you use an NPT\n"
1661	>	"\tensemble, you must set tauThermostat.\n");
1662	>	painCave.isFatal = 1;
1663	>	simError();
1664	>	}
1665	>
1666	>	if (globals->haveTauBarostat())
1667	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1668	>	else{
1669	>	sprintf(painCave.errMsg,
1670	>	"SimSetup error: If you use an NPT\n"
1671	>	"\tensemble, you must set tauBarostat.\n");
1672	>	painCave.isFatal = 1;
1673	>	simError();
1674	>	}
1675	>
1676	>	info->the_integrator = myNPTxyz;
1677	>	break;
1678	>
1679	>	default:
1680	>	sprintf(painCave.errMsg,
1681	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1682	>	painCave.isFatal = 1;
1683	>	simError();
1684		}
1685		}
1686		}
1687
1688	<	void SimSetup::initFortran( void ){
1740	<
1688	>	void SimSetup::initFortran(void){
1689		info[0].refreshSim();
1690	<
1691	<	if( !strcmp( info[0].mixingRule, "standard") ){
1692	<	the_ff->initForceField( LB_MIXING_RULE );
1690	>
1691	>	if (!strcmp(info[0].mixingRule, "standard")){
1692	>	the_ff->initForceField(LB_MIXING_RULE);
1693		}
1694	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1695	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1694	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1695	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1696		}
1697		else{
1698	<	sprintf( painCave.errMsg,
1699	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	<	info[0].mixingRule );
1698	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1699	>	info[0].mixingRule);
1700		painCave.isFatal = 1;
1701		simError();
1702		}
1703
1704
1705		#ifdef IS_MPI
1706	<	strcpy( checkPointMsg,
1760	<	"Successfully intialized the mixingRule for Fortran." );
1706	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1707		MPIcheckPoint();
1708		#endif // is_mpi
1709	+	}
1710
1711	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1712	+	int nZConstraints;
1713	+	ZconStamp** zconStamp;
1714	+
1715	+	if (globals->haveZconstraintTime()){
1716	+	//add sample time of z-constraint  into SimInfo's property list
1717	+	DoubleData* zconsTimeProp = new DoubleData();
1718	+	zconsTimeProp->setID(ZCONSTIME_ID);
1719	+	zconsTimeProp->setData(globals->getZconsTime());
1720	+	theInfo.addProperty(zconsTimeProp);
1721	+	}
1722	+	else{
1723	+	sprintf(painCave.errMsg,
1724	+	"ZConstraint error: If you use a ZConstraint,\n"
1725	+	"\tyou must set zconsTime.\n");
1726	+	painCave.isFatal = 1;
1727	+	simError();
1728	+	}
1729	+
1730	+	//push zconsTol into siminfo, if user does not specify
1731	+	//value for zconsTol, a default value will be used
1732	+	DoubleData* zconsTol = new DoubleData();
1733	+	zconsTol->setID(ZCONSTOL_ID);
1734	+	if (globals->haveZconsTol()){
1735	+	zconsTol->setData(globals->getZconsTol());
1736	+	}
1737	+	else{
1738	+	double defaultZConsTol = 0.01;
1739	+	sprintf(painCave.errMsg,
1740	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1741	+	"\tOOPSE will use a default value of %f.\n"
1742	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1743	+	defaultZConsTol);
1744	+	painCave.isFatal = 0;
1745	+	simError();
1746	+
1747	+	zconsTol->setData(defaultZConsTol);
1748	+	}
1749	+	theInfo.addProperty(zconsTol);
1750	+
1751	+	//set Force Subtraction Policy
1752	+	StringData* zconsForcePolicy = new StringData();
1753	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1754	+
1755	+	if (globals->haveZconsForcePolicy()){
1756	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1757	+	}
1758	+	else{
1759	+	sprintf(painCave.errMsg,
1760	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1761	+	"\tOOPSE will use PolicyByMass.\n"
1762	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1763	+	painCave.isFatal = 0;
1764	+	simError();
1765	+	zconsForcePolicy->setData("BYMASS");
1766	+	}
1767	+
1768	+	theInfo.addProperty(zconsForcePolicy);
1769	+
1770	+	//set zcons gap
1771	+	DoubleData* zconsGap = new DoubleData();
1772	+	zconsGap->setID(ZCONSGAP_ID);
1773	+
1774	+	if (globals->haveZConsGap()){
1775	+	zconsGap->setData(globals->getZconsGap());
1776	+	theInfo.addProperty(zconsGap);
1777	+	}
1778	+
1779	+	//set zcons fixtime
1780	+	DoubleData* zconsFixtime = new DoubleData();
1781	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1782	+
1783	+	if (globals->haveZConsFixTime()){
1784	+	zconsFixtime->setData(globals->getZconsFixtime());
1785	+	theInfo.addProperty(zconsFixtime);
1786	+	}
1787	+
1788	+	//set zconsUsingSMD
1789	+	IntData* zconsUsingSMD = new IntData();
1790	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1791	+
1792	+	if (globals->haveZConsUsingSMD()){
1793	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1794	+	theInfo.addProperty(zconsUsingSMD);
1795	+	}
1796	+
1797	+	//Determine the name of ouput file and add it into SimInfo's property list
1798	+	//Be careful, do not use inFileName, since it is a pointer which
1799	+	//point to a string at master node, and slave nodes do not contain that string
1800	+
1801	+	string zconsOutput(theInfo.finalName);
1802	+
1803	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1804	+
1805	+	StringData* zconsFilename = new StringData();
1806	+	zconsFilename->setID(ZCONSFILENAME_ID);
1807	+	zconsFilename->setData(zconsOutput);
1808	+
1809	+	theInfo.addProperty(zconsFilename);
1810	+
1811	+	//setup index, pos and other parameters of z-constraint molecules
1812	+	nZConstraints = globals->getNzConstraints();
1813	+	theInfo.nZconstraints = nZConstraints;
1814	+
1815	+	zconStamp = globals->getZconStamp();
1816	+	ZConsParaItem tempParaItem;
1817	+
1818	+	ZConsParaData* zconsParaData = new ZConsParaData();
1819	+	zconsParaData->setID(ZCONSPARADATA_ID);
1820	+
1821	+	for (int i = 0; i < nZConstraints; i++){
1822	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1823	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1824	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1825	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1826	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1827	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1828	+	zconsParaData->addItem(tempParaItem);
1829	+	}
1830	+
1831	+	//check the uniqueness of index
1832	+	if(!zconsParaData->isIndexUnique()){
1833	+	sprintf(painCave.errMsg,
1834	+	"ZConstraint Error: molIndex is not unique!\n");
1835	+	painCave.isFatal = 1;
1836	+	simError();
1837	+	}
1838	+
1839	+	//sort the parameters by index of molecules
1840	+	zconsParaData->sortByIndex();
1841	+
1842	+	//push data into siminfo, therefore, we can retrieve later
1843	+	theInfo.addProperty(zconsParaData);
1844		}
1845
1846	<	void SimSetup::setupZConstraint()
1767	<	{
1768	<	int k;
1846	>	void SimSetup::makeMinimizer(){
1847
1848	<	for(k=0; k<nInfo; k++){
1848	>	OOPSEMinimizer* myOOPSEMinimizer;
1849	>	MinimizerParameterSet* param;
1850	>	char minimizerName[100];
1851	>
1852	>	for (int i = 0; i < nInfo; i++){
1853
1854	<	if(globals->haveZConsTime()){
1855	<
1856	<	//add sample time of z-constraint  into SimInfo's property list
1857	<	DoubleData* zconsTimeProp = new DoubleData();
1858	<	zconsTimeProp->setID("zconstime");
1859	<	zconsTimeProp->setData(globals->getZConsTime());
1778	<	info[k].addProperty(zconsTimeProp);
1854	>	//prepare parameter set for minimizer
1855	>	param = new MinimizerParameterSet();
1856	>	param->setDefaultParameter();
1857	>
1858	>	if (globals->haveMinimizer()){
1859	>	param->setFTol(globals->getMinFTol());
1860		}
1861	<	else{
1862	<	sprintf( painCave.errMsg,
1863	<	"ZConstraint error: If you use an ZConstraint\n"
1783	<	" , you must set sample time.\n");
1784	<	painCave.isFatal = 1;
1785	<	simError();
1861	>
1862	>	if (globals->haveMinGTol()){
1863	>	param->setGTol(globals->getMinGTol());
1864		}
1865	+
1866	+	if (globals->haveMinMaxIter()){
1867	+	param->setMaxIteration(globals->getMinMaxIter());
1868	+	}
1869	+
1870	+	if (globals->haveMinWriteFrq()){
1871	+	param->setMaxIteration(globals->getMinMaxIter());
1872	+	}
1873	+
1874	+	if (globals->haveMinWriteFrq()){
1875	+	param->setWriteFrq(globals->getMinWriteFrq());
1876	+	}
1877
1878	<	if(globals->haveIndexOfAllZConsMols()){
1879	<
1790	<	//add index of z-constraint molecules into SimInfo's property list
1791	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792	<
1793	<	//sort the index
1794	<	sort(tempIndex.begin(), tempIndex.end());
1795	<
1796	<	IndexData* zconsIndex = new IndexData();
1797	<	zconsIndex->setID("zconsindex");
1798	<	zconsIndex->setIndexData(tempIndex);
1799	<	info[k].addProperty(zconsIndex);
1878	>	if (globals->haveMinStepSize()){
1879	>	param->setStepSize(globals->getMinStepSize());
1880		}
1881	+
1882	+	if (globals->haveMinLSMaxIter()){
1883	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1884	+	}
1885	+
1886	+	if (globals->haveMinLSTol()){
1887	+	param->setLineSearchTol(globals->getMinLSTol());
1888	+	}
1889	+
1890	+	strcpy(minimizerName, globals->getMinimizer());
1891	+
1892	+	if (!strcasecmp(minimizerName, "CG")){
1893	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1894	+	}
1895	+	else if (!strcasecmp(minimizerName, "SD")){
1896	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1897	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1898	+	}
1899		else{
1900	<	sprintf( painCave.errMsg,
1901	<	"SimSetup error: If you use an ZConstraint\n"
1902	<	" , you must set index of z-constraint molecules.\n");
1903	<	painCave.isFatal = 1;
1904	<	simError();
1905	<
1900	>	sprintf(painCave.errMsg,
1901	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1902	>	painCave.isFatal = 0;
1903	>	simError();
1904	>
1905	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1906		}
1907	<
1908	<	//Determine the name of ouput file and add it into SimInfo's property list
1909	<	//Be careful, do not use inFileName, since it is a pointer which
1910	<	//point to a string at master node, and slave nodes do not contain that string
1911	<
1814	<	string zconsOutput(info[k].finalName);
1815	<
1816	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1817	<
1818	<	StringData* zconsFilename = new StringData();
1819	<	zconsFilename->setID("zconsfilename");
1820	<	zconsFilename->setData(zconsOutput);
1821	<
1822	<	info[k].addProperty(zconsFilename);
1907	>	info[i].the_integrator = myOOPSEMinimizer;
1908	>
1909	>	//store the minimizer into simInfo
1910	>	info[i].the_minimizer = myOOPSEMinimizer;
1911	>	info[i].has_minimizer = true;
1912		}
1913	+
1914		}

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