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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 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 21 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#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 50 | 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 ){
61	<
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();
89	<	mpiEventLoop();
90	<
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
97	–	int i, j, k, globalAtomIndex;
98	–
126		// gather all of the information from the Bass file
127
101	–	std::cerr << "gathering info\n";
102	–
128		gatherInfo();
129
130		// creation of complex system objects
131
107	–	std::cerr << "creating system objects\n";
108	–
132		sysObjectsCreation();
133
134		// check on the post processing info
112	–
113	–	std::cerr << "performing final info check.\n";
135
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	std::cerr << "about to init coords\n";
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	<	if( !isInfoArray ) initSystemCoords();
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145	>	}
146
147		// make the output filenames
148
149		makeOutNames();
150	<
151	<	// make the integrator
150	>
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157
129	–	makeIntegrator();
130	–
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
#	Line 135 | Line 162 | void SimSetup::createSim(void){
162		// initialize the Fortran
163
164		initFortran();
138	–
139	–
140	–
165		}
166
167
168	<	void SimSetup::makeMolecules( void ){
169	<
170	<	int k,l;
171	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174		molInit molInfo;
175		DirectionalAtom* dAtom;
176	+	RigidBody* myRB;
177	+	StuntDouble* mySD;
178		LinkedAssign* extras;
179		LinkedAssign* current_extra;
180		AtomStamp* currentAtom;
181		BondStamp* currentBond;
182		BendStamp* currentBend;
183		TorsionStamp* currentTorsion;
184	+	RigidBodyStamp* currentRigidBody;
185
186		bond_pair* theBonds;
187		bend_set* theBends;
188		torsion_set* theTorsions;
189
190	<
190	>	set<int> skipList;
191	>
192	>	double phi, theta, psi;
193	>	char* molName;
194	>	char rbName[100];
195	>
196		//init the forceField paramters
197
198		the_ff->readParams();
199
166	–
200		// init the atoms
201
202	<	double ux, uy, uz, u, uSqr;
170	<
171	<	for(k=0; k<nInfo; k++){
172	<
173	<	the_ff->setSimInfo( &(info[k]) );
202	>	int nMembers, nNew, rb1, rb2;
203
204	+	for (k = 0; k < nInfo; k++){
205	+	the_ff->setSimInfo(&(info[k]));
206	+
207		atomOffset = 0;
208	<	excludeOffset = 0;
209	<	for(i=0; i<info[k].n_mol; i++){
178	<
208	>
209	>	for (i = 0; i < info[k].n_mol; i++){
210		stampID = info[k].molecules[i].getStampID();
211	+	molName = comp_stamps[stampID]->getID();
212
213	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
214	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
215	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
213	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
214	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
215	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
216		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
217	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
217	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
218
219		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	–	molInfo.myBends = new Bend*[molInfo.nBends];
191	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
220
221	+	if (molInfo.nBonds > 0)
222	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
223	+	else
224	+	molInfo.myBonds = NULL;
225	+
226	+	if (molInfo.nBends > 0)
227	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
228	+	else
229	+	molInfo.myBends = NULL;
230	+
231	+	if (molInfo.nTorsions > 0)
232	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
233	+	else
234	+	molInfo.myTorsions = NULL;
235	+
236		theBonds = new bond_pair[molInfo.nBonds];
237		theBends = new bend_set[molInfo.nBends];
238		theTorsions = new torsion_set[molInfo.nTorsions];
239	<
239	>
240		// make the Atoms
241	<
242	<	for(j=0; j<molInfo.nAtoms; j++){
243	<
244	<	currentAtom = comp_stamps[stampID]->getAtom( j );
245	<	if( currentAtom->haveOrientation() ){
246	<
247	<	dAtom = new DirectionalAtom( (j + atomOffset),
248	<	info[k].getConfiguration() );
249	<	info[k].n_oriented++;
250	<	molInfo.myAtoms[j] = dAtom;
251	<
252	<	ux = currentAtom->getOrntX();
253	<	uy = currentAtom->getOrntY();
254	<	uz = currentAtom->getOrntZ();
255	<
256	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257	<
258	<	u = sqrt( uSqr );
259	<	ux = ux / u;
260	<	uy = uy / u;
261	<	uz = uz / u;
262	<
263	<	dAtom->setSUx( ux );
264	<	dAtom->setSUy( uy );
265	<	dAtom->setSUz( uz );
266	<	}
267	<	else{
268	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	<	info[k].getConfiguration() );
227	<	}
228	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	<
241	>
242	>	for (j = 0; j < molInfo.nAtoms; j++){
243	>	currentAtom = comp_stamps[stampID]->getAtom(j);
244	>
245	>	if (currentAtom->haveOrientation()){
246	>	dAtom = new DirectionalAtom((j + atomOffset),
247	>	info[k].getConfiguration());
248	>	info[k].n_oriented++;
249	>	molInfo.myAtoms[j] = dAtom;
250	>
251	>	// Directional Atoms have standard unit vectors which are oriented
252	>	// in space using the three Euler angles.  We assume the standard
253	>	// unit vector was originally along the z axis below.
254	>
255	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
256	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
257	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
258	>
259	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
260	>
261	>	}
262	>	else{
263	>
264	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
265	>	}
266	>
267	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
268	>
269		#ifdef IS_MPI
270	<
271	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
272	<
270	>
271	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
272	>
273		#endif // is_mpi
274		}
275	<
276	<	// make the bonds
277	<	for(j=0; j<molInfo.nBonds; j++){
278	<
279	<	currentBond = comp_stamps[stampID]->getBond( j );
280	<	theBonds[j].a = currentBond->getA() + atomOffset;
281	<	theBonds[j].b = currentBond->getB() + atomOffset;
282	<
283	<	exI = theBonds[j].a;
284	<	exJ = theBonds[j].b;
285	<
286	<	// exclude_I must always be the smaller of the pair
287	<	if( exI > exJ ){
288	<	tempEx = exI;
289	<	exI = exJ;
290	<	exJ = tempEx;
291	<	}
292	<	#ifdef IS_MPI
293	<	tempEx = exI;
255	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	<	tempEx = exJ;
257	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	<
259	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260	<	#else  // isn't MPI
261	<
262	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263	<	#endif  //is_mpi
275	>
276	>	// make the bonds
277	>	for (j = 0; j < molInfo.nBonds; j++){
278	>	currentBond = comp_stamps[stampID]->getBond(j);
279	>	theBonds[j].a = currentBond->getA() + atomOffset;
280	>	theBonds[j].b = currentBond->getB() + atomOffset;
281	>
282	>	tempI = theBonds[j].a;
283	>	tempJ = theBonds[j].b;
284	>
285	>	#ifdef IS_MPI
286	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
287	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
288	>	#else
289	>	exI = tempI + 1;
290	>	exJ = tempJ + 1;
291	>	#endif
292	>
293	>	info[k].excludes->addPair(exI, exJ);
294		}
295	<	excludeOffset += molInfo.nBonds;
266	<
295	>
296		//make the bends
297	<	for(j=0; j<molInfo.nBends; j++){
298	<
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	<
306	<	extras = currentBend->getExtras();
307	<	current_extra = extras;
308	<
309	<	while( current_extra != NULL ){
310	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
311	<
312	<	switch( current_extra->getType() ){
313	<
314	<	case 0:
315	<	theBends[j].ghost =
316	<	current_extra->getInt() + atomOffset;
317	<	theBends[j].isGhost = 1;
318	<	break;
319	<
320	<	case 1:
321	<	theBends[j].ghost =
322	<	(int)current_extra->getDouble() + atomOffset;
323	<	theBends[j].isGhost = 1;
324	<	break;
325	<
326	<	default:
327	<	sprintf( painCave.errMsg,
328	<	"SimSetup Error: ghostVectorSource was neither a "
329	<	"double nor an int.\n"
330	<	"-->Bend[%d] in %s\n",
331	<	j, comp_stamps[stampID]->getID() );
332	<	painCave.isFatal = 1;
333	<	simError();
334	<	}
335	<	}
336	<
337	<	else{
338	<
339	<	sprintf( painCave.errMsg,
340	<	"SimSetup Error: unhandled bend assignment:\n"
341	<	"    -->%s in Bend[%d] in %s\n",
342	<	current_extra->getlhs(),
343	<	j, comp_stamps[stampID]->getID() );
344	<	painCave.isFatal = 1;
345	<	simError();
346	<	}
347	<
348	<	current_extra = current_extra->getNext();
320	<	}
321	<	}
322	<
323	<	if( !theBends[j].isGhost ){
324	<
325	<	exI = theBends[j].a;
326	<	exJ = theBends[j].c;
327	<	}
328	<	else{
329	<
330	<	exI = theBends[j].a;
331	<	exJ = theBends[j].b;
332	<	}
333	<
334	<	// exclude_I must always be the smaller of the pair
335	<	if( exI > exJ ){
336	<	tempEx = exI;
337	<	exI = exJ;
338	<	exJ = tempEx;
339	<	}
297	>	for (j = 0; j < molInfo.nBends; j++){
298	>	currentBend = comp_stamps[stampID]->getBend(j);
299	>	theBends[j].a = currentBend->getA() + atomOffset;
300	>	theBends[j].b = currentBend->getB() + atomOffset;
301	>	theBends[j].c = currentBend->getC() + atomOffset;
302	>
303	>	if (currentBend->haveExtras()){
304	>	extras = currentBend->getExtras();
305	>	current_extra = extras;
306	>
307	>	while (current_extra != NULL){
308	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
309	>	switch (current_extra->getType()){
310	>	case 0:
311	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
312	>	theBends[j].isGhost = 1;
313	>	break;
314	>
315	>	case 1:
316	>	theBends[j].ghost = (int) current_extra->getDouble() +
317	>	atomOffset;
318	>	theBends[j].isGhost = 1;
319	>	break;
320	>
321	>	default:
322	>	sprintf(painCave.errMsg,
323	>	"SimSetup Error: ghostVectorSource was neither a "
324	>	"double nor an int.\n"
325	>	"-->Bend[%d] in %s\n",
326	>	j, comp_stamps[stampID]->getID());
327	>	painCave.isFatal = 1;
328	>	simError();
329	>	}
330	>	}
331	>	else{
332	>	sprintf(painCave.errMsg,
333	>	"SimSetup Error: unhandled bend assignment:\n"
334	>	"    -->%s in Bend[%d] in %s\n",
335	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>
340	>	current_extra = current_extra->getNext();
341	>	}
342	>	}
343	>
344	>	if (theBends[j].isGhost) {
345	>
346	>	tempI = theBends[j].a;
347	>	tempJ = theBends[j].b;
348	>
349		#ifdef IS_MPI
350	<	tempEx = exI;
351	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352	<	tempEx = exJ;
353	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
354	<
355	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
356	<	#else  // isn't MPI
357	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
358	<	#endif  //is_mpi
350	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
351	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
352	>	#else
353	>	exI = tempI + 1;
354	>	exJ = tempJ + 1;
355	>	#endif
356	>	info[k].excludes->addPair(exI, exJ);
357	>
358	>	} else {
359	>
360	>	tempI = theBends[j].a;
361	>	tempJ = theBends[j].b;
362	>	tempK = theBends[j].c;
363	>
364	>	#ifdef IS_MPI
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
368	>	#else
369	>	exI = tempI + 1;
370	>	exJ = tempJ + 1;
371	>	exK = tempK + 1;
372	>	#endif
373	>
374	>	info[k].excludes->addPair(exI, exK);
375	>	info[k].excludes->addPair(exI, exJ);
376	>	info[k].excludes->addPair(exJ, exK);
377	>	}
378		}
379	<	excludeOffset += molInfo.nBends;
380	<
381	<	for(j=0; j<molInfo.nTorsions; j++){
382	<
383	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
384	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
385	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
386	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
387	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
388	<
389	<	exI = theTorsions[j].a;
390	<	exJ = theTorsions[j].d;
391	<
364	<	// exclude_I must always be the smaller of the pair
365	<	if( exI > exJ ){
366	<	tempEx = exI;
367	<	exI = exJ;
368	<	exJ = tempEx;
369	<	}
379	>
380	>	for (j = 0; j < molInfo.nTorsions; j++){
381	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
382	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
383	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
384	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
385	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
386	>
387	>	tempI = theTorsions[j].a;
388	>	tempJ = theTorsions[j].b;
389	>	tempK = theTorsions[j].c;
390	>	tempL = theTorsions[j].d;
391	>
392		#ifdef IS_MPI
393	<	tempEx = exI;
394	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
395	<	tempEx = exJ;
396	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
397	<
398	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
399	<	#else  // isn't MPI
400	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
401	<	#endif  //is_mpi
393	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
394	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
395	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
396	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	exL = tempL + 1;
402	>	#endif
403	>
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exI, exK);
406	>	info[k].excludes->addPair(exI, exL);
407	>	info[k].excludes->addPair(exJ, exK);
408	>	info[k].excludes->addPair(exJ, exL);
409	>	info[k].excludes->addPair(exK, exL);
410		}
411	<	excludeOffset += molInfo.nTorsions;
411	>
412	>	for (j = 0; j < molInfo.nRigidBodies; j++){
413	>
414	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
415	>	nMembers = currentRigidBody->getNMembers();
416	>
417	>	// Create the Rigid Body:
418	>
419	>	myRB = new RigidBody();
420	>
421	>	sprintf(rbName,"%s_RB_%s", molName, j);
422	>	myRB->setType(rbName);
423	>
424	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
425	>
426	>	// molI is atom numbering inside this molecule
427	>	molI = currentRigidBody->getMember(rb1);
428	>
429	>	// tempI is atom numbering on local processor
430	>	tempI = molI + atomOffset;
431	>
432	>	// currentAtom is the AtomStamp (which we need for
433	>	// rigid body reference positions)
434	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
435	>
436	>	// When we add to the rigid body, add the atom itself and
437	>	// the stamp info:
438	>
439	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
440	>
441	>	// Add this atom to the Skip List for the integrators
442	>	#ifdef IS_MPI
443	>	slI = info[k].atoms[tempI]->getGlobalIndex();
444	>	#else
445	>	slI = tempI;
446	>	#endif
447	>	skipList.insert(slI);
448	>
449	>	}
450	>
451	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
452	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
453	>
454	>	tempI = currentRigidBody->getMember(rb1);
455	>	tempJ = currentRigidBody->getMember(rb2);
456	>
457	>	// Some explanation is required here.
458	>	// Fortran indexing starts at 1, while c indexing starts at 0
459	>	// Also, in parallel computations, the GlobalIndex is
460	>	// used for the exclude list:
461	>
462	>	#ifdef IS_MPI
463	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
464	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
465	>	#else
466	>	exI = tempI + 1;
467	>	exJ = tempJ + 1;
468	>	#endif
469	>
470	>	info[k].excludes->addPair(exI, exJ);
471	>
472	>	}
473	>	}
474	>
475	>	molInfo.myRigidBodies.push_back(myRB);
476	>	info[k].rigidBodies.push_back(myRB);
477	>	}
478
479	+
480	+	// After this is all set up, scan through the atoms to
481	+	// see if they can be added to the integrableObjects:
482	+
483	+	for (j = 0; j < molInfo.nAtoms; j++){
484	+
485	+	#ifdef IS_MPI
486	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
487	+	#else
488	+	slJ = j+atomOffset;
489	+	#endif
490	+
491	+	// if they aren't on the skip list, then they can be integrated
492	+
493	+	if (skipList.find(slJ) == skipList.end()) {
494	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
495	+	info[k].integrableObjects.push_back(mySD);
496	+	molInfo.myIntegrableObjects.push_back(mySD);
497	+	}
498	+	}
499	+
500	+	// all rigid bodies are integrated:
501	+
502	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
503	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
504	+	info[k].integrableObjects.push_back(mySD);
505	+	molInfo.myIntegrableObjects.push_back(mySD);
506	+	}
507	+
508
509		// send the arrays off to the forceField for init.
510
511	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
512	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
513	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
514	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
515	<
391	<
392	<	info[k].molecules[i].initialize( molInfo );
511	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
512	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
513	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
514	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
515	>	theTorsions);
516
517	<
517	>	info[k].molecules[i].initialize(molInfo);
518	>
519	>
520		atomOffset += molInfo.nAtoms;
521		delete[] theBonds;
522		delete[] theBends;
523		delete[] theTorsions;
524	<	}
524	>	}
525		}
526	<
526	>
527		#ifdef IS_MPI
528	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
528	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
529		MPIcheckPoint();
530		#endif // is_mpi
531	<
531	>
532		// clean up the forcefield
533
534	<	the_ff->calcRcut();
534	>	if (!globals->haveLJrcut()){
535	>
536	>	the_ff->calcRcut();
537	>
538	>	} else {
539	>
540	>	the_ff->setRcut( globals->getLJrcut() );
541	>	}
542	>
543		the_ff->cleanMe();
411	–
544		}
545
546	<	void SimSetup::initFromBass( void ){
415	<
546	>	void SimSetup::initFromBass(void){
547		int i, j, k;
548		int n_cells;
549		double cellx, celly, cellz;
#	Line 426 | Line 557 | void SimSetup::initFromBass( void ){
557		vel[1] = 0.0;
558		vel[2] = 0.0;
559
560	<	temp1 = (double)tot_nmol / 4.0;
561	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
562	<	temp3 = ceil( temp2 );
560	>	temp1 = (double) tot_nmol / 4.0;
561	>	temp2 = pow(temp1, (1.0 / 3.0));
562	>	temp3 = ceil(temp2);
563
564	<	have_extra =0;
565	<	if( temp2 < temp3 ){ // we have a non-complete lattice
566	<	have_extra =1;
564	>	have_extra = 0;
565	>	if (temp2 < temp3){
566	>	// we have a non-complete lattice
567	>	have_extra = 1;
568
569	<	n_cells = (int)temp3 - 1;
569	>	n_cells = (int) temp3 - 1;
570		cellx = info[0].boxL[0] / temp3;
571		celly = info[0].boxL[1] / temp3;
572		cellz = info[0].boxL[2] / temp3;
573	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
574	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
575	<	n_per_extra = (int)ceil( temp1 );
573	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
574	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
575	>	n_per_extra = (int) ceil(temp1);
576
577	<	if( n_per_extra > 4){
578	<	sprintf( painCave.errMsg,
579	<	"SimSetup error. There has been an error in constructing"
580	<	" the non-complete lattice.\n" );
577	>	if (n_per_extra > 4){
578	>	sprintf(painCave.errMsg,
579	>	"SimSetup error. There has been an error in constructing"
580	>	" the non-complete lattice.\n");
581		painCave.isFatal = 1;
582		simError();
583		}
584		}
585		else{
586	<	n_cells = (int)temp3;
586	>	n_cells = (int) temp3;
587		cellx = info[0].boxL[0] / temp3;
588		celly = info[0].boxL[1] / temp3;
589		cellz = info[0].boxL[2] / temp3;
#	Line 462 | Line 594 | void SimSetup::initFromBass( void ){
594		current_comp = 0;
595		current_atom_ndx = 0;
596
597	<	for( i=0; i < n_cells ; i++ ){
598	<	for( j=0; j < n_cells; j++ ){
599	<	for( k=0; k < n_cells; k++ ){
597	>	for (i = 0; i < n_cells ; i++){
598	>	for (j = 0; j < n_cells; j++){
599	>	for (k = 0; k < n_cells; k++){
600	>	makeElement(i * cellx, j * celly, k * cellz);
601
602	<	makeElement( i * cellx,
470	<	j * celly,
471	<	k * cellz );
602	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
603
604	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly + 0.5 * celly,
475	<	k * cellz );
604	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
605
606	<	makeElement( i * cellx,
478	<	j * celly + 0.5 * celly,
479	<	k * cellz + 0.5 * cellz );
480	<
481	<	makeElement( i * cellx + 0.5 * cellx,
482	<	j * celly,
483	<	k * cellz + 0.5 * cellz );
606	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
607		}
608		}
609		}
610
611	<	if( have_extra ){
611	>	if (have_extra){
612		done = 0;
613
614		int start_ndx;
615	<	for( i=0; i < (n_cells+1) && !done; i++ ){
616	<	for( j=0; j < (n_cells+1) && !done; j++ ){
615	>	for (i = 0; i < (n_cells + 1) && !done; i++){
616	>	for (j = 0; j < (n_cells + 1) && !done; j++){
617	>	if (i < n_cells){
618	>	if (j < n_cells){
619	>	start_ndx = n_cells;
620	>	}
621	>	else
622	>	start_ndx = 0;
623	>	}
624	>	else
625	>	start_ndx = 0;
626
627	<	if( i < n_cells ){
627	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
628	>	makeElement(i * cellx, j * celly, k * cellz);
629	>	done = (current_mol >= tot_nmol);
630
631	<	if( j < n_cells ){
632	<	start_ndx = n_cells;
633	<	}
634	<	else start_ndx = 0;
635	<	}
502	<	else start_ndx = 0;
631	>	if (!done && n_per_extra > 1){
632	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
633	>	k * cellz);
634	>	done = (current_mol >= tot_nmol);
635	>	}
636
637	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
637	>	if (!done && n_per_extra > 2){
638	>	makeElement(i * cellx, j * celly + 0.5 * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642
643	<	makeElement( i * cellx,
644	<	j * celly,
645	<	k * cellz );
646	<	done = ( current_mol >= tot_nmol );
647	<
648	<	if( !done && n_per_extra > 1 ){
512	<	makeElement( i * cellx + 0.5 * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
517	<
518	<	if( !done && n_per_extra > 2){
519	<	makeElement( i * cellx,
520	<	j * celly + 0.5 * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<
525	<	if( !done && n_per_extra > 3){
526	<	makeElement( i * cellx + 0.5 * cellx,
527	<	j * celly,
528	<	k * cellz + 0.5 * cellz );
529	<	done = ( current_mol >= tot_nmol );
530	<	}
531	<	}
643	>	if (!done && n_per_extra > 3){
644	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
645	>	k * cellz + 0.5 * cellz);
646	>	done = (current_mol >= tot_nmol);
647	>	}
648	>	}
649		}
650		}
651		}
652
653	<	for( i=0; i<info[0].n_atoms; i++ ){
654	<	info[0].atoms[i]->setVel( vel );
653	>	for (i = 0; i < info[0].n_atoms; i++){
654	>	info[0].atoms[i]->setVel(vel);
655		}
656		}
657
658	<	void SimSetup::makeElement( double x, double y, double z ){
542	<
658	>	void SimSetup::makeElement(double x, double y, double z){
659		int k;
660		AtomStamp* current_atom;
661		DirectionalAtom* dAtom;
662		double rotMat[3][3];
663		double pos[3];
664
665	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
666	<
667	<	current_atom = comp_stamps[current_comp]->getAtom( k );
668	<	if( !current_atom->havePosition() ){
669	<	sprintf( painCave.errMsg,
670	<	"SimSetup:initFromBass error.\n"
671	<	"\tComponent %s, atom %s does not have a position specified.\n"
672	<	"\tThe initialization routine is unable to give a start"
673	<	" position.\n",
558	<	comp_stamps[current_comp]->getID(),
559	<	current_atom->getType() );
665	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
666	>	current_atom = comp_stamps[current_comp]->getAtom(k);
667	>	if (!current_atom->havePosition()){
668	>	sprintf(painCave.errMsg,
669	>	"SimSetup:initFromBass error.\n"
670	>	"\tComponent %s, atom %s does not have a position specified.\n"
671	>	"\tThe initialization routine is unable to give a start"
672	>	" position.\n",
673	>	comp_stamps[current_comp]->getID(), current_atom->getType());
674		painCave.isFatal = 1;
675		simError();
676		}
677	<
677	>
678		pos[0] = x + current_atom->getPosX();
679		pos[1] = y + current_atom->getPosY();
680		pos[2] = z + current_atom->getPosZ();
567	–
568	–	info[0].atoms[current_atom_ndx]->setPos( pos );
681
682	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
682	>	info[0].atoms[current_atom_ndx]->setPos(pos);
683
684	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
684	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
685	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
686
687		rotMat[0][0] = 1.0;
688		rotMat[0][1] = 0.0;
#	Line 583 | Line 696 | void SimSetup::makeElement( double x, double y, double
696		rotMat[2][1] = 0.0;
697		rotMat[2][2] = 1.0;
698
699	<	dAtom->setA( rotMat );
699	>	dAtom->setA(rotMat);
700		}
701
702		current_atom_ndx++;
#	Line 592 | Line 705 | void SimSetup::makeElement( double x, double y, double
705		current_mol++;
706		current_comp_mol++;
707
708	<	if( current_comp_mol >= components_nmol[current_comp] ){
596	<
708	>	if (current_comp_mol >= components_nmol[current_comp]){
709		current_comp_mol = 0;
710		current_comp++;
711		}
712		}
713
714
715	<	void SimSetup::gatherInfo( void ){
716	<	int i,j,k;
715	>	void SimSetup::gatherInfo(void){
716	>	int i;
717
718		ensembleCase = -1;
719		ffCase = -1;
720
721		// set the easy ones first
722
723	<	for( i=0; i<nInfo; i++){
723	>	for (i = 0; i < nInfo; i++){
724		info[i].target_temp = globals->getTargetTemp();
725		info[i].dt = globals->getDt();
726		info[i].run_time = globals->getRunTime();
#	Line 618 | Line 730 | void SimSetup::gatherInfo( void ){
730
731		// get the forceField
732
733	<	strcpy( force_field, globals->getForceField() );
733	>	strcpy(force_field, globals->getForceField());
734
735	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
736	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
737	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
735	>	if (!strcasecmp(force_field, "DUFF")){
736	>	ffCase = FF_DUFF;
737	>	}
738	>	else if (!strcasecmp(force_field, "LJ")){
739	>	ffCase = FF_LJ;
740	>	}
741	>	else if (!strcasecmp(force_field, "EAM")){
742	>	ffCase = FF_EAM;
743	>	}
744	>	else if (!strcasecmp(force_field, "WATER")){
745	>	ffCase = FF_H2O;
746	>	}
747		else{
748	<	sprintf( painCave.errMsg,
749	<	"SimSetup Error. Unrecognized force field -> %s\n",
750	<	force_field );
751	<	painCave.isFatal = 1;
631	<	simError();
748	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
749	>	force_field);
750	>	painCave.isFatal = 1;
751	>	simError();
752		}
753
754	<	// get the ensemble
754	>	// get the ensemble
755
756	<	strcpy( ensemble, globals->getEnsemble() );
756	>	strcpy(ensemble, globals->getEnsemble());
757
758	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
759	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
760	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
758	>	if (!strcasecmp(ensemble, "NVE")){
759	>	ensembleCase = NVE_ENS;
760	>	}
761	>	else if (!strcasecmp(ensemble, "NVT")){
762	>	ensembleCase = NVT_ENS;
763	>	}
764	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
765		ensembleCase = NPTi_ENS;
766	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
767	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
768	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
766	>	}
767	>	else if (!strcasecmp(ensemble, "NPTf")){
768	>	ensembleCase = NPTf_ENS;
769	>	}
770	>	else if (!strcasecmp(ensemble, "NPTxyz")){
771	>	ensembleCase = NPTxyz_ENS;
772	>	}
773		else{
774	<	sprintf( painCave.errMsg,
775	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
776	<	"reverting to NVE for this simulation.\n",
777	<	ensemble );
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	strcpy( ensemble, "NVE" );
781	<	ensembleCase = NVE_ENS;
774	>	sprintf(painCave.errMsg,
775	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
776	>	"\treverting to NVE for this simulation.\n",
777	>	ensemble);
778	>	painCave.isFatal = 0;
779	>	simError();
780	>	strcpy(ensemble, "NVE");
781	>	ensembleCase = NVE_ENS;
782		}
655	–
656	–	for(i=0; i<nInfo; i++){
657	–
658	–	strcpy( info[i].ensemble, ensemble );
783
784	+	for (i = 0; i < nInfo; i++){
785	+	strcpy(info[i].ensemble, ensemble);
786	+
787		// get the mixing rule
788
789	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
789	>	strcpy(info[i].mixingRule, globals->getMixingRule());
790		info[i].usePBC = globals->getPBC();
791		}
792	<
792	>
793		// get the components and calculate the tot_nMol and indvidual n_mol
794	<
794	>
795		the_components = globals->getComponents();
796		components_nmol = new int[n_components];
797
798
799	<	if( !globals->haveNMol() ){
799	>	if (!globals->haveNMol()){
800		// we don't have the total number of molecules, so we assume it is
801		// given in each component
802
803		tot_nmol = 0;
804	<	for( i=0; i<n_components; i++ ){
805	<
806	<	if( !the_components[i]->haveNMol() ){
807	<	// we have a problem
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup Error. No global NMol or component NMol"
810	<	" given. Cannot calculate the number of atoms.\n" );
811	<	painCave.isFatal = 1;
685	<	simError();
804	>	for (i = 0; i < n_components; i++){
805	>	if (!the_components[i]->haveNMol()){
806	>	// we have a problem
807	>	sprintf(painCave.errMsg,
808	>	"SimSetup Error. No global NMol or component NMol given.\n"
809	>	"\tCannot calculate the number of atoms.\n");
810	>	painCave.isFatal = 1;
811	>	simError();
812		}
813
814		tot_nmol += the_components[i]->getNMol();
#	Line 690 | Line 816 | void SimSetup::gatherInfo( void ){
816		}
817		}
818		else{
819	<	sprintf( painCave.errMsg,
820	<	"SimSetup error.\n"
821	<	"\tSorry, the ability to specify total"
822	<	" nMols and then give molfractions in the components\n"
823	<	"\tis not currently supported."
824	<	" Please give nMol in the components.\n" );
819	>	sprintf(painCave.errMsg,
820	>	"SimSetup error.\n"
821	>	"\tSorry, the ability to specify total"
822	>	" nMols and then give molfractions in the components\n"
823	>	"\tis not currently supported."
824	>	" Please give nMol in the components.\n");
825		painCave.isFatal = 1;
826		simError();
827		}
828
829	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
830	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
831	+	sprintf(painCave.errMsg,
832	+	"Sample time is not divisible by dt.\n"
833	+	"\tThis will result in samples that are not uniformly\n"
834	+	"\tdistributed in time.  If this is a problem, change\n"
835	+	"\tyour sampleTime variable.\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	}
839	+
840	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
841	+	sprintf(painCave.errMsg,
842	+	"Status time is not divisible by dt.\n"
843	+	"\tThis will result in status reports that are not uniformly\n"
844	+	"\tdistributed in time.  If this is a problem, change \n"
845	+	"\tyour statusTime variable.\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	}
849	+
850	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
851	+	sprintf(painCave.errMsg,
852	+	"Thermal time is not divisible by dt.\n"
853	+	"\tThis will result in thermalizations that are not uniformly\n"
854	+	"\tdistributed in time.  If this is a problem, change \n"
855	+	"\tyour thermalTime variable.\n");
856	+	painCave.isFatal = 0;
857	+	simError();
858	+	}
859	+
860	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
861	+	sprintf(painCave.errMsg,
862	+	"Reset time is not divisible by dt.\n"
863	+	"\tThis will result in integrator resets that are not uniformly\n"
864	+	"\tdistributed in time.  If this is a problem, change\n"
865	+	"\tyour resetTime variable.\n");
866	+	painCave.isFatal = 0;
867	+	simError();
868	+	}
869	+
870		// set the status, sample, and thermal kick times
704	–
705	–	for(i=0; i<nInfo; i++){
871
872	<	if( globals->haveSampleTime() ){
872	>	for (i = 0; i < nInfo; i++){
873	>	if (globals->haveSampleTime()){
874		info[i].sampleTime = globals->getSampleTime();
875		info[i].statusTime = info[i].sampleTime;
876		info[i].thermalTime = info[i].sampleTime;
#	Line 714 | Line 880 | void SimSetup::gatherInfo( void ){
880		info[i].statusTime = info[i].sampleTime;
881		info[i].thermalTime = info[i].sampleTime;
882		}
883	<
884	<	if( globals->haveStatusTime() ){
883	>
884	>	if (globals->haveStatusTime()){
885		info[i].statusTime = globals->getStatusTime();
886		}
887	<
888	<	if( globals->haveThermalTime() ){
887	>
888	>	if (globals->haveThermalTime()){
889		info[i].thermalTime = globals->getThermalTime();
890		}
891
892	+	info[i].resetIntegrator = 0;
893	+	if( globals->haveResetTime() ){
894	+	info[i].resetTime = globals->getResetTime();
895	+	info[i].resetIntegrator = 1;
896	+	}
897	+
898		// check for the temperature set flag
899	+
900	+	if (globals->haveTempSet())
901	+	info[i].setTemp = globals->getTempSet();
902
903	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
903	>	// check for the extended State init
904	>
905	>	info[i].useInitXSstate = globals->getUseInitXSstate();
906	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
907
730	–	// get some of the tricky things that may still be in the globals
731	–
732	–	double boxVector[3];
733	–	if( globals->haveBox() ){
734	–	boxVector[0] = globals->getBox();
735	–	boxVector[1] = globals->getBox();
736	–	boxVector[2] = globals->getBox();
737	–
738	–	info[i].setBox( boxVector );
739	–	}
740	–	else if( globals->haveDensity() ){
741	–
742	–	double vol;
743	–	vol = (double)tot_nmol / globals->getDensity();
744	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	–	boxVector[1] = boxVector[0];
746	–	boxVector[2] = boxVector[0];
747	–
748	–	info[i].setBox( boxVector );
908		}
909	<	else{
910	<	if( !globals->haveBoxX() ){
911	<	sprintf( painCave.errMsg,
912	<	"SimSetup error, no periodic BoxX size given.\n" );
913	<	painCave.isFatal = 1;
914	<	simError();
915	<	}
916	<	boxVector[0] = globals->getBoxX();
917	<
918	<	if( !globals->haveBoxY() ){
919	<	sprintf( painCave.errMsg,
920	<	"SimSetup error, no periodic BoxY size given.\n" );
921	<	painCave.isFatal = 1;
922	<	simError();
909	>
910	>	//setup seed for random number generator
911	>	int seedValue;
912	>
913	>	if (globals->haveSeed()){
914	>	seedValue = globals->getSeed();
915	>
916	>	if(seedValue / 1E9 == 0){
917	>	sprintf(painCave.errMsg,
918	>	"Seed for sprng library should contain at least 9 digits\n"
919	>	"OOPSE will generate a seed for user\n");
920	>	painCave.isFatal = 0;
921	>	simError();
922	>
923	>	//using seed generated by system instead of invalid seed set by user
924	>	#ifndef IS_MPI
925	>	seedValue = make_sprng_seed();
926	>	#else
927	>	if (worldRank == 0){
928	>	seedValue = make_sprng_seed();
929		}
930	<	boxVector[1] = globals->getBoxY();
931	<
767	<	if( !globals->haveBoxZ() ){
768	<	sprintf( painCave.errMsg,
769	<	"SimSetup error, no periodic BoxZ size given.\n" );
770	<	painCave.isFatal = 1;
771	<	simError();
772	<	}
773	<	boxVector[2] = globals->getBoxZ();
774	<
775	<	info[i].setBox( boxVector );
930	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
931	>	#endif
932		}
933	+	}//end of if branch of globals->haveSeed()
934	+	else{
935	+
936	+	#ifndef IS_MPI
937	+	seedValue = make_sprng_seed();
938	+	#else
939	+	if (worldRank == 0){
940	+	seedValue = make_sprng_seed();
941	+	}
942	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
943	+	#endif
944	+	}//end of globals->haveSeed()
945
946	+	for (int i = 0; i < nInfo; i++){
947	+	info[i].setSeed(seedValue);
948		}
949	<
949	>
950		#ifdef IS_MPI
951	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
951	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
952		MPIcheckPoint();
953		#endif // is_mpi
784	–
954		}
955
956
957	<	void SimSetup::finalInfoCheck( void ){
957	>	void SimSetup::finalInfoCheck(void){
958		int index;
959		int usesDipoles;
960		int i;
961
962	<	for(i=0; i<nInfo; i++){
962	>	for (i = 0; i < nInfo; i++){
963		// check electrostatic parameters
964	<
964	>
965		index = 0;
966		usesDipoles = 0;
967	<	while( (index < info[i].n_atoms) && !usesDipoles ){
967	>	while ((index < info[i].n_atoms) && !usesDipoles){
968		usesDipoles = (info[i].atoms[index])->hasDipole();
969		index++;
970		}
971	<
971	>
972		#ifdef IS_MPI
973		int myUse = usesDipoles;
974	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
974	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
975		#endif //is_mpi
976	<
976	>
977		double theEcr, theEst;
978	<
979	<	if (globals->getUseRF() ) {
978	>
979	>	if (globals->getUseRF()){
980		info[i].useReactionField = 1;
981	<
982	<	if( !globals->haveECR() ){
983	<	sprintf( painCave.errMsg,
984	<	"SimSetup Warning: using default value of 1/2 the smallest "
985	<	"box length for the electrostaticCutoffRadius.\n"
986	<	"I hope you have a very fast processor!\n");
987	<	painCave.isFatal = 0;
988	<	simError();
989	<	double smallest;
821	<	smallest = info[i].boxL[0];
822	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
981	>
982	>	if (!globals->haveECR()){
983	>	sprintf(painCave.errMsg,
984	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
985	>	"\tOOPSE will use a default value of 15.0 angstroms"
986	>	"\tfor the electrostaticCutoffRadius.\n");
987	>	painCave.isFatal = 0;
988	>	simError();
989	>	theEcr = 15.0;
990		}
991	<
992	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	<	);
834	<	painCave.isFatal = 0;
835	<	simError();
836	<	theEst = 0.05 * theEcr;
837	<	} else {
838	<	theEst= globals->getEST();
991	>	else{
992	>	theEcr = globals->getECR();
993		}
994	<
995	<	info[i].setEcr( theEcr, theEst );
996	<
997	<	if(!globals->haveDielectric() ){
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: You are trying to use Reaction Field without"
1000	<	"setting a dielectric constant!\n"
1001	<	);
1002	<	painCave.isFatal = 1;
1003	<	simError();
994	>
995	>	if (!globals->haveEST()){
996	>	sprintf(painCave.errMsg,
997	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
998	>	"\tOOPSE will use a default value of\n"
999	>	"\t0.05 * electrostaticCutoffRadius\n"
1000	>	"\tfor the electrostaticSkinThickness\n");
1001	>	painCave.isFatal = 0;
1002	>	simError();
1003	>	theEst = 0.05 * theEcr;
1004		}
1005	<	info[i].dielectric = globals->getDielectric();
1006	<	}
1007	<	else {
1008	<	if (usesDipoles) {
1009	<
1010	<	if( !globals->haveECR() ){
1011	<	sprintf( painCave.errMsg,
1012	<	"SimSetup Warning: using default value of 1/2 the smallest "
1013	<	"box length for the electrostaticCutoffRadius.\n"
1014	<	"I hope you have a very fast processor!\n");
1005	>	else{
1006	>	theEst = globals->getEST();
1007	>	}
1008	>
1009	>	info[i].setDefaultEcr(theEcr, theEst);
1010	>
1011	>	if (!globals->haveDielectric()){
1012	>	sprintf(painCave.errMsg,
1013	>	"SimSetup Error: No Dielectric constant was set.\n"
1014	>	"\tYou are trying to use Reaction Field without"
1015	>	"\tsetting a dielectric constant!\n");
1016	>	painCave.isFatal = 1;
1017	>	simError();
1018	>	}
1019	>	info[i].dielectric = globals->getDielectric();
1020	>	}
1021	>	else{
1022	>	if (usesDipoles){
1023	>	if (!globals->haveECR()){
1024	>	sprintf(painCave.errMsg,
1025	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the electrostaticCutoffRadius.\n");
1028		painCave.isFatal = 0;
1029		simError();
1030	<	double smallest;
1031	<	smallest = info[i].boxL[0];
1032	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
1033	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
1034	<	theEcr = 0.5 * smallest;
868	<	} else {
869	<	theEcr = globals->getECR();
870	<	}
1030	>	theEcr = 15.0;
1031	>	}
1032	>	else{
1033	>	theEcr = globals->getECR();
1034	>	}
1035
1036	<	if( !globals->haveEST() ){
1037	<	sprintf( painCave.errMsg,
1038	<	"SimSetup Warning: using default value of 0.05 * the "
1039	<	"electrostaticCutoffRadius for the "
1040	<	"electrostaticSkinThickness\n"
1041	<	);
1042	<	painCave.isFatal = 0;
1043	<	simError();
1044	<	theEst = 0.05 * theEcr;
1045	<	} else {
1046	<	theEst= globals->getEST();
1047	<	}
1036	>	if (!globals->haveEST()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1039	>	"\tOOPSE will use a default value of\n"
1040	>	"\t0.05 * electrostaticCutoffRadius\n"
1041	>	"\tfor the electrostaticSkinThickness\n");
1042	>	painCave.isFatal = 0;
1043	>	simError();
1044	>	theEst = 0.05 * theEcr;
1045	>	}
1046	>	else{
1047	>	theEst = globals->getEST();
1048	>	}
1049
1050	<	info[i].setEcr( theEcr, theEst );
1050	>	info[i].setDefaultEcr(theEcr, theEst);
1051		}
1052	<	}
1052	>	}
1053		}
889	–
1054		#ifdef IS_MPI
1055	<	strcpy( checkPointMsg, "post processing checks out" );
1055	>	strcpy(checkPointMsg, "post processing checks out");
1056		MPIcheckPoint();
1057		#endif // is_mpi
894	–
1058		}
896	–
897	–	void SimSetup::initSystemCoords( void ){
898	–	int i;
1059
1060	+	void SimSetup::initSystemCoords(void){
1061	+	int i;
1062	+
1063		char* inName;
1064
1065	<	std::cerr << "Setting atom Coords\n";
1065	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1066
1067	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1068	<
1069	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1070	<
908	<	if( globals->haveInitialConfig() ){
909	<
1067	>	for (i = 0; i < info[0].n_atoms; i++)
1068	>	info[0].atoms[i]->setCoords();
1069	>
1070	>	if (globals->haveInitialConfig()){
1071		InitializeFromFile* fileInit;
1072		#ifdef IS_MPI // is_mpi
1073	<	if( worldRank == 0 ){
1073	>	if (worldRank == 0){
1074		#endif //is_mpi
1075		inName = globals->getInitialConfig();
1076	<	fileInit = new InitializeFromFile( inName );
1076	>	fileInit = new InitializeFromFile(inName);
1077		#ifdef IS_MPI
1078	<	}else fileInit = new InitializeFromFile( NULL );
1078	>	}
1079	>	else
1080	>	fileInit = new InitializeFromFile(NULL);
1081		#endif
1082	<	fileInit->readInit( info ); // default velocities on
1083	<
1082	>	fileInit->readInit(info); // default velocities on
1083	>
1084		delete fileInit;
1085		}
1086		else{
1087
925	–	#ifdef IS_MPI
926	–
1088		// no init from bass
1089
1090	<	sprintf( painCave.errMsg,
1091	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1092	<	painCave.isFatal;
1090	>	sprintf(painCave.errMsg,
1091	>	"Cannot intialize a simulation without an initial configuration file.\n");
1092	>	painCave.isFatal = 1;;
1093		simError();
1094
934	–	#else
935	–
936	–	initFromBass();
937	–
938	–
939	–	#endif
1095		}
1096	<
1096	>
1097		#ifdef IS_MPI
1098	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1098	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1099		MPIcheckPoint();
1100		#endif // is_mpi
946	–
1101		}
1102
1103
1104	<	void SimSetup::makeOutNames( void ){
951	<
1104	>	void SimSetup::makeOutNames(void){
1105		int k;
1106
954	–
955	–	for(k=0; k<nInfo; k++){
1107
1108	+	for (k = 0; k < nInfo; k++){
1109		#ifdef IS_MPI
1110	<	if( worldRank == 0 ){
1110	>	if (worldRank == 0){
1111		#endif // is_mpi
1112	<
1113	<	if( globals->haveFinalConfig() ){
1114	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1112	>
1113	>	if (globals->haveFinalConfig()){
1114	>	strcpy(info[k].finalName, globals->getFinalConfig());
1115		}
1116		else{
1117	<	strcpy( info[k].finalName, inFileName );
1118	<	char* endTest;
1119	<	int nameLength = strlen( info[k].finalName );
1120	<	endTest = &(info[k].finalName[nameLength - 5]);
1121	<	if( !strcmp( endTest, ".bass" ) ){
1122	<	strcpy( endTest, ".eor" );
1123	<	}
1124	<	else if( !strcmp( endTest, ".BASS" ) ){
1125	<	strcpy( endTest, ".eor" );
1126	<	}
1127	<	else{
1128	<	endTest = &(info[k].finalName[nameLength - 4]);
1129	<	if( !strcmp( endTest, ".bss" ) ){
1130	<	strcpy( endTest, ".eor" );
1131	<	}
1132	<	else if( !strcmp( endTest, ".mdl" ) ){
1133	<	strcpy( endTest, ".eor" );
1134	<	}
1135	<	else{
1136	<	strcat( info[k].finalName, ".eor" );
1137	<	}
1138	<	}
1117	>	strcpy(info[k].finalName, inFileName);
1118	>	char* endTest;
1119	>	int nameLength = strlen(info[k].finalName);
1120	>	endTest = &(info[k].finalName[nameLength - 5]);
1121	>	if (!strcmp(endTest, ".bass")){
1122	>	strcpy(endTest, ".eor");
1123	>	}
1124	>	else if (!strcmp(endTest, ".BASS")){
1125	>	strcpy(endTest, ".eor");
1126	>	}
1127	>	else{
1128	>	endTest = &(info[k].finalName[nameLength - 4]);
1129	>	if (!strcmp(endTest, ".bss")){
1130	>	strcpy(endTest, ".eor");
1131	>	}
1132	>	else if (!strcmp(endTest, ".mdl")){
1133	>	strcpy(endTest, ".eor");
1134	>	}
1135	>	else{
1136	>	strcat(info[k].finalName, ".eor");
1137	>	}
1138	>	}
1139		}
1140	<
1140	>
1141		// make the sample and status out names
1142	<
1143	<	strcpy( info[k].sampleName, inFileName );
1142	>
1143	>	strcpy(info[k].sampleName, inFileName);
1144		char* endTest;
1145	<	int nameLength = strlen( info[k].sampleName );
1145	>	int nameLength = strlen(info[k].sampleName);
1146		endTest = &(info[k].sampleName[nameLength - 5]);
1147	<	if( !strcmp( endTest, ".bass" ) ){
1148	<	strcpy( endTest, ".dump" );
1147	>	if (!strcmp(endTest, ".bass")){
1148	>	strcpy(endTest, ".dump");
1149		}
1150	<	else if( !strcmp( endTest, ".BASS" ) ){
1151	<	strcpy( endTest, ".dump" );
1150	>	else if (!strcmp(endTest, ".BASS")){
1151	>	strcpy(endTest, ".dump");
1152		}
1153		else{
1154	<	endTest = &(info[k].sampleName[nameLength - 4]);
1155	<	if( !strcmp( endTest, ".bss" ) ){
1156	<	strcpy( endTest, ".dump" );
1157	<	}
1158	<	else if( !strcmp( endTest, ".mdl" ) ){
1159	<	strcpy( endTest, ".dump" );
1160	<	}
1161	<	else{
1162	<	strcat( info[k].sampleName, ".dump" );
1163	<	}
1154	>	endTest = &(info[k].sampleName[nameLength - 4]);
1155	>	if (!strcmp(endTest, ".bss")){
1156	>	strcpy(endTest, ".dump");
1157	>	}
1158	>	else if (!strcmp(endTest, ".mdl")){
1159	>	strcpy(endTest, ".dump");
1160	>	}
1161	>	else{
1162	>	strcat(info[k].sampleName, ".dump");
1163	>	}
1164		}
1165	<
1166	<	strcpy( info[k].statusName, inFileName );
1167	<	nameLength = strlen( info[k].statusName );
1165	>
1166	>	strcpy(info[k].statusName, inFileName);
1167	>	nameLength = strlen(info[k].statusName);
1168		endTest = &(info[k].statusName[nameLength - 5]);
1169	<	if( !strcmp( endTest, ".bass" ) ){
1170	<	strcpy( endTest, ".stat" );
1169	>	if (!strcmp(endTest, ".bass")){
1170	>	strcpy(endTest, ".stat");
1171		}
1172	<	else if( !strcmp( endTest, ".BASS" ) ){
1173	<	strcpy( endTest, ".stat" );
1172	>	else if (!strcmp(endTest, ".BASS")){
1173	>	strcpy(endTest, ".stat");
1174		}
1175		else{
1176	<	endTest = &(info[k].statusName[nameLength - 4]);
1177	<	if( !strcmp( endTest, ".bss" ) ){
1178	<	strcpy( endTest, ".stat" );
1179	<	}
1180	<	else if( !strcmp( endTest, ".mdl" ) ){
1181	<	strcpy( endTest, ".stat" );
1182	<	}
1183	<	else{
1184	<	strcat( info[k].statusName, ".stat" );
1185	<	}
1176	>	endTest = &(info[k].statusName[nameLength - 4]);
1177	>	if (!strcmp(endTest, ".bss")){
1178	>	strcpy(endTest, ".stat");
1179	>	}
1180	>	else if (!strcmp(endTest, ".mdl")){
1181	>	strcpy(endTest, ".stat");
1182	>	}
1183	>	else{
1184	>	strcat(info[k].statusName, ".stat");
1185	>	}
1186		}
1187	<
1187	>
1188		#ifdef IS_MPI
1189	+
1190		}
1191		#endif // is_mpi
1192		}
1193		}
1194
1195
1196	<	void SimSetup::sysObjectsCreation( void ){
1197	<
1198	<	int i,k;
1046	<
1196	>	void SimSetup::sysObjectsCreation(void){
1197	>	int i, k;
1198	>
1199		// create the forceField
1200
1201		createFF();
#	Line 1058 | Line 1210 | void SimSetup::sysObjectsCreation( void ){
1210
1211		#ifdef IS_MPI
1212		// divide the molecules among the processors
1213	<
1213	>
1214		mpiMolDivide();
1215		#endif //is_mpi
1216	<
1216	>
1217		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1218	<
1218	>
1219		makeSysArrays();
1220
1221		// make and initialize the molecules (all but atomic coordinates)
1222	<
1222	>
1223		makeMolecules();
1224	<
1225	<	for(k=0; k<nInfo; k++){
1224	>
1225	>	for (k = 0; k < nInfo; k++){
1226		info[k].identArray = new int[info[k].n_atoms];
1227	<	for(i=0; i<info[k].n_atoms; i++){
1227	>	for (i = 0; i < info[k].n_atoms; i++){
1228		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1229		}
1230		}
1231		}
1232
1233
1234	<	void SimSetup::createFF( void ){
1234	>	void SimSetup::createFF(void){
1235	>	switch (ffCase){
1236	>	case FF_DUFF:
1237	>	the_ff = new DUFF();
1238	>	break;
1239
1240	<	switch( ffCase ){
1240	>	case FF_LJ:
1241	>	the_ff = new LJFF();
1242	>	break;
1243
1244	<	case FF_DUFF:
1245	<	the_ff = new DUFF();
1246	<	break;
1244	>	case FF_EAM:
1245	>	the_ff = new EAM_FF();
1246	>	break;
1247
1248	<	case FF_LJ:
1249	<	the_ff = new LJFF();
1250	<	break;
1248	>	case FF_H2O:
1249	>	the_ff = new WATER();
1250	>	break;
1251
1252	<	case FF_EAM:
1253	<	the_ff = new EAM_FF();
1254	<	break;
1255	<
1256	<	default:
1099	<	sprintf( painCave.errMsg,
1100	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	<	painCave.isFatal = 1;
1102	<	simError();
1252	>	default:
1253	>	sprintf(painCave.errMsg,
1254	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1255	>	painCave.isFatal = 1;
1256	>	simError();
1257		}
1258
1259		#ifdef IS_MPI
1260	<	strcpy( checkPointMsg, "ForceField creation successful" );
1260	>	strcpy(checkPointMsg, "ForceField creation successful");
1261		MPIcheckPoint();
1262		#endif // is_mpi
1109	–
1263		}
1264
1265
1266	<	void SimSetup::compList( void ){
1114	<
1266	>	void SimSetup::compList(void){
1267		int i;
1268		char* id;
1269		LinkedMolStamp* headStamp = new LinkedMolStamp();
1270		LinkedMolStamp* currentStamp = NULL;
1271	<	comp_stamps = new MoleculeStamp*[n_components];
1272	<
1271	>	comp_stamps = new MoleculeStamp * [n_components];
1272	>
1273		// make an array of molecule stamps that match the components used.
1274		// also extract the used stamps out into a separate linked list
1275	<
1276	<	for(i=0; i<nInfo; i++){
1275	>
1276	>	for (i = 0; i < nInfo; i++){
1277		info[i].nComponents = n_components;
1278		info[i].componentsNmol = components_nmol;
1279		info[i].compStamps = comp_stamps;
1280		info[i].headStamp = headStamp;
1281		}
1130	–
1282
1132	–	for( i=0; i<n_components; i++ ){
1283
1284	+	for (i = 0; i < n_components; i++){
1285		id = the_components[i]->getType();
1286		comp_stamps[i] = NULL;
1287	<
1287	>
1288		// check to make sure the component isn't already in the list
1289
1290	<	comp_stamps[i] = headStamp->match( id );
1291	<	if( comp_stamps[i] == NULL ){
1141	<
1290	>	comp_stamps[i] = headStamp->match(id);
1291	>	if (comp_stamps[i] == NULL){
1292		// extract the component from the list;
1293	<
1294	<	currentStamp = stamps->extractMolStamp( id );
1295	<	if( currentStamp == NULL ){
1296	<	sprintf( painCave.errMsg,
1297	<	"SimSetup error: Component \"%s\" was not found in the "
1298	<	"list of declared molecules\n",
1299	<	id );
1300	<	painCave.isFatal = 1;
1301	<	simError();
1293	>
1294	>	currentStamp = stamps->extractMolStamp(id);
1295	>	if (currentStamp == NULL){
1296	>	sprintf(painCave.errMsg,
1297	>	"SimSetup error: Component \"%s\" was not found in the "
1298	>	"list of declared molecules\n",
1299	>	id);
1300	>	painCave.isFatal = 1;
1301	>	simError();
1302		}
1303	<
1304	<	headStamp->add( currentStamp );
1305	<	comp_stamps[i] = headStamp->match( id );
1303	>
1304	>	headStamp->add(currentStamp);
1305	>	comp_stamps[i] = headStamp->match(id);
1306		}
1307		}
1308
1309		#ifdef IS_MPI
1310	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1310	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1311		MPIcheckPoint();
1312		#endif // is_mpi
1313	+	}
1314
1315	+	void SimSetup::calcSysValues(void){
1316	+	int i;
1317
1318	<	}
1318	>	int* molMembershipArray;
1319
1167	–	void SimSetup::calcSysValues( void ){
1168	–	int i, j, k;
1169	–
1170	–	int *molMembershipArray;
1171	–
1320		tot_atoms = 0;
1321		tot_bonds = 0;
1322		tot_bends = 0;
1323		tot_torsions = 0;
1324	<	for( i=0; i<n_components; i++ ){
1325	<
1326	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1327	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1328	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1324	>	tot_rigid = 0;
1325	>	for (i = 0; i < n_components; i++){
1326	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1327	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1328	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1329		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1330	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1331		}
1332
1333		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1334		molMembershipArray = new int[tot_atoms];
1335	<
1336	<	for(i=0; i<nInfo; i++){
1335	>
1336	>	for (i = 0; i < nInfo; i++){
1337		info[i].n_atoms = tot_atoms;
1338		info[i].n_bonds = tot_bonds;
1339		info[i].n_bends = tot_bends;
1340		info[i].n_torsions = tot_torsions;
1341		info[i].n_SRI = tot_SRI;
1342		info[i].n_mol = tot_nmol;
1343	<
1343	>
1344		info[i].molMembershipArray = molMembershipArray;
1345	<	}
1345	>	}
1346		}
1347
1348		#ifdef IS_MPI
1349
1350	<	void SimSetup::mpiMolDivide( void ){
1202	<
1350	>	void SimSetup::mpiMolDivide(void){
1351		int i, j, k;
1352		int localMol, allMol;
1353		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1354	+	int local_rigid;
1355	+	vector<int> globalAtomIndex;
1356	+	vector<int> globalMolIndex;
1357
1358	<	mpiSim = new mpiSimulation( info );
1208	<
1209	<	globalIndex = mpiSim->divideLabor();
1358	>	mpiSim = new mpiSimulation(info);
1359
1360	+	mpiSim->divideLabor();
1361	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1362	+	globalMolIndex = mpiSim->getGlobalMolIndex();
1363	+
1364		// set up the local variables
1365	<
1365	>
1366		mol2proc = mpiSim->getMolToProcMap();
1367		molCompType = mpiSim->getMolComponentType();
1368	<
1368	>
1369		allMol = 0;
1370		localMol = 0;
1371		local_atoms = 0;
1372		local_bonds = 0;
1373		local_bends = 0;
1374		local_torsions = 0;
1375	<	globalAtomIndex = 0;
1375	>	local_rigid = 0;
1376	>	globalAtomCounter = 0;
1377
1378	<
1379	<	for( i=0; i<n_components; i++ ){
1380	<
1381	<	for( j=0; j<components_nmol[i]; j++ ){
1382	<
1383	<	if( mol2proc[allMol] == worldRank ){
1384	<
1385	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1386	<	local_bonds +=    comp_stamps[i]->getNBonds();
1233	<	local_bends +=    comp_stamps[i]->getNBends();
1234	<	local_torsions += comp_stamps[i]->getNTorsions();
1235	<	localMol++;
1378	>	for (i = 0; i < n_components; i++){
1379	>	for (j = 0; j < components_nmol[i]; j++){
1380	>	if (mol2proc[allMol] == worldRank){
1381	>	local_atoms += comp_stamps[i]->getNAtoms();
1382	>	local_bonds += comp_stamps[i]->getNBonds();
1383	>	local_bends += comp_stamps[i]->getNBends();
1384	>	local_torsions += comp_stamps[i]->getNTorsions();
1385	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1386	>	localMol++;
1387		}
1388	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1389	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1390	<	globalAtomIndex++;
1388	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1389	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1390	>	globalAtomCounter++;
1391		}
1392
1393	<	allMol++;
1393	>	allMol++;
1394		}
1395		}
1396		local_SRI = local_bonds + local_bends + local_torsions;
1397	<
1397	>
1398		info[0].n_atoms = mpiSim->getMyNlocal();
1399
1400	<	if( local_atoms != info[0].n_atoms ){
1401	<	sprintf( painCave.errMsg,
1402	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1403	<	" localAtom (%d) are not equal.\n",
1404	<	info[0].n_atoms,
1405	<	local_atoms );
1400	>
1401	>	if (local_atoms != info[0].n_atoms){
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1404	>	"\tlocalAtom (%d) are not equal.\n",
1405	>	info[0].n_atoms, local_atoms);
1406		painCave.isFatal = 1;
1407		simError();
1408		}
#	Line 1262 | Line 1413 | void SimSetup::mpiMolDivide( void ){
1413		info[0].n_SRI = local_SRI;
1414		info[0].n_mol = localMol;
1415
1416	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1416	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1417		MPIcheckPoint();
1418		}
1419	<
1419	>
1420		#endif // is_mpi
1421
1422
1423	<	void SimSetup::makeSysArrays( void ){
1424	<	int i, j, k, l;
1423	>	void SimSetup::makeSysArrays(void){
1424	>
1425	>	#ifndef IS_MPI
1426	>	int k, j;
1427	>	#endif // is_mpi
1428	>	int i, l;
1429
1430		Atom** the_atoms;
1431		Molecule* the_molecules;
1277	–	Exclude** the_excludes;
1432
1433	<
1280	<	for(l=0; l<nInfo; l++){
1281	<
1433	>	for (l = 0; l < nInfo; l++){
1434		// create the atom and short range interaction arrays
1435	<
1436	<	the_atoms = new Atom*[info[l].n_atoms];
1435	>
1436	>	the_atoms = new Atom * [info[l].n_atoms];
1437		the_molecules = new Molecule[info[l].n_mol];
1438		int molIndex;
1439
1440		// initialize the molecule's stampID's
1441	<
1441	>
1442		#ifdef IS_MPI
1443	<
1444	<
1443	>
1444	>
1445		molIndex = 0;
1446	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1447	<
1448	<	if(mol2proc[i] == worldRank ){
1449	<	the_molecules[molIndex].setStampID( molCompType[i] );
1450	<	the_molecules[molIndex].setMyIndex( molIndex );
1451	<	the_molecules[molIndex].setGlobalIndex( i );
1300	<	molIndex++;
1446	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1447	>	if (mol2proc[i] == worldRank){
1448	>	the_molecules[molIndex].setStampID(molCompType[i]);
1449	>	the_molecules[molIndex].setMyIndex(molIndex);
1450	>	the_molecules[molIndex].setGlobalIndex(i);
1451	>	molIndex++;
1452		}
1453		}
1454	<
1454	>
1455		#else // is_mpi
1456	<
1456	>
1457		molIndex = 0;
1458	<	globalAtomIndex = 0;
1459	<	for(i=0; i<n_components; i++){
1460	<	for(j=0; j<components_nmol[i]; j++ ){
1461	<	the_molecules[molIndex].setStampID( i );
1462	<	the_molecules[molIndex].setMyIndex( molIndex );
1463	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1464	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1465	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1466	<	globalAtomIndex++;
1467	<	}
1468	<	molIndex++;
1458	>	globalAtomCounter = 0;
1459	>	for (i = 0; i < n_components; i++){
1460	>	for (j = 0; j < components_nmol[i]; j++){
1461	>	the_molecules[molIndex].setStampID(i);
1462	>	the_molecules[molIndex].setMyIndex(molIndex);
1463	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1464	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1465	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1466	>	globalAtomCounter++;
1467	>	}
1468	>	molIndex++;
1469		}
1470		}
1320	–
1321	–
1322	–	#endif // is_mpi
1471
1472
1473	<	if( info[l].n_SRI ){
1326	<
1327	<	Exclude::createArray(info[l].n_SRI);
1328	<	the_excludes = new Exclude*[info[l].n_SRI];
1329	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	<	the_excludes[ex] = new Exclude(ex);
1331	<	}
1332	<	info[l].globalExcludes = new int;
1333	<	info[l].n_exclude = info[l].n_SRI;
1334	<	}
1335	<	else{
1336	<
1337	<	Exclude::createArray( 1 );
1338	<	the_excludes = new Exclude*;
1339	<	the_excludes[0] = new Exclude(0);
1340	<	the_excludes[0]->setPair( 0,0 );
1341	<	info[l].globalExcludes = new int;
1342	<	info[l].globalExcludes[0] = 0;
1343	<	info[l].n_exclude = 0;
1344	<	}
1473	>	#endif // is_mpi
1474
1475	+	info[l].globalExcludes = new int;
1476	+	info[l].globalExcludes[0] = 0;
1477	+
1478		// set the arrays into the SimInfo object
1479
1480		info[l].atoms = the_atoms;
1481		info[l].molecules = the_molecules;
1482		info[l].nGlobalExcludes = 0;
1351	–	info[l].excludes = the_excludes;
1483
1484	<	the_ff->setSimInfo( info );
1354	<
1484	>	the_ff->setSimInfo(info);
1485		}
1486		}
1487
1488	<	void SimSetup::makeIntegrator( void ){
1359	<
1488	>	void SimSetup::makeIntegrator(void){
1489		int k;
1490
1491	<	NVT<RealIntegrator>*  myNVT = NULL;
1492	<	NPTi<RealIntegrator>* myNPTi = NULL;
1493	<	NPTf<RealIntegrator>* myNPTf = NULL;
1494	<	NPTim<RealIntegrator>* myNPTim = NULL;
1495	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1496	<
1497	<	for(k=0; k<nInfo; k++){
1498	<
1499	<	switch( ensembleCase ){
1500	<
1501	<	case NVE_ENS:
1502	<	if (globals->haveZconstraints()){
1503	<	setupZConstraint(info[k]);
1504	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1491	>	NVE<RealIntegrator>* myNVE = NULL;
1492	>	NVT<RealIntegrator>* myNVT = NULL;
1493	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1494	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1495	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1496	>
1497	>	for (k = 0; k < nInfo; k++){
1498	>	switch (ensembleCase){
1499	>	case NVE_ENS:
1500	>	if (globals->haveZconstraints()){
1501	>	setupZConstraint(info[k]);
1502	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1503	>	}
1504	>	else{
1505	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1506		}
1507	+
1508	+	info->the_integrator = myNVE;
1509	+	break;
1510
1511	<	else
1512	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1513	<	break;
1514	<
1515	<	case NVT_ENS:
1516	<	if (globals->haveZconstraints()){
1517	<	setupZConstraint(info[k]);
1385	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	<	}
1387	<	else
1388	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1511	>	case NVT_ENS:
1512	>	if (globals->haveZconstraints()){
1513	>	setupZConstraint(info[k]);
1514	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1515	>	}
1516	>	else
1517	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1518
1519	<	myNVT->setTargetTemp(globals->getTargetTemp());
1391	<
1392	<	if (globals->haveTauThermostat())
1393	<	myNVT->setTauThermostat(globals->getTauThermostat());
1394	<
1395	<	else {
1396	<	sprintf( painCave.errMsg,
1397	<	"SimSetup error: If you use the NVT\n"
1398	<	"    ensemble, you must set tauThermostat.\n");
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1402	<	break;
1403	<
1404	<	case NPTi_ENS:
1405	<	if (globals->haveZconstraints()){
1406	<	setupZConstraint(info[k]);
1407	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	<	}
1409	<	else
1410	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1519	>	myNVT->setTargetTemp(globals->getTargetTemp());
1520
1521	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1522	<
1523	<	if (globals->haveTargetPressure())
1524	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1525	<	else {
1526	<	sprintf( painCave.errMsg,
1527	<	"SimSetup error: If you use a constant pressure\n"
1528	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1529	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1423	<
1424	<	if( globals->haveTauThermostat() )
1425	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	<	else{
1427	<	sprintf( painCave.errMsg,
1428	<	"SimSetup error: If you use an NPT\n"
1429	<	"    ensemble, you must set tauThermostat.\n");
1430	<	painCave.isFatal = 1;
1431	<	simError();
1432	<	}
1433	<
1434	<	if( globals->haveTauBarostat() )
1435	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	<	else{
1437	<	sprintf( painCave.errMsg,
1438	<	"SimSetup error: If you use an NPT\n"
1439	<	"    ensemble, you must set tauBarostat.\n");
1440	<	painCave.isFatal = 1;
1441	<	simError();
1442	<	}
1443	<	break;
1444	<
1445	<	case NPTf_ENS:
1446	<	if (globals->haveZconstraints()){
1447	<	setupZConstraint(info[k]);
1448	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	<	}
1450	<	else
1451	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1521	>	if (globals->haveTauThermostat())
1522	>	myNVT->setTauThermostat(globals->getTauThermostat());
1523	>	else{
1524	>	sprintf(painCave.errMsg,
1525	>	"SimSetup error: If you use the NVT\n"
1526	>	"\tensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530
1531	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1532	<
1455	<	if (globals->haveTargetPressure())
1456	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	<	else {
1458	<	sprintf( painCave.errMsg,
1459	<	"SimSetup error: If you use a constant pressure\n"
1460	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	<	painCave.isFatal = 1;
1462	<	simError();
1463	<	}
1464	<
1465	<	if( globals->haveTauThermostat() )
1466	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	<	else{
1468	<	sprintf( painCave.errMsg,
1469	<	"SimSetup error: If you use an NPT\n"
1470	<	"    ensemble, you must set tauThermostat.\n");
1471	<	painCave.isFatal = 1;
1472	<	simError();
1473	<	}
1474	<
1475	<	if( globals->haveTauBarostat() )
1476	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	<	else{
1478	<	sprintf( painCave.errMsg,
1479	<	"SimSetup error: If you use an NPT\n"
1480	<	"    ensemble, you must set tauBarostat.\n");
1481	<	painCave.isFatal = 1;
1482	<	simError();
1483	<	}
1484	<	break;
1485	<
1486	<	case NPTim_ENS:
1487	<	if (globals->haveZconstraints()){
1488	<	setupZConstraint(info[k]);
1489	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	<	}
1491	<	else
1492	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1531	>	info->the_integrator = myNVT;
1532	>	break;
1533
1534	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1535	<
1536	<	if (globals->haveTargetPressure())
1537	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1538	<	else {
1539	<	sprintf( painCave.errMsg,
1540	<	"SimSetup error: If you use a constant pressure\n"
1501	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	<	painCave.isFatal = 1;
1503	<	simError();
1504	<	}
1505	<
1506	<	if( globals->haveTauThermostat() )
1507	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	<	else{
1509	<	sprintf( painCave.errMsg,
1510	<	"SimSetup error: If you use an NPT\n"
1511	<	"    ensemble, you must set tauThermostat.\n");
1512	<	painCave.isFatal = 1;
1513	<	simError();
1514	<	}
1515	<
1516	<	if( globals->haveTauBarostat() )
1517	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	<	else{
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use an NPT\n"
1521	<	"    ensemble, you must set tauBarostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1525	<	break;
1526	<
1527	<	case NPTfm_ENS:
1528	<	if (globals->haveZconstraints()){
1529	<	setupZConstraint(info[k]);
1530	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	<	}
1532	<	else
1533	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534	>	case NPTi_ENS:
1535	>	if (globals->haveZconstraints()){
1536	>	setupZConstraint(info[k]);
1537	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1538	>	}
1539	>	else
1540	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1541
1542	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1543	<
1544	<	if (globals->haveTargetPressure())
1545	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1546	<	else {
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use a constant pressure\n"
1549	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1553	<
1554	<	if( globals->haveTauThermostat() )
1555	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1556	<	else{
1557	<	sprintf( painCave.errMsg,
1558	<	"SimSetup error: If you use an NPT\n"
1559	<	"    ensemble, you must set tauThermostat.\n");
1560	<	painCave.isFatal = 1;
1561	<	simError();
1562	<	}
1563	<
1564	<	if( globals->haveTauBarostat() )
1565	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1566	<	else{
1567	<	sprintf( painCave.errMsg,
1568	<	"SimSetup error: If you use an NPT\n"
1569	<	"    ensemble, you must set tauBarostat.\n");
1570	<	painCave.isFatal = 1;
1571	<	simError();
1572	<	}
1573	<	break;
1574	<
1575	<	default:
1576	<	sprintf( painCave.errMsg,
1577	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1578	<	painCave.isFatal = 1;
1579	<	simError();
1542	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1543	>
1544	>	if (globals->haveTargetPressure())
1545	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1546	>	else{
1547	>	sprintf(painCave.errMsg,
1548	>	"SimSetup error: If you use a constant pressure\n"
1549	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553	>
1554	>	if (globals->haveTauThermostat())
1555	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1556	>	else{
1557	>	sprintf(painCave.errMsg,
1558	>	"SimSetup error: If you use an NPT\n"
1559	>	"\tensemble, you must set tauThermostat.\n");
1560	>	painCave.isFatal = 1;
1561	>	simError();
1562	>	}
1563	>
1564	>	if (globals->haveTauBarostat())
1565	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1566	>	else{
1567	>	sprintf(painCave.errMsg,
1568	>	"SimSetup error: If you use an NPT\n"
1569	>	"\tensemble, you must set tauBarostat.\n");
1570	>	painCave.isFatal = 1;
1571	>	simError();
1572	>	}
1573	>
1574	>	info->the_integrator = myNPTi;
1575	>	break;
1576	>
1577	>	case NPTf_ENS:
1578	>	if (globals->haveZconstraints()){
1579	>	setupZConstraint(info[k]);
1580	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1581	>	}
1582	>	else
1583	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1584	>
1585	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1586	>
1587	>	if (globals->haveTargetPressure())
1588	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1589	>	else{
1590	>	sprintf(painCave.errMsg,
1591	>	"SimSetup error: If you use a constant pressure\n"
1592	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1593	>	painCave.isFatal = 1;
1594	>	simError();
1595	>	}
1596	>
1597	>	if (globals->haveTauThermostat())
1598	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1599	>
1600	>	else{
1601	>	sprintf(painCave.errMsg,
1602	>	"SimSetup error: If you use an NPT\n"
1603	>	"\tensemble, you must set tauThermostat.\n");
1604	>	painCave.isFatal = 1;
1605	>	simError();
1606	>	}
1607	>
1608	>	if (globals->haveTauBarostat())
1609	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1610	>
1611	>	else{
1612	>	sprintf(painCave.errMsg,
1613	>	"SimSetup error: If you use an NPT\n"
1614	>	"\tensemble, you must set tauBarostat.\n");
1615	>	painCave.isFatal = 1;
1616	>	simError();
1617	>	}
1618	>
1619	>	info->the_integrator = myNPTf;
1620	>	break;
1621	>
1622	>	case NPTxyz_ENS:
1623	>	if (globals->haveZconstraints()){
1624	>	setupZConstraint(info[k]);
1625	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1626	>	}
1627	>	else
1628	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1629	>
1630	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1631	>
1632	>	if (globals->haveTargetPressure())
1633	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1634	>	else{
1635	>	sprintf(painCave.errMsg,
1636	>	"SimSetup error: If you use a constant pressure\n"
1637	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1638	>	painCave.isFatal = 1;
1639	>	simError();
1640	>	}
1641	>
1642	>	if (globals->haveTauThermostat())
1643	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1644	>	else{
1645	>	sprintf(painCave.errMsg,
1646	>	"SimSetup error: If you use an NPT\n"
1647	>	"\tensemble, you must set tauThermostat.\n");
1648	>	painCave.isFatal = 1;
1649	>	simError();
1650	>	}
1651	>
1652	>	if (globals->haveTauBarostat())
1653	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1654	>	else{
1655	>	sprintf(painCave.errMsg,
1656	>	"SimSetup error: If you use an NPT\n"
1657	>	"\tensemble, you must set tauBarostat.\n");
1658	>	painCave.isFatal = 1;
1659	>	simError();
1660	>	}
1661	>
1662	>	info->the_integrator = myNPTxyz;
1663	>	break;
1664	>
1665	>	default:
1666	>	sprintf(painCave.errMsg,
1667	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1668	>	painCave.isFatal = 1;
1669	>	simError();
1670		}
1671		}
1672		}
1673
1674	<	void SimSetup::initFortran( void ){
1578	<
1674	>	void SimSetup::initFortran(void){
1675		info[0].refreshSim();
1676	<
1677	<	if( !strcmp( info[0].mixingRule, "standard") ){
1678	<	the_ff->initForceField( LB_MIXING_RULE );
1676	>
1677	>	if (!strcmp(info[0].mixingRule, "standard")){
1678	>	the_ff->initForceField(LB_MIXING_RULE);
1679		}
1680	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1681	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1680	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1681	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1682		}
1683		else{
1684	<	sprintf( painCave.errMsg,
1685	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	<	info[0].mixingRule );
1684	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1685	>	info[0].mixingRule);
1686		painCave.isFatal = 1;
1687		simError();
1688		}
1689
1690
1691		#ifdef IS_MPI
1692	<	strcpy( checkPointMsg,
1598	<	"Successfully intialized the mixingRule for Fortran." );
1692	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1693		MPIcheckPoint();
1694		#endif // is_mpi
1601	–
1695		}
1696
1697	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1698	<	{
1699	<	int nZConstraints;
1607	<	ZconStamp** zconStamp;
1608	<
1609	<	if(globals->haveZconstraintTime()){
1610	<
1611	<	//add sample time of z-constraint  into SimInfo's property list
1612	<	DoubleData* zconsTimeProp = new DoubleData();
1613	<	zconsTimeProp->setID(ZCONSTIME_ID);
1614	<	zconsTimeProp->setData(globals->getZconsTime());
1615	<	theInfo.addProperty(zconsTimeProp);
1616	<	}
1617	<	else{
1618	<	sprintf( painCave.errMsg,
1619	<	"ZConstraint error: If you use an ZConstraint\n"
1620	<	" , you must set sample time.\n");
1621	<	painCave.isFatal = 1;
1622	<	simError();
1623	<	}
1697	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1698	>	int nZConstraints;
1699	>	ZconStamp** zconStamp;
1700
1701	<	//
1702	<	nZConstraints = globals->getNzConstraints();
1703	<	zconStamp = globals->getZconStamp();
1704	<	ZConsParaItem tempParaItem;
1701	>	if (globals->haveZconstraintTime()){
1702	>	//add sample time of z-constraint  into SimInfo's property list
1703	>	DoubleData* zconsTimeProp = new DoubleData();
1704	>	zconsTimeProp->setID(ZCONSTIME_ID);
1705	>	zconsTimeProp->setData(globals->getZconsTime());
1706	>	theInfo.addProperty(zconsTimeProp);
1707	>	}
1708	>	else{
1709	>	sprintf(painCave.errMsg,
1710	>	"ZConstraint error: If you use a ZConstraint,\n"
1711	>	"\tyou must set zconsTime.\n");
1712	>	painCave.isFatal = 1;
1713	>	simError();
1714	>	}
1715
1716	<	ZConsParaData* zconsParaData = new ZConsParaData();
1717	<	zconsParaData->setID(ZCONSPARADATA_ID);
1718	<
1719	<	for(int i = 0; i < nZConstraints; i++){
1716	>	//push zconsTol into siminfo, if user does not specify
1717	>	//value for zconsTol, a default value will be used
1718	>	DoubleData* zconsTol = new DoubleData();
1719	>	zconsTol->setID(ZCONSTOL_ID);
1720	>	if (globals->haveZconsTol()){
1721	>	zconsTol->setData(globals->getZconsTol());
1722	>	}
1723	>	else{
1724	>	double defaultZConsTol = 0.01;
1725	>	sprintf(painCave.errMsg,
1726	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1727	>	"\tOOPSE will use a default value of %f.\n"
1728	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1729	>	defaultZConsTol);
1730	>	painCave.isFatal = 0;
1731	>	simError();
1732	>
1733	>	zconsTol->setData(defaultZConsTol);
1734	>	}
1735	>	theInfo.addProperty(zconsTol);
1736	>
1737	>	//set Force Subtraction Policy
1738	>	StringData* zconsForcePolicy = new StringData();
1739	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1740	>
1741	>	if (globals->haveZconsForcePolicy()){
1742	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1743	>	}
1744	>	else{
1745	>	sprintf(painCave.errMsg,
1746	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1747	>	"\tOOPSE will use PolicyByMass.\n"
1748	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1749	>	painCave.isFatal = 0;
1750	>	simError();
1751	>	zconsForcePolicy->setData("BYMASS");
1752	>	}
1753	>
1754	>	theInfo.addProperty(zconsForcePolicy);
1755	>
1756	>	//set zcons gap
1757	>	DoubleData* zconsGap = new DoubleData();
1758	>	zconsGap->setID(ZCONSGAP_ID);
1759	>
1760	>	if (globals->haveZConsGap()){
1761	>	zconsGap->setData(globals->getZconsGap());
1762	>	theInfo.addProperty(zconsGap);
1763	>	}
1764	>
1765	>	//set zcons fixtime
1766	>	DoubleData* zconsFixtime = new DoubleData();
1767	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
1768	>
1769	>	if (globals->haveZConsFixTime()){
1770	>	zconsFixtime->setData(globals->getZconsFixtime());
1771	>	theInfo.addProperty(zconsFixtime);
1772	>	}
1773	>
1774	>	//set zconsUsingSMD
1775	>	IntData* zconsUsingSMD = new IntData();
1776	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1777	>
1778	>	if (globals->haveZConsUsingSMD()){
1779	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1780	>	theInfo.addProperty(zconsUsingSMD);
1781	>	}
1782	>
1783	>	//Determine the name of ouput file and add it into SimInfo's property list
1784	>	//Be careful, do not use inFileName, since it is a pointer which
1785	>	//point to a string at master node, and slave nodes do not contain that string
1786	>
1787	>	string zconsOutput(theInfo.finalName);
1788	>
1789	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1790	>
1791	>	StringData* zconsFilename = new StringData();
1792	>	zconsFilename->setID(ZCONSFILENAME_ID);
1793	>	zconsFilename->setData(zconsOutput);
1794	>
1795	>	theInfo.addProperty(zconsFilename);
1796	>
1797	>	//setup index, pos and other parameters of z-constraint molecules
1798	>	nZConstraints = globals->getNzConstraints();
1799	>	theInfo.nZconstraints = nZConstraints;
1800	>
1801	>	zconStamp = globals->getZconStamp();
1802	>	ZConsParaItem tempParaItem;
1803	>
1804	>	ZConsParaData* zconsParaData = new ZConsParaData();
1805	>	zconsParaData->setID(ZCONSPARADATA_ID);
1806	>
1807	>	for (int i = 0; i < nZConstraints; i++){
1808		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1809		tempParaItem.zPos = zconStamp[i]->getZpos();
1810		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1811		tempParaItem.kRatio = zconStamp[i]->getKratio();
1812	<
1812	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1813	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1814		zconsParaData->addItem(tempParaItem);
1815	+	}
1816	+
1817	+	//check the uniqueness of index
1818	+	if(!zconsParaData->isIndexUnique()){
1819	+	sprintf(painCave.errMsg,
1820	+	"ZConstraint Error: molIndex is not unique!\n");
1821	+	painCave.isFatal = 1;
1822	+	simError();
1823	+	}
1824	+
1825	+	//sort the parameters by index of molecules
1826	+	zconsParaData->sortByIndex();
1827	+
1828	+	//push data into siminfo, therefore, we can retrieve later
1829	+	theInfo.addProperty(zconsParaData);
1830	+	}
1831	+
1832	+	void SimSetup::makeMinimizer(){
1833	+
1834	+	OOPSEMinimizer* myOOPSEMinimizer;
1835	+	MinimizerParameterSet* param;
1836	+	char minimizerName[100];
1837	+
1838	+	for (int i = 0; i < nInfo; i++){
1839	+
1840	+	//prepare parameter set for minimizer
1841	+	param = new MinimizerParameterSet();
1842	+	param->setDefaultParameter();
1843	+
1844	+	if (globals->haveMinimizer()){
1845	+	param->setFTol(globals->getMinFTol());
1846		}
1847
1848	<	//sort the parameters by index of molecules
1849	<	zconsParaData->sortByIndex();
1850	<
1645	<	//push data into siminfo, therefore, we can retrieve later
1646	<	theInfo.addProperty(zconsParaData);
1848	>	if (globals->haveMinGTol()){
1849	>	param->setGTol(globals->getMinGTol());
1850	>	}
1851
1852	<	//push zconsTol into siminfo, if user does not specify
1853	<	//value for zconsTol, a default value will be used
1650	<	DoubleData* zconsTol = new DoubleData();
1651	<	zconsTol->setID(ZCONSTOL_ID);
1652	<	if(globals->haveZconsTol()){
1653	<	zconsTol->setData(globals->getZconsTol());
1852	>	if (globals->haveMinMaxIter()){
1853	>	param->setMaxIteration(globals->getMinMaxIter());
1854		}
1655	–	else{
1656	–	double defaultZConsTol = 1E-6;
1657	–	sprintf( painCave.errMsg,
1658	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	–	" , default value %f is used.\n", defaultZConsTol);
1660	–	painCave.isFatal = 0;
1661	–	simError();
1855
1856	<	zconsTol->setData(defaultZConsTol);
1857	<	}
1858	<	theInfo.addProperty(zconsTol);
1859	<
1860	<	//Determine the name of ouput file and add it into SimInfo's property list
1861	<	//Be careful, do not use inFileName, since it is a pointer which
1862	<	//point to a string at master node, and slave nodes do not contain that string
1856	>	if (globals->haveMinWriteFrq()){
1857	>	param->setMaxIteration(globals->getMinMaxIter());
1858	>	}
1859	>
1860	>	if (globals->haveMinWriteFrq()){
1861	>	param->setWriteFrq(globals->getMinWriteFrq());
1862	>	}
1863
1864	<	string zconsOutput(theInfo.finalName);
1865	<
1866	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1867	<
1868	<	StringData* zconsFilename = new StringData();
1869	<	zconsFilename->setID(ZCONSFILENAME_ID);
1870	<	zconsFilename->setData(zconsOutput);
1871	<
1872	<	theInfo.addProperty(zconsFilename);
1864	>	if (globals->haveMinStepSize()){
1865	>	param->setStepSize(globals->getMinStepSize());
1866	>	}
1867	>
1868	>	if (globals->haveMinLSMaxIter()){
1869	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1870	>	}
1871	>
1872	>	if (globals->haveMinLSTol()){
1873	>	param->setLineSearchTol(globals->getMinLSTol());
1874	>	}
1875	>
1876	>	strcpy(minimizerName, globals->getMinimizer());
1877	>
1878	>	if (!strcasecmp(minimizerName, "CG")){
1879	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1880	>	}
1881	>	else if (!strcasecmp(minimizerName, "SD")){
1882	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1883	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1884	>	}
1885	>	else{
1886	>	sprintf(painCave.errMsg,
1887	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1888	>	painCave.isFatal = 0;
1889	>	simError();
1890	>
1891	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	>	}
1893	>	info[i].the_integrator = myOOPSEMinimizer;
1894	>
1895	>	//store the minimizer into simInfo
1896	>	info[i].the_minimizer = myOOPSEMinimizer;
1897	>	info[i].has_minimizer = true;
1898	>	}
1899	>
1900		}

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