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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
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"
18		#include "mpiSimulation.hpp"
19		#endif
20
21	+	// some defines for ensemble and Forcefield  cases
22	+
23	+	#define NVE_ENS        0
24	+	#define NVT_ENS        1
25	+	#define NPTi_ENS       2
26	+	#define NPTf_ENS       3
27	+	#define NPTxyz_ENS     4
28	+
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	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
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 27 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
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){
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();
59	<	mpiEventLoop();
60	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
132	>	sysObjectsCreation();
133
134	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
134	>	// check on the post processing info
135
136	+	finalInfoCheck();
137
138	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
138	>	// initialize the system coordinates
139
140	<	#ifdef IS_MPI
141	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
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();
150
151	+	#ifdef IS_MPI
152	+	mpiSim->mpiRefresh();
153	+	#endif
154
155	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
155	>	// initialize the Fortran
156
157	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
157	>	initFortran();
158
159	<	tot_nmol = 0;
160	<	for( i=0; i<n_components; i++ ){
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
166	>	}
167
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
168
169	<	#ifdef IS_MPI
170	<	strcpy( checkPointMsg, "Have the number of components" );
171	<	MPIcheckPoint();
172	<	#endif // is_mpi
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	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	// make an array of molecule stamps that match the components used.
192	<	// also extract the used stamps out into a separate linked list
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194
195	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
195	>	set<int> skipList;
196
197	<	id = the_components[i]->getType();
198	<	comp_stamps[i] = NULL;
199	<
181	<	// check to make sure the component isn't already in the list
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200
201	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
201	>	//init the forceField paramters
202
203	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
203	>	the_ff->readParams();
204
205	+	// init the atoms
206
207	+	int nMembers, nNew, rb1, rb2;
208
209	<	// caclulate the number of atoms, bonds, bends and torsions
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211
212	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
212	>	atomOffset = 0;
213
214	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	simnfo->n_atoms = tot_atoms;
219	<	simnfo->n_bonds = tot_bonds;
220	<	simnfo->n_bends = tot_bends;
221	<	simnfo->n_torsions = tot_torsions;
222	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	<
225	<	#ifdef IS_MPI
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	>
226	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
227
228	<	// divide the molecules among processors here.
229	<
230	<	mpiSim = new mpiSimulation( simnfo );
231	<
241	<
228	>	if (molInfo.nBonds > 0)
229	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	>	else
231	>	molInfo.myBonds = NULL;
232
233	<	globalIndex = mpiSim->divideLabor();
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new Bend*[molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242
243	<
244	<	// set up the local variables
245	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
247	>	// make the Atoms
248
249	<	simnfo->n_atoms = mpiSim->getMyNlocal();
250	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	<	simnfo->n_bonds = local_bonds;
253	<	simnfo->n_bends = local_bends;
254	<	simnfo->n_torsions = local_torsions;
255	<	simnfo->n_SRI = local_SRI;
256	<	simnfo->n_mol = localMol;
252	>	if (currentAtom->haveOrientation()){
253	>	dAtom = new DirectionalAtom((j + atomOffset),
254	>	info[k].getConfiguration());
255	>	info[k].n_oriented++;
256	>	molInfo.myAtoms[j] = dAtom;
257
258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
259	<	MPIcheckPoint();
260	<
298	<
299	<	#endif // is_mpi
300	<
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261
262	<	// create the atom and short range interaction arrays
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	Atom::createArrays(simnfo->n_atoms);
267	<	the_atoms = new Atom*[simnfo->n_atoms];
268	<	the_molecules = new Molecule[simnfo->n_mol];
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	<	if( simnfo->n_SRI ){
310	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
273	>	}
274
275	<	simnfo->n_exclude = 1;
276	<	}
275	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
276	>	#ifdef IS_MPI
277
278	<	// set the arrays into the SimInfo object
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280	<	simnfo->atoms = the_atoms;
281	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
280	>	#endif // is_mpi
281	>	}
282
283	+	// make the bonds
284	+	for (j = 0; j < molInfo.nBonds; j++){
285	+	currentBond = comp_stamps[stampID]->getBond(j);
286	+	theBonds[j].a = currentBond->getA() + atomOffset;
287	+	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	// get some of the tricky things that may still be in the globals
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
336	–
337	–	if( the_globals->haveBox() ){
338	–	simnfo->box_x = the_globals->getBox();
339	–	simnfo->box_y = the_globals->getBox();
340	–	simnfo->box_z = the_globals->getBox();
341	–	}
342	–	else if( the_globals->haveDensity() ){
343	–
344	–	double vol;
345	–	vol = (double)tot_nmol / the_globals->getDensity();
346	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	–	simnfo->box_y = simnfo->box_x;
348	–	simnfo->box_z = simnfo->box_x;
349	–	}
350	–	else{
351	–	if( !the_globals->haveBoxX() ){
352	–	sprintf( painCave.errMsg,
353	–	"SimSetup error, no periodic BoxX size given.\n" );
354	–	painCave.isFatal = 1;
355	–	simError();
356	–	}
357	–	simnfo->box_x = the_globals->getBoxX();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
292		#ifdef IS_MPI
293	<	strcpy( checkPointMsg, "Box size set up" );
294	<	MPIcheckPoint();
295	<	#endif // is_mpi
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	+	info[k].excludes->addPair(exI, exJ);
301	+	}
302
303	<	// initialize the arrays
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<	the_ff->setSimInfo( simnfo );
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	makeAtoms();
315	<	simnfo->identArray = new int[simnfo->n_atoms];
316	<	for(i=0; i<simnfo->n_atoms; i++){
317	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
318	<	}
319	<
320	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	if( tot_bends ){
323	<	makeBends();
324	<	}
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	<	if( tot_torsions ){
329	<	makeTorsions();
330	<	}
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350
351	<	if (the_globals->getUseRF() ) {
352	<	simnfo->useReactionField = 1;
353	<
354	<	if( !the_globals->haveECR() ){
355	<	sprintf( painCave.errMsg,
356	<	"SimSetup Warning: using default value of 1/2 the smallest "
357	<	"box length for the electrostaticCutoffRadius.\n"
358	<	"I hope you have a very fast processor!\n");
359	<	painCave.isFatal = 0;
360	<	simError();
361	<	double smallest;
362	<	smallest = simnfo->box_x;
363	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356	>	#ifdef IS_MPI
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
365	>	} else {
366
367	+	tempI = theBends[j].a;
368	+	tempJ = theBends[j].b;
369	+	tempK = theBends[j].c;
370	+
371		#ifdef IS_MPI
372	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
373	<	MPIcheckPoint();
374	<	#endif // is_mpi
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385	>	}
386
387	<	if( the_globals->haveInitialConfig() ){
388	<
389	<	InitializeFromFile* fileInit;
390	<	#ifdef IS_MPI // is_mpi
391	<	if( worldRank == 0 ){
392	<	#endif //is_mpi
393	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393	>
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398	>
399		#ifdef IS_MPI
400	<	}else fileInit = new InitializeFromFile( NULL );
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
410
411	<	delete fileInit;
412	<	}
413	<	else{
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	<	#ifdef IS_MPI
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	<	// no init from bass
425	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426
427	<	initFromBass();
427	>	// Create the Rigid Body:
428
429	+	myRB = new RigidBody();
430
431	<	#endif
432	<	}
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438
439	+	// tempI is atom numbering on local processor
440	+	tempI = molI + atomOffset;
441
442	<
443	<
444	<
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445
446	<
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452		#ifdef IS_MPI
453	<	if( worldRank == 0 ){
454	<	#endif // is_mpi
455	<
456	<	if( the_globals->haveFinalConfig() ){
457	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
458	<	}
459	<	else{
460	<	strcpy( simnfo->finalName, inFileName );
461	<	char* endTest;
462	<	int nameLength = strlen( simnfo->finalName );
463	<	endTest = &(simnfo->finalName[nameLength - 5]);
464	<	if( !strcmp( endTest, ".bass" ) ){
465	<	strcpy( endTest, ".eor" );
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487		}
488	<	else if( !strcmp( endTest, ".BASS" ) ){
489	<	strcpy( endTest, ".eor" );
490	<	}
491	<	else{
492	<	endTest = &(simnfo->finalName[nameLength - 4]);
493	<	if( !strcmp( endTest, ".bss" ) ){
494	<	strcpy( endTest, ".eor" );
495	<	}
496	<	else if( !strcmp( endTest, ".mdl" ) ){
497	<	strcpy( endTest, ".eor" );
498	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
608	<	}
609	<	#endif // is_mpi
610	<
611	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
617	<	}
618	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
488	>
489	>
490	>	//create cutoff group for molecule
491	>
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499
500	<	if( the_globals->haveStatusTime() ){
501	<	simnfo->statusTime = the_globals->getStatusTime();
502	<	}
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503
504	<	if( the_globals->haveThermalTime() ){
505	<	simnfo->thermalTime = the_globals->getThermalTime();
630	<	}
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506
507	<	// check for the temperature set flag
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511
512	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514
515	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517
518	<	//   // make the longe range forces and the integrator
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519
520	<	//   new AllLong( simnfo );
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521
522	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
523	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
524	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
525	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528	>	}
529
530	+
531
532
533	<	// initialize the Fortran
534	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
654	<	}
655	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	<	}
658	<	else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
662	<	painCave.isFatal = 1;
663	<	simError();
664	<	}
533	>	// After this is all set up, scan through the atoms to
534	>	// see if they can be added to the integrableObjects:
535
536	+	molInfo.myIntegrableObjects.clear();
537	+
538
539	+	for (j = 0; j < molInfo.nAtoms; j++){
540	+
541		#ifdef IS_MPI
542	<	strcpy( checkPointMsg,
543	<	"Successfully intialized the mixingRule for Fortran." );
544	<	MPIcheckPoint();
545	<	#endif // is_mpi
672	<	}
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545	>	#endif
546
547	+	// if they aren't on the skip list, then they can be integrated
548
549	<	void SimSetup::makeMolecules( void ){
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
684	<
685	<	//init the forceField paramters
556	>	// all rigid bodies are integrated:
557
558	<	the_ff->readParams();
559	<
560	<
561	<	// init the molecules
691	<
692	<	atomOffset = 0;
693	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
696	<
697	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	<	info.nBends    = comp_stamps[stampID]->getNBends();
700	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	<
702	<	info.myAtoms = &the_atoms[atomOffset];
703	<	info.myBonds = new Bond*[info.nBonds];
704	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
706	<
707	<	theBonds = new bond_pair[info.nBonds];
708	<	theBends = new bend_set[info.nBends];
709	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
714	<
715	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562		}
737	–	else{
738	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	–	}
740	–	info.myAtoms[j]->setType( currentAtom->getType() );
563
742	–	#ifdef IS_MPI
564
565	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
565	>	// send the arrays off to the forceField for init.
566
567	<	#endif // is_mpi
568	<	}
569	<
570	<	// make the bonds
571	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	<	exI = theBonds[i].a;
757	<	exJ = theBonds[i].b;
573	>	info[k].molecules[i].initialize(molInfo);
574
759	–	// exclude_I must always be the smaller of the pair
760	–	if( exI > exJ ){
761	–	tempEx = exI;
762	–	exI = exJ;
763	–	exJ = tempEx;
764	–	}
765	–	#ifdef IS_MPI
766	–
767	–	the_excludes[index*2] =
768	–	the_atoms[exI]->getGlobalIndex() + 1;
769	–	the_excludes[index*2 + 1] =
770	–	the_atoms[exJ]->getGlobalIndex() + 1;
771	–
772	–	#else  // isn't MPI
773	–
774	–	the_excludes[index*2] =     exI + 1;
775	–	the_excludes[index*2 + 1] = exJ + 1;
776	–	// fortran index from 1 (hence the +1 in the indexing)
575
576	<	#endif  //is_mpi
577	<
576	>	atomOffset += molInfo.nAtoms;
577	>	delete[] theBonds;
578	>	delete[] theBends;
579	>	delete[] theTorsions;
580	>	}
581		}
582
583	+	#ifdef IS_MPI
584	+	sprintf(checkPointMsg, "all molecules initialized succesfully");
585	+	MPIcheckPoint();
586	+	#endif // is_mpi
587
588	+	}
589
590	+	void SimSetup::initFromBass(void){
591	+	int i, j, k;
592	+	int n_cells;
593	+	double cellx, celly, cellz;
594	+	double temp1, temp2, temp3;
595	+	int n_per_extra;
596	+	int n_extra;
597	+	int have_extra, done;
598
599	+	double vel[3];
600	+	vel[0] = 0.0;
601	+	vel[1] = 0.0;
602	+	vel[2] = 0.0;
603
604	+	temp1 = (double) tot_nmol / 4.0;
605	+	temp2 = pow(temp1, (1.0 / 3.0));
606	+	temp3 = ceil(temp2);
607
608	+	have_extra = 0;
609	+	if (temp2 < temp3){
610	+	// we have a non-complete lattice
611	+	have_extra = 1;
612
613	+	n_cells = (int) temp3 - 1;
614	+	cellx = info[0].boxL[0] / temp3;
615	+	celly = info[0].boxL[1] / temp3;
616	+	cellz = info[0].boxL[2] / temp3;
617	+	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	+	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	+	n_per_extra = (int) ceil(temp1);
620
621	+	if (n_per_extra > 4){
622	+	sprintf(painCave.errMsg,
623	+	"SimSetup error. There has been an error in constructing"
624	+	" the non-complete lattice.\n");
625	+	painCave.isFatal = 1;
626	+	simError();
627	+	}
628	+	}
629	+	else{
630	+	n_cells = (int) temp3;
631	+	cellx = info[0].boxL[0] / temp3;
632	+	celly = info[0].boxL[1] / temp3;
633	+	cellz = info[0].boxL[2] / temp3;
634	+	}
635
636	+	current_mol = 0;
637	+	current_comp_mol = 0;
638	+	current_comp = 0;
639	+	current_atom_ndx = 0;
640
641	+	for (i = 0; i < n_cells ; i++){
642	+	for (j = 0; j < n_cells; j++){
643	+	for (k = 0; k < n_cells; k++){
644	+	makeElement(i * cellx, j * celly, k * cellz);
645
646	+	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	+	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651	+	}
652	+	}
653	+	}
654
655	+	if (have_extra){
656	+	done = 0;
657
658	<	void SimSetup::makeAtoms( void ){
658	>	int start_ndx;
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	int i, j, k, index;
672	<	double ux, uy, uz, uSqr, u;
673	<	AtomStamp* current_atom;
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	DirectionalAtom* dAtom;
676	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	lMolIndex = 0;
682	<	molIndex = 0;
683	<	index = 0;
684	<	for( i=0; i<n_components; i++ ){
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	for( j=0; j<components_nmol[i]; j++ ){
688	<
689	<	#ifdef IS_MPI
690	<	if( mpiSim->getMyMolStart() <= molIndex &&
691	<	molIndex <= mpiSim->getMyMolEnd() ){
692	<	#endif // is_mpi
816	<
817	<	molStart = index;
818	<	nMemb = comp_stamps[i]->getNAtoms();
819	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
820	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
859	<
860	<	#ifdef IS_MPI
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693		}
862	–	#endif //is_mpi
863	–
864	–	molIndex++;
694		}
695		}
696
697	<	#ifdef IS_MPI
698	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
699	<
871	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699	>	}
700		}
701
702	<	void SimSetup::makeBonds( void ){
702	>	void SimSetup::makeElement(double x, double y, double z){
703	>	int k;
704	>	AtomStamp* current_atom;
705	>	DirectionalAtom* dAtom;
706	>	double rotMat[3][3];
707	>	double pos[3];
708
709	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
710	<	bond_pair* the_bonds;
711	<	BondStamp* current_bond;
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718	>	painCave.isFatal = 1;
719	>	simError();
720	>	}
721
722	<	the_bonds = new bond_pair[tot_bonds];
723	<	index = 0;
724	<	offset = 0;
888	<	molIndex = 0;
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	<	for( i=0; i<n_components; i++ ){
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	for( j=0; j<components_nmol[i]; j++ ){
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731	<	#ifdef IS_MPI
732	<	if( mpiSim->getMyMolStart() <= molIndex &&
733	<	molIndex <= mpiSim->getMyMolEnd() ){
897	<	#endif // is_mpi
898	<
899	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
731	>	rotMat[0][0] = 1.0;
732	>	rotMat[0][1] = 0.0;
733	>	rotMat[0][2] = 0.0;
734
735	<	exI = the_bonds[index].a;
736	<	exJ = the_bonds[index].b;
735	>	rotMat[1][0] = 0.0;
736	>	rotMat[1][1] = 1.0;
737	>	rotMat[1][2] = 0.0;
738
739	<	// exclude_I must always be the smaller of the pair
740	<	if( exI > exJ ){
741	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
739	>	rotMat[2][0] = 0.0;
740	>	rotMat[2][1] = 0.0;
741	>	rotMat[2][2] = 1.0;
742
743	<
744	<	#ifdef IS_MPI
743	>	dAtom->setA(rotMat);
744	>	}
745
746	<	the_excludes[index*2] =
919	<	the_atoms[exI]->getGlobalIndex() + 1;
920	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
922	<
923	<	#else  // isn't MPI
924	<
925	<	the_excludes[index*2] =     exI + 1;
926	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
936	<	}
937	<	#endif //is_mpi
938	<
939	<	molIndex++;
940	<	}
746	>	current_atom_ndx++;
747		}
748
749	<	the_ff->initializeBonds( the_bonds );
749	>	current_mol++;
750	>	current_comp_mol++;
751	>
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753	>	current_comp_mol = 0;
754	>	current_comp++;
755	>	}
756		}
757
946	–	void SimSetup::makeBends( void ){
758
759	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
760	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762	<	the_bends = new bend_set[tot_bends];
763	<	index = 0;
957	<	offset = 0;
958	<	molIndex = 0;
959	<	for( i=0; i<n_components; i++ ){
762	>	ensembleCase = -1;
763	>	ffCase = -1;
764
765	<	for( j=0; j<components_nmol[i]; j++ ){
765	>	// set the easy ones first
766
767	<	#ifdef IS_MPI
768	<	if( mpiSim->getMyMolStart() <= molIndex &&
769	<	molIndex <= mpiSim->getMyMolEnd() ){
770	<	#endif // is_mpi
767	>	for (i = 0; i < nInfo; i++){
768	>	info[i].target_temp = globals->getTargetTemp();
769	>	info[i].dt = globals->getDt();
770	>	info[i].run_time = globals->getRunTime();
771	>	}
772	>	n_components = globals->getNComponents();
773
774	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
775	<
776	<	current_bend = comp_stamps[i]->getBend( k );
777	<	the_bends[index].a = current_bend->getA() + offset;
778	<	the_bends[index].b = current_bend->getB() + offset;
779	<	the_bends[index].c = current_bend->getC() + offset;
780	<
781	<	if( current_bend->haveExtras() ){
782	<
783	<	extras = current_bend->getExtras();
784	<	current_extra = extras;
785	<
786	<	while( current_extra != NULL ){
787	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
788	<
789	<	switch( current_extra->getType() ){
790	<
791	<	case 0:
792	<	the_bends[index].ghost =
793	<	current_extra->getInt() + offset;
794	<	the_bends[index].isGhost = 1;
795	<	break;
796	<
797	<	case 1:
798	<	the_bends[index].ghost =
799	<	(int)current_extra->getDouble() + offset;
800	<	the_bends[index].isGhost = 1;
801	<	break;
802	<
803	<	default:
804	<	sprintf( painCave.errMsg,
805	<	"SimSetup Error: ghostVectorSource was neiter a "
806	<	"double nor an int.\n"
807	<	"-->Bend[%d] in %s\n",
808	<	k, comp_stamps[i]->getID() );
809	<	painCave.isFatal = 1;
810	<	simError();
811	<	}
812	<	}
813	<
814	<	else{
815	<
816	<	sprintf( painCave.errMsg,
817	<	"SimSetup Error: unhandled bend assignment:\n"
818	<	"    -->%s in Bend[%d] in %s\n",
819	<	current_extra->getlhs(),
820	<	k, comp_stamps[i]->getID() );
821	<	painCave.isFatal = 1;
822	<	simError();
823	<	}
824	<
825	<	current_extra = current_extra->getNext();
826	<	}
827	<	}
828	<
829	<	if( !the_bends[index].isGhost ){
830	<
831	<	exI = the_bends[index].a;
832	<	exJ = the_bends[index].c;
833	<	}
834	<	else{
835	<
836	<	exI = the_bends[index].a;
837	<	exJ = the_bends[index].b;
838	<	}
839	<
840	<	// exclude_I must always be the smaller of the pair
841	<	if( exI > exJ ){
842	<	tempEx = exI;
843	<	exI = exJ;
844	<	exJ = tempEx;
845	<	}
774	>
775	>	// get the forceField
776	>
777	>	strcpy(force_field, globals->getForceField());
778	>
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791	>	else{
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796	>	}
797	>
798	>	// get the ensemble
799	>
800	>	strcpy(ensemble, globals->getEnsemble());
801	>
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	>	ensembleCase = NPTi_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817	>	else{
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826	>	}
827	>
828	>	for (i = 0; i < nInfo; i++){
829	>	strcpy(info[i].ensemble, ensemble);
830	>
831	>	// get the mixing rule
832	>
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834	>	info[i].usePBC = globals->getPBC();
835	>	}
836	>
837	>	// get the components and calculate the tot_nMol and indvidual n_mol
838	>
839	>	the_components = globals->getComponents();
840	>	components_nmol = new int[n_components];
841	>
842	>
843	>	if (!globals->haveNMol()){
844	>	// we don't have the total number of molecules, so we assume it is
845	>	// given in each component
846	>
847	>	tot_nmol = 0;
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>
858	>	tot_nmol += the_components[i]->getNMol();
859	>	components_nmol[i] = the_components[i]->getNMol();
860	>	}
861	>	}
862	>	else{
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869	>	painCave.isFatal = 1;
870	>	simError();
871	>	}
872
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883
884	<	#ifdef IS_MPI
884	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	>	sprintf(painCave.errMsg,
886	>	"Status time is not divisible by dt.\n"
887	>	"\tThis will result in status reports that are not uniformly\n"
888	>	"\tdistributed in time.  If this is a problem, change \n"
889	>	"\tyour statusTime variable.\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	}
893
894	<	the_excludes[(index + tot_bonds)*2] =
895	<	the_atoms[exI]->getGlobalIndex() + 1;
896	<	the_excludes[(index + tot_bonds)*2 + 1] =
897	<	the_atoms[exJ]->getGlobalIndex() + 1;
898	<
899	<	#else  // isn't MPI
900	<
901	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
902	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
903	<	// fortran index from 1 (hence the +1 in the indexing)
904	<	#endif  //is_mpi
905	<
906	<
907	<	// increment the index and repeat;
908	<	index++;
909	<	}
910	<	offset += comp_stamps[i]->getNAtoms();
894	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	>	sprintf(painCave.errMsg,
896	>	"Thermal time is not divisible by dt.\n"
897	>	"\tThis will result in thermalizations that are not uniformly\n"
898	>	"\tdistributed in time.  If this is a problem, change \n"
899	>	"\tyour thermalTime variable.\n");
900	>	painCave.isFatal = 0;
901	>	simError();
902	>	}
903	>
904	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	>	sprintf(painCave.errMsg,
906	>	"Reset time is not divisible by dt.\n"
907	>	"\tThis will result in integrator resets that are not uniformly\n"
908	>	"\tdistributed in time.  If this is a problem, change\n"
909	>	"\tyour resetTime variable.\n");
910	>	painCave.isFatal = 0;
911	>	simError();
912	>	}
913	>
914	>	// set the status, sample, and thermal kick times
915	>
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918	>	info[i].sampleTime = globals->getSampleTime();
919	>	info[i].statusTime = info[i].sampleTime;
920	>	}
921	>	else{
922	>	info[i].sampleTime = globals->getRunTime();
923	>	info[i].statusTime = info[i].sampleTime;
924	>	}
925	>
926	>	if (globals->haveStatusTime()){
927	>	info[i].statusTime = globals->getStatusTime();
928	>	}
929	>
930	>	if (globals->haveThermalTime()){
931	>	info[i].thermalTime = globals->getThermalTime();
932	>	} else {
933	>	info[i].thermalTime = globals->getRunTime();
934	>	}
935	>
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941	>
942	>	// check for the temperature set flag
943	>
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952	>	// check for thermodynamic integration
953	>	if (globals->getUseThermInt()) {
954	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	>	info[i].useThermInt = globals->getUseThermInt();
956	>	info[i].thermIntLambda = globals->getThermIntLambda();
957	>	info[i].thermIntK = globals->getThermIntK();
958
959	<	#ifdef IS_MPI
959	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	>	info[i].restraint = myRestraint;
961		}
962	<	#endif //is_mpi
963	<
964	<	molIndex++;
962	>	else {
963	>	sprintf(painCave.errMsg,
964	>	"SimSetup Error:\n"
965	>	"\tKeyword useThermInt was set to 'true' but\n"
966	>	"\tthermodynamicIntegrationLambda (and/or\n"
967	>	"\tthermodynamicIntegrationK) was not specified.\n"
968	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
969	>	painCave.isFatal = 1;
970	>	simError();
971	>	}
972		}
973	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974	+	sprintf(painCave.errMsg,
975	+	"SimSetup Warning: If you want to use Thermodynamic\n"
976	+	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	+	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	+	"\tlambda and/or k values are being ignored.\n");
979	+	painCave.isFatal = 0;
980	+	simError();
981	+	}
982		}
983	+
984	+	//setup seed for random number generator
985	+	int seedValue;
986
987	+	if (globals->haveSeed()){
988	+	seedValue = globals->getSeed();
989	+
990	+	if(seedValue / 1E9 == 0){
991	+	sprintf(painCave.errMsg,
992	+	"Seed for sprng library should contain at least 9 digits\n"
993	+	"OOPSE will generate a seed for user\n");
994	+	painCave.isFatal = 0;
995	+	simError();
996	+
997	+	//using seed generated by system instead of invalid seed set by user
998	+	#ifndef IS_MPI
999	+	seedValue = make_sprng_seed();
1000	+	#else
1001	+	if (worldRank == 0){
1002	+	seedValue = make_sprng_seed();
1003	+	}
1004	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1005	+	#endif
1006	+	}
1007	+	}//end of if branch of globals->haveSeed()
1008	+	else{
1009	+
1010	+	#ifndef IS_MPI
1011	+	seedValue = make_sprng_seed();
1012	+	#else
1013	+	if (worldRank == 0){
1014	+	seedValue = make_sprng_seed();
1015	+	}
1016	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1017	+	#endif
1018	+	}//end of globals->haveSeed()
1019	+
1020	+	for (int i = 0; i < nInfo; i++){
1021	+	info[i].setSeed(seedValue);
1022	+	}
1023	+
1024		#ifdef IS_MPI
1025	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
1025	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026		MPIcheckPoint();
1027		#endif // is_mpi
1075	–
1076	–
1077	–	the_ff->initializeBends( the_bends );
1028		}
1029
1080	–	void SimSetup::makeTorsions( void ){
1030
1031	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1032	<	torsion_set* the_torsions;
1033	<	TorsionStamp* current_torsion;
1031	>	void SimSetup::finalInfoCheck(void){
1032	>	int index;
1033	>	int usesDipoles;
1034	>	int usesCharges;
1035	>	int i;
1036
1037	<	the_torsions = new torsion_set[tot_torsions];
1038	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1037	>	for (i = 0; i < nInfo; i++){
1038	>	// check electrostatic parameters
1039
1040	<	for( j=0; j<components_nmol[i]; j++ ){
1041	<
1040	>	index = 0;
1041	>	usesDipoles = 0;
1042	>	while ((index < info[i].n_atoms) && !usesDipoles){
1043	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1044	>	index++;
1045	>	}
1046	>	index = 0;
1047	>	usesCharges = 0;
1048	>	while ((index < info[i].n_atoms) && !usesCharges){
1049	>	usesCharges= (info[i].atoms[index])->hasCharge();
1050	>	index++;
1051	>	}
1052		#ifdef IS_MPI
1053	<	if( mpiSim->getMyMolStart() <= molIndex &&
1054	<	molIndex <= mpiSim->getMyMolEnd() ){
1055	<	#endif // is_mpi
1053	>	int myUse = usesDipoles;
1054	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055	>	#endif //is_mpi
1056
1057	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1057	>	double theRcut, theRsw;
1058
1059	<	current_torsion = comp_stamps[i]->getTorsion( k );
1060	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1059	>	if (globals->haveRcut()) {
1060	>	theRcut = globals->getRcut();
1061
1062	<	exI = the_torsions[index].a;
1063	<	exJ = the_torsions[index].d;
1062	>	if (globals->haveRsw())
1063	>	theRsw = globals->getRsw();
1064	>	else
1065	>	theRsw = theRcut;
1066	>
1067	>	info[i].setDefaultRcut(theRcut, theRsw);
1068
1069	<
1070	<	// exclude_I must always be the smaller of the pair
1071	<	if( exI > exJ ){
1072	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1069	>	} else {
1070	>
1071	>	the_ff->calcRcut();
1072	>	theRcut = info[i].getRcut();
1073
1074	+	if (globals->haveRsw())
1075	+	theRsw = globals->getRsw();
1076	+	else
1077	+	theRsw = theRcut;
1078	+
1079	+	info[i].setDefaultRcut(theRcut, theRsw);
1080	+	}
1081
1082	<	#ifdef IS_MPI
1083	<
1084	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1085	<	the_atoms[exI]->getGlobalIndex() + 1;
1086	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1087	<	the_atoms[exJ]->getGlobalIndex() + 1;
1088	<
1089	<	#else  // isn't MPI
1090	<
1091	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1092	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1093	<	// fortran indexes from 1 (hence the +1 in the indexing)
1094	<	#endif  //is_mpi
1095	<
1082	>	if (globals->getUseRF()){
1083	>	info[i].useReactionField = 1;
1084	>
1085	>	if (!globals->haveRcut()){
1086	>	sprintf(painCave.errMsg,
1087	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088	>	"\tOOPSE will use a default value of 15.0 angstroms"
1089	>	"\tfor the cutoffRadius.\n");
1090	>	painCave.isFatal = 0;
1091	>	simError();
1092	>	theRcut = 15.0;
1093	>	}
1094	>	else{
1095	>	theRcut = globals->getRcut();
1096	>	}
1097
1098	<	// increment the index and repeat;
1099	<	index++;
1098	>	if (!globals->haveRsw()){
1099	>	sprintf(painCave.errMsg,
1100	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1101	>	"\tOOPSE will use a default value of\n"
1102	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103	>	painCave.isFatal = 0;
1104	>	simError();
1105	>	theRsw = 0.95 * theRcut;
1106		}
1107	<	offset += comp_stamps[i]->getNAtoms();
1107	>	else{
1108	>	theRsw = globals->getRsw();
1109	>	}
1110
1111	<	#ifdef IS_MPI
1111	>	info[i].setDefaultRcut(theRcut, theRsw);
1112	>
1113	>	if (!globals->haveDielectric()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error: No Dielectric constant was set.\n"
1116	>	"\tYou are trying to use Reaction Field without"
1117	>	"\tsetting a dielectric constant!\n");
1118	>	painCave.isFatal = 1;
1119	>	simError();
1120		}
1121	<	#endif //is_mpi
1121	>	info[i].dielectric = globals->getDielectric();
1122	>	}
1123	>	else{
1124	>	if (usesDipoles || usesCharges){
1125
1126	<	molIndex++;
1126	>	if (!globals->haveRcut()){
1127	>	sprintf(painCave.errMsg,
1128	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129	>	"\tOOPSE will use a default value of 15.0 angstroms"
1130	>	"\tfor the cutoffRadius.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	theRcut = 15.0;
1134	>	}
1135	>	else{
1136	>	theRcut = globals->getRcut();
1137	>	}
1138	>
1139	>	if (!globals->haveRsw()){
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1142	>	"\tOOPSE will use a default value of\n"
1143	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144	>	painCave.isFatal = 0;
1145	>	simError();
1146	>	theRsw = 0.95 * theRcut;
1147	>	}
1148	>	else{
1149	>	theRsw = globals->getRsw();
1150	>	}
1151	>
1152	>	info[i].setDefaultRcut(theRcut, theRsw);
1153	>
1154	>	}
1155		}
1156		}
1157	+	#ifdef IS_MPI
1158	+	strcpy(checkPointMsg, "post processing checks out");
1159	+	MPIcheckPoint();
1160	+	#endif // is_mpi
1161
1162	<	the_ff->initializeTorsions( the_torsions );
1162	>	// clean up the forcefield
1163	>	the_ff->cleanMe();
1164		}
1165	+
1166	+	void SimSetup::initSystemCoords(void){
1167	+	int i;
1168
1169	<	void SimSetup::initFromBass( void ){
1169	>	char* inName;
1170
1171	<	int i, j, k;
1153	<	int n_cells;
1154	<	double cellx, celly, cellz;
1155	<	double temp1, temp2, temp3;
1156	<	int n_per_extra;
1157	<	int n_extra;
1158	<	int have_extra, done;
1171	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1172
1173	<	temp1 = (double)tot_nmol / 4.0;
1174	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	<	temp3 = ceil( temp2 );
1173	>	for (i = 0; i < info[0].n_atoms; i++)
1174	>	info[0].atoms[i]->setCoords();
1175
1176	<	have_extra =0;
1177	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1178	<	have_extra =1;
1179	<
1180	<	n_cells = (int)temp3 - 1;
1181	<	cellx = simnfo->box_x / temp3;
1182	<	celly = simnfo->box_y / temp3;
1183	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
1175	<
1176	<	if( n_per_extra > 4){
1177	<	sprintf( painCave.errMsg,
1178	<	"SimSetup error. There has been an error in constructing"
1179	<	" the non-complete lattice.\n" );
1180	<	painCave.isFatal = 1;
1181	<	simError();
1176	>	if (globals->haveInitialConfig()){
1177	>	InitializeFromFile* fileInit;
1178	>	#ifdef IS_MPI // is_mpi
1179	>	if (worldRank == 0){
1180	>	#endif //is_mpi
1181	>	inName = globals->getInitialConfig();
1182	>	fileInit = new InitializeFromFile(inName);
1183	>	#ifdef IS_MPI
1184		}
1185	+	else
1186	+	fileInit = new InitializeFromFile(NULL);
1187	+	#endif
1188	+	fileInit->readInit(info); // default velocities on
1189	+
1190	+	delete fileInit;
1191		}
1192		else{
1193	<	n_cells = (int)temp3;
1194	<	cellx = simnfo->box_x / temp3;
1195	<	celly = simnfo->box_y / temp3;
1196	<	cellz = simnfo->box_z / temp3;
1193	>
1194	>	// no init from bass
1195	>
1196	>	sprintf(painCave.errMsg,
1197	>	"Cannot intialize a simulation without an initial configuration file.\n");
1198	>	painCave.isFatal = 1;;
1199	>	simError();
1200	>
1201		}
1202
1203	<	current_mol = 0;
1204	<	current_comp_mol = 0;
1205	<	current_comp = 0;
1206	<	current_atom_ndx = 0;
1203	>	#ifdef IS_MPI
1204	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1205	>	MPIcheckPoint();
1206	>	#endif // is_mpi
1207	>	}
1208
1196	–	for( i=0; i < n_cells ; i++ ){
1197	–	for( j=0; j < n_cells; j++ ){
1198	–	for( k=0; k < n_cells; k++ ){
1209
1210	<	makeElement( i * cellx,
1211	<	j * celly,
1202	<	k * cellz );
1210	>	void SimSetup::makeOutNames(void){
1211	>	int k;
1212
1204	–	makeElement( i * cellx + 0.5 * cellx,
1205	–	j * celly + 0.5 * celly,
1206	–	k * cellz );
1213
1214	<	makeElement( i * cellx,
1215	<	j * celly + 0.5 * celly,
1216	<	k * cellz + 0.5 * cellz );
1214	>	for (k = 0; k < nInfo; k++){
1215	>	#ifdef IS_MPI
1216	>	if (worldRank == 0){
1217	>	#endif // is_mpi
1218	>
1219	>	if (globals->haveFinalConfig()){
1220	>	strcpy(info[k].finalName, globals->getFinalConfig());
1221	>	}
1222	>	else{
1223	>	strcpy(info[k].finalName, inFileName);
1224	>	char* endTest;
1225	>	int nameLength = strlen(info[k].finalName);
1226	>	endTest = &(info[k].finalName[nameLength - 5]);
1227	>	if (!strcmp(endTest, ".bass")){
1228	>	strcpy(endTest, ".eor");
1229	>	}
1230	>	else if (!strcmp(endTest, ".BASS")){
1231	>	strcpy(endTest, ".eor");
1232	>	}
1233	>	else{
1234	>	endTest = &(info[k].finalName[nameLength - 4]);
1235	>	if (!strcmp(endTest, ".bss")){
1236	>	strcpy(endTest, ".eor");
1237	>	}
1238	>	else if (!strcmp(endTest, ".mdl")){
1239	>	strcpy(endTest, ".eor");
1240	>	}
1241	>	else{
1242	>	strcat(info[k].finalName, ".eor");
1243	>	}
1244	>	}
1245	>	}
1246
1247	<	makeElement( i * cellx + 0.5 * cellx,
1248	<	j * celly,
1249	<	k * cellz + 0.5 * cellz );
1247	>	// make the sample and status out names
1248	>
1249	>	strcpy(info[k].sampleName, inFileName);
1250	>	char* endTest;
1251	>	int nameLength = strlen(info[k].sampleName);
1252	>	endTest = &(info[k].sampleName[nameLength - 5]);
1253	>	if (!strcmp(endTest, ".bass")){
1254	>	strcpy(endTest, ".dump");
1255		}
1256	+	else if (!strcmp(endTest, ".BASS")){
1257	+	strcpy(endTest, ".dump");
1258	+	}
1259	+	else{
1260	+	endTest = &(info[k].sampleName[nameLength - 4]);
1261	+	if (!strcmp(endTest, ".bss")){
1262	+	strcpy(endTest, ".dump");
1263	+	}
1264	+	else if (!strcmp(endTest, ".mdl")){
1265	+	strcpy(endTest, ".dump");
1266	+	}
1267	+	else{
1268	+	strcat(info[k].sampleName, ".dump");
1269	+	}
1270	+	}
1271	+
1272	+	strcpy(info[k].statusName, inFileName);
1273	+	nameLength = strlen(info[k].statusName);
1274	+	endTest = &(info[k].statusName[nameLength - 5]);
1275	+	if (!strcmp(endTest, ".bass")){
1276	+	strcpy(endTest, ".stat");
1277	+	}
1278	+	else if (!strcmp(endTest, ".BASS")){
1279	+	strcpy(endTest, ".stat");
1280	+	}
1281	+	else{
1282	+	endTest = &(info[k].statusName[nameLength - 4]);
1283	+	if (!strcmp(endTest, ".bss")){
1284	+	strcpy(endTest, ".stat");
1285	+	}
1286	+	else if (!strcmp(endTest, ".mdl")){
1287	+	strcpy(endTest, ".stat");
1288	+	}
1289	+	else{
1290	+	strcat(info[k].statusName, ".stat");
1291	+	}
1292	+	}
1293	+
1294	+	strcpy(info[k].rawPotName, inFileName);
1295	+	nameLength = strlen(info[k].rawPotName);
1296	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	+	if (!strcmp(endTest, ".bass")){
1298	+	strcpy(endTest, ".raw");
1299	+	}
1300	+	else if (!strcmp(endTest, ".BASS")){
1301	+	strcpy(endTest, ".raw");
1302	+	}
1303	+	else{
1304	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	+	if (!strcmp(endTest, ".bss")){
1306	+	strcpy(endTest, ".raw");
1307	+	}
1308	+	else if (!strcmp(endTest, ".mdl")){
1309	+	strcpy(endTest, ".raw");
1310	+	}
1311	+	else{
1312	+	strcat(info[k].rawPotName, ".raw");
1313	+	}
1314	+	}
1315	+
1316	+	#ifdef IS_MPI
1317	+
1318		}
1319	+	#endif // is_mpi
1320		}
1321	+	}
1322
1219	–	if( have_extra ){
1220	–	done = 0;
1323
1324	<	int start_ndx;
1325	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1224	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1324	>	void SimSetup::sysObjectsCreation(void){
1325	>	int i, k;
1326
1327	<	if( i < n_cells ){
1327	>	// create the forceField
1328
1329	<	if( j < n_cells ){
1229	<	start_ndx = n_cells;
1230	<	}
1231	<	else start_ndx = 0;
1232	<	}
1233	<	else start_ndx = 0;
1329	>	createFF();
1330
1331	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1331	>	// extract componentList
1332
1333	<	makeElement( i * cellx,
1238	<	j * celly,
1239	<	k * cellz );
1240	<	done = ( current_mol >= tot_nmol );
1333	>	compList();
1334
1335	<	if( !done && n_per_extra > 1 ){
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1335	>	// calc the number of atoms, bond, bends, and torsions
1336
1337	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1337	>	calcSysValues();
1338
1339	<	if( !done && n_per_extra > 3){
1340	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly,
1259	<	k * cellz + 0.5 * cellz );
1260	<	done = ( current_mol >= tot_nmol );
1261	<	}
1262	<	}
1263	<	}
1264	<	}
1265	<	}
1339	>	#ifdef IS_MPI
1340	>	// divide the molecules among the processors
1341
1342	+	mpiMolDivide();
1343	+	#endif //is_mpi
1344
1345	<	for( i=0; i<simnfo->n_atoms; i++ ){
1346	<	simnfo->atoms[i]->set_vx( 0.0 );
1347	<	simnfo->atoms[i]->set_vy( 0.0 );
1348	<	simnfo->atoms[i]->set_vz( 0.0 );
1345	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1346	>
1347	>	makeSysArrays();
1348	>
1349	>	// make and initialize the molecules (all but atomic coordinates)
1350	>
1351	>	makeMolecules();
1352	>
1353	>	for (k = 0; k < nInfo; k++){
1354	>	info[k].identArray = new int[info[k].n_atoms];
1355	>	for (i = 0; i < info[k].n_atoms; i++){
1356	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1357	>	}
1358		}
1359		}
1360
1275	–	void SimSetup::makeElement( double x, double y, double z ){
1361
1362	<	int k;
1363	<	AtomStamp* current_atom;
1364	<	DirectionalAtom* dAtom;
1365	<	double rotMat[3][3];
1362	>	void SimSetup::createFF(void){
1363	>	switch (ffCase){
1364	>	case FF_DUFF:
1365	>	the_ff = new DUFF();
1366	>	break;
1367
1368	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1368	>	case FF_LJ:
1369	>	the_ff = new LJFF();
1370	>	break;
1371
1372	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1373	<	if( !current_atom->havePosition() ){
1374	<	sprintf( painCave.errMsg,
1375	<	"SimSetup:initFromBass error.\n"
1376	<	"\tComponent %s, atom %s does not have a position specified.\n"
1377	<	"\tThe initialization routine is unable to give a start"
1378	<	" position.\n",
1379	<	comp_stamps[current_comp]->getID(),
1380	<	current_atom->getType() );
1372	>	case FF_EAM:
1373	>	the_ff = new EAM_FF();
1374	>	break;
1375	>
1376	>	case FF_H2O:
1377	>	the_ff = new WATER();
1378	>	break;
1379	>
1380	>	default:
1381	>	sprintf(painCave.errMsg,
1382	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1383		painCave.isFatal = 1;
1384		simError();
1385	+	}
1386	+
1387	+	#ifdef IS_MPI
1388	+	strcpy(checkPointMsg, "ForceField creation successful");
1389	+	MPIcheckPoint();
1390	+	#endif // is_mpi
1391	+	}
1392	+
1393	+
1394	+	void SimSetup::compList(void){
1395	+	int i;
1396	+	char* id;
1397	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1398	+	LinkedMolStamp* currentStamp = NULL;
1399	+	comp_stamps = new MoleculeStamp * [n_components];
1400	+	bool haveCutoffGroups;
1401	+
1402	+	haveCutoffGroups = false;
1403	+
1404	+	// make an array of molecule stamps that match the components used.
1405	+	// also extract the used stamps out into a separate linked list
1406	+
1407	+	for (i = 0; i < nInfo; i++){
1408	+	info[i].nComponents = n_components;
1409	+	info[i].componentsNmol = components_nmol;
1410	+	info[i].compStamps = comp_stamps;
1411	+	info[i].headStamp = headStamp;
1412	+	}
1413	+
1414	+
1415	+	for (i = 0; i < n_components; i++){
1416	+	id = the_components[i]->getType();
1417	+	comp_stamps[i] = NULL;
1418	+
1419	+	// check to make sure the component isn't already in the list
1420	+
1421	+	comp_stamps[i] = headStamp->match(id);
1422	+	if (comp_stamps[i] == NULL){
1423	+	// extract the component from the list;
1424	+
1425	+	currentStamp = stamps->extractMolStamp(id);
1426	+	if (currentStamp == NULL){
1427	+	sprintf(painCave.errMsg,
1428	+	"SimSetup error: Component \"%s\" was not found in the "
1429	+	"list of declared molecules\n",
1430	+	id);
1431	+	painCave.isFatal = 1;
1432	+	simError();
1433	+	}
1434	+
1435	+	headStamp->add(currentStamp);
1436	+	comp_stamps[i] = headStamp->match(id);
1437		}
1438
1439	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1440	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1441	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1439	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	>	haveCutoffGroups = true;
1441	>	}
1442	>
1443	>	for (i = 0; i < nInfo; i++)
1444	>	info[i].haveCutoffGroups = haveCutoffGroups;
1445
1446	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1446	>	#ifdef IS_MPI
1447	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1448	>	MPIcheckPoint();
1449	>	#endif // is_mpi
1450	>	}
1451
1452	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1452	>	void SimSetup::calcSysValues(void){
1453	>	int i;
1454
1455	<	rotMat[0][0] = 1.0;
1306	<	rotMat[0][1] = 0.0;
1307	<	rotMat[0][2] = 0.0;
1455	>	int* molMembershipArray;
1456
1457	<	rotMat[1][0] = 0.0;
1458	<	rotMat[1][1] = 1.0;
1459	<	rotMat[1][2] = 0.0;
1457	>	tot_atoms = 0;
1458	>	tot_bonds = 0;
1459	>	tot_bends = 0;
1460	>	tot_torsions = 0;
1461	>	tot_rigid = 0;
1462	>	for (i = 0; i < n_components; i++){
1463	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1464	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1465	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1466	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1467	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1468	>	}
1469	>
1470	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1471	>	molMembershipArray = new int[tot_atoms];
1472
1473	<	rotMat[2][0] = 0.0;
1474	<	rotMat[2][1] = 0.0;
1475	<	rotMat[2][2] = 1.0;
1473	>	for (i = 0; i < nInfo; i++){
1474	>	info[i].n_atoms = tot_atoms;
1475	>	info[i].n_bonds = tot_bonds;
1476	>	info[i].n_bends = tot_bends;
1477	>	info[i].n_torsions = tot_torsions;
1478	>	info[i].n_SRI = tot_SRI;
1479	>	info[i].n_mol = tot_nmol;
1480
1481	<	dAtom->setA( rotMat );
1481	>	info[i].molMembershipArray = molMembershipArray;
1482	>	}
1483	>	}
1484	>
1485	>	#ifdef IS_MPI
1486	>
1487	>	void SimSetup::mpiMolDivide(void){
1488	>	int i, j, k;
1489	>	int localMol, allMol;
1490	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1491	>	int local_rigid;
1492	>	vector<int> globalMolIndex;
1493	>
1494	>	mpiSim = new mpiSimulation(info);
1495	>
1496	>	mpiSim->divideLabor();
1497	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1498	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1499	>
1500	>	// set up the local variables
1501	>
1502	>	mol2proc = mpiSim->getMolToProcMap();
1503	>	molCompType = mpiSim->getMolComponentType();
1504	>
1505	>	allMol = 0;
1506	>	localMol = 0;
1507	>	local_atoms = 0;
1508	>	local_bonds = 0;
1509	>	local_bends = 0;
1510	>	local_torsions = 0;
1511	>	local_rigid = 0;
1512	>	globalAtomCounter = 0;
1513	>
1514	>	for (i = 0; i < n_components; i++){
1515	>	for (j = 0; j < components_nmol[i]; j++){
1516	>	if (mol2proc[allMol] == worldRank){
1517	>	local_atoms += comp_stamps[i]->getNAtoms();
1518	>	local_bonds += comp_stamps[i]->getNBonds();
1519	>	local_bends += comp_stamps[i]->getNBends();
1520	>	local_torsions += comp_stamps[i]->getNTorsions();
1521	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1522	>	localMol++;
1523	>	}
1524	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1525	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1526	>	globalAtomCounter++;
1527	>	}
1528	>
1529	>	allMol++;
1530		}
1531	+	}
1532	+	local_SRI = local_bonds + local_bends + local_torsions;
1533
1534	<	current_atom_ndx++;
1534	>	info[0].n_atoms = mpiSim->getMyNlocal();
1535	>
1536	>
1537	>	if (local_atoms != info[0].n_atoms){
1538	>	sprintf(painCave.errMsg,
1539	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1540	>	"\tlocalAtom (%d) are not equal.\n",
1541	>	info[0].n_atoms, local_atoms);
1542	>	painCave.isFatal = 1;
1543	>	simError();
1544		}
1545
1546	<	current_mol++;
1547	<	current_comp_mol++;
1546	>	info[0].n_bonds = local_bonds;
1547	>	info[0].n_bends = local_bends;
1548	>	info[0].n_torsions = local_torsions;
1549	>	info[0].n_SRI = local_SRI;
1550	>	info[0].n_mol = localMol;
1551
1552	<	if( current_comp_mol >= components_nmol[current_comp] ){
1552	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1553	>	MPIcheckPoint();
1554	>	}
1555
1556	<	current_comp_mol = 0;
1557	<	current_comp++;
1556	>	#endif // is_mpi
1557	>
1558	>
1559	>	void SimSetup::makeSysArrays(void){
1560	>
1561	>	#ifndef IS_MPI
1562	>	int k, j;
1563	>	#endif // is_mpi
1564	>	int i, l;
1565	>
1566	>	Atom** the_atoms;
1567	>	Molecule* the_molecules;
1568	>
1569	>	for (l = 0; l < nInfo; l++){
1570	>	// create the atom and short range interaction arrays
1571	>
1572	>	the_atoms = new Atom * [info[l].n_atoms];
1573	>	the_molecules = new Molecule[info[l].n_mol];
1574	>	int molIndex;
1575	>
1576	>	// initialize the molecule's stampID's
1577	>
1578	>	#ifdef IS_MPI
1579	>
1580	>
1581	>	molIndex = 0;
1582	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1583	>	if (mol2proc[i] == worldRank){
1584	>	the_molecules[molIndex].setStampID(molCompType[i]);
1585	>	the_molecules[molIndex].setMyIndex(molIndex);
1586	>	the_molecules[molIndex].setGlobalIndex(i);
1587	>	molIndex++;
1588	>	}
1589	>	}
1590	>
1591	>	#else // is_mpi
1592	>
1593	>	molIndex = 0;
1594	>	globalAtomCounter = 0;
1595	>	for (i = 0; i < n_components; i++){
1596	>	for (j = 0; j < components_nmol[i]; j++){
1597	>	the_molecules[molIndex].setStampID(i);
1598	>	the_molecules[molIndex].setMyIndex(molIndex);
1599	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1600	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1601	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1602	>	globalAtomCounter++;
1603	>	}
1604	>	molIndex++;
1605	>	}
1606	>	}
1607	>
1608	>
1609	>	#endif // is_mpi
1610	>
1611	>	info[l].globalExcludes = new int;
1612	>	info[l].globalExcludes[0] = 0;
1613	>
1614	>	// set the arrays into the SimInfo object
1615	>
1616	>	info[l].atoms = the_atoms;
1617	>	info[l].molecules = the_molecules;
1618	>	info[l].nGlobalExcludes = 0;
1619	>
1620	>	the_ff->setSimInfo(info);
1621		}
1622		}
1623	+
1624	+	void SimSetup::makeIntegrator(void){
1625	+	int k;
1626	+
1627	+	NVE<RealIntegrator>* myNVE = NULL;
1628	+	NVT<RealIntegrator>* myNVT = NULL;
1629	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1630	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1631	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1632	+
1633	+	for (k = 0; k < nInfo; k++){
1634	+	switch (ensembleCase){
1635	+	case NVE_ENS:
1636	+	if (globals->haveZconstraints()){
1637	+	setupZConstraint(info[k]);
1638	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1639	+	}
1640	+	else{
1641	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1642	+	}
1643	+
1644	+	info->the_integrator = myNVE;
1645	+	break;
1646	+
1647	+	case NVT_ENS:
1648	+	if (globals->haveZconstraints()){
1649	+	setupZConstraint(info[k]);
1650	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1651	+	}
1652	+	else
1653	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1654	+
1655	+	myNVT->setTargetTemp(globals->getTargetTemp());
1656	+
1657	+	if (globals->haveTauThermostat())
1658	+	myNVT->setTauThermostat(globals->getTauThermostat());
1659	+	else{
1660	+	sprintf(painCave.errMsg,
1661	+	"SimSetup error: If you use the NVT\n"
1662	+	"\tensemble, you must set tauThermostat.\n");
1663	+	painCave.isFatal = 1;
1664	+	simError();
1665	+	}
1666	+
1667	+	info->the_integrator = myNVT;
1668	+	break;
1669	+
1670	+	case NPTi_ENS:
1671	+	if (globals->haveZconstraints()){
1672	+	setupZConstraint(info[k]);
1673	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1674	+	}
1675	+	else
1676	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1677	+
1678	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1679	+
1680	+	if (globals->haveTargetPressure())
1681	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1682	+	else{
1683	+	sprintf(painCave.errMsg,
1684	+	"SimSetup error: If you use a constant pressure\n"
1685	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1686	+	painCave.isFatal = 1;
1687	+	simError();
1688	+	}
1689	+
1690	+	if (globals->haveTauThermostat())
1691	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1692	+	else{
1693	+	sprintf(painCave.errMsg,
1694	+	"SimSetup error: If you use an NPT\n"
1695	+	"\tensemble, you must set tauThermostat.\n");
1696	+	painCave.isFatal = 1;
1697	+	simError();
1698	+	}
1699	+
1700	+	if (globals->haveTauBarostat())
1701	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1702	+	else{
1703	+	sprintf(painCave.errMsg,
1704	+	"SimSetup error: If you use an NPT\n"
1705	+	"\tensemble, you must set tauBarostat.\n");
1706	+	painCave.isFatal = 1;
1707	+	simError();
1708	+	}
1709	+
1710	+	info->the_integrator = myNPTi;
1711	+	break;
1712	+
1713	+	case NPTf_ENS:
1714	+	if (globals->haveZconstraints()){
1715	+	setupZConstraint(info[k]);
1716	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1717	+	}
1718	+	else
1719	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1720	+
1721	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1722	+
1723	+	if (globals->haveTargetPressure())
1724	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1725	+	else{
1726	+	sprintf(painCave.errMsg,
1727	+	"SimSetup error: If you use a constant pressure\n"
1728	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1729	+	painCave.isFatal = 1;
1730	+	simError();
1731	+	}
1732	+
1733	+	if (globals->haveTauThermostat())
1734	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1735	+
1736	+	else{
1737	+	sprintf(painCave.errMsg,
1738	+	"SimSetup error: If you use an NPT\n"
1739	+	"\tensemble, you must set tauThermostat.\n");
1740	+	painCave.isFatal = 1;
1741	+	simError();
1742	+	}
1743	+
1744	+	if (globals->haveTauBarostat())
1745	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1746	+
1747	+	else{
1748	+	sprintf(painCave.errMsg,
1749	+	"SimSetup error: If you use an NPT\n"
1750	+	"\tensemble, you must set tauBarostat.\n");
1751	+	painCave.isFatal = 1;
1752	+	simError();
1753	+	}
1754	+
1755	+	info->the_integrator = myNPTf;
1756	+	break;
1757	+
1758	+	case NPTxyz_ENS:
1759	+	if (globals->haveZconstraints()){
1760	+	setupZConstraint(info[k]);
1761	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1762	+	}
1763	+	else
1764	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1765	+
1766	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1767	+
1768	+	if (globals->haveTargetPressure())
1769	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1770	+	else{
1771	+	sprintf(painCave.errMsg,
1772	+	"SimSetup error: If you use a constant pressure\n"
1773	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1774	+	painCave.isFatal = 1;
1775	+	simError();
1776	+	}
1777	+
1778	+	if (globals->haveTauThermostat())
1779	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1780	+	else{
1781	+	sprintf(painCave.errMsg,
1782	+	"SimSetup error: If you use an NPT\n"
1783	+	"\tensemble, you must set tauThermostat.\n");
1784	+	painCave.isFatal = 1;
1785	+	simError();
1786	+	}
1787	+
1788	+	if (globals->haveTauBarostat())
1789	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1790	+	else{
1791	+	sprintf(painCave.errMsg,
1792	+	"SimSetup error: If you use an NPT\n"
1793	+	"\tensemble, you must set tauBarostat.\n");
1794	+	painCave.isFatal = 1;
1795	+	simError();
1796	+	}
1797	+
1798	+	info->the_integrator = myNPTxyz;
1799	+	break;
1800	+
1801	+	default:
1802	+	sprintf(painCave.errMsg,
1803	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1804	+	painCave.isFatal = 1;
1805	+	simError();
1806	+	}
1807	+	}
1808	+	}
1809	+
1810	+	void SimSetup::initFortran(void){
1811	+	info[0].refreshSim();
1812	+
1813	+	if (!strcmp(info[0].mixingRule, "standard")){
1814	+	the_ff->initForceField(LB_MIXING_RULE);
1815	+	}
1816	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1817	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1818	+	}
1819	+	else{
1820	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1821	+	info[0].mixingRule);
1822	+	painCave.isFatal = 1;
1823	+	simError();
1824	+	}
1825	+
1826	+
1827	+	#ifdef IS_MPI
1828	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1829	+	MPIcheckPoint();
1830	+	#endif // is_mpi
1831	+	}
1832	+
1833	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1834	+	int nZConstraints;
1835	+	ZconStamp** zconStamp;
1836	+
1837	+	if (globals->haveZconstraintTime()){
1838	+	//add sample time of z-constraint  into SimInfo's property list
1839	+	DoubleData* zconsTimeProp = new DoubleData();
1840	+	zconsTimeProp->setID(ZCONSTIME_ID);
1841	+	zconsTimeProp->setData(globals->getZconsTime());
1842	+	theInfo.addProperty(zconsTimeProp);
1843	+	}
1844	+	else{
1845	+	sprintf(painCave.errMsg,
1846	+	"ZConstraint error: If you use a ZConstraint,\n"
1847	+	"\tyou must set zconsTime.\n");
1848	+	painCave.isFatal = 1;
1849	+	simError();
1850	+	}
1851	+
1852	+	//push zconsTol into siminfo, if user does not specify
1853	+	//value for zconsTol, a default value will be used
1854	+	DoubleData* zconsTol = new DoubleData();
1855	+	zconsTol->setID(ZCONSTOL_ID);
1856	+	if (globals->haveZconsTol()){
1857	+	zconsTol->setData(globals->getZconsTol());
1858	+	}
1859	+	else{
1860	+	double defaultZConsTol = 0.01;
1861	+	sprintf(painCave.errMsg,
1862	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1863	+	"\tOOPSE will use a default value of %f.\n"
1864	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1865	+	defaultZConsTol);
1866	+	painCave.isFatal = 0;
1867	+	simError();
1868	+
1869	+	zconsTol->setData(defaultZConsTol);
1870	+	}
1871	+	theInfo.addProperty(zconsTol);
1872	+
1873	+	//set Force Subtraction Policy
1874	+	StringData* zconsForcePolicy = new StringData();
1875	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1876	+
1877	+	if (globals->haveZconsForcePolicy()){
1878	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1879	+	}
1880	+	else{
1881	+	sprintf(painCave.errMsg,
1882	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1883	+	"\tOOPSE will use PolicyByMass.\n"
1884	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1885	+	painCave.isFatal = 0;
1886	+	simError();
1887	+	zconsForcePolicy->setData("BYMASS");
1888	+	}
1889	+
1890	+	theInfo.addProperty(zconsForcePolicy);
1891	+
1892	+	//set zcons gap
1893	+	DoubleData* zconsGap = new DoubleData();
1894	+	zconsGap->setID(ZCONSGAP_ID);
1895	+
1896	+	if (globals->haveZConsGap()){
1897	+	zconsGap->setData(globals->getZconsGap());
1898	+	theInfo.addProperty(zconsGap);
1899	+	}
1900	+
1901	+	//set zcons fixtime
1902	+	DoubleData* zconsFixtime = new DoubleData();
1903	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1904	+
1905	+	if (globals->haveZConsFixTime()){
1906	+	zconsFixtime->setData(globals->getZconsFixtime());
1907	+	theInfo.addProperty(zconsFixtime);
1908	+	}
1909	+
1910	+	//set zconsUsingSMD
1911	+	IntData* zconsUsingSMD = new IntData();
1912	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1913	+
1914	+	if (globals->haveZConsUsingSMD()){
1915	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1916	+	theInfo.addProperty(zconsUsingSMD);
1917	+	}
1918	+
1919	+	//Determine the name of ouput file and add it into SimInfo's property list
1920	+	//Be careful, do not use inFileName, since it is a pointer which
1921	+	//point to a string at master node, and slave nodes do not contain that string
1922	+
1923	+	string zconsOutput(theInfo.finalName);
1924	+
1925	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1926	+
1927	+	StringData* zconsFilename = new StringData();
1928	+	zconsFilename->setID(ZCONSFILENAME_ID);
1929	+	zconsFilename->setData(zconsOutput);
1930	+
1931	+	theInfo.addProperty(zconsFilename);
1932	+
1933	+	//setup index, pos and other parameters of z-constraint molecules
1934	+	nZConstraints = globals->getNzConstraints();
1935	+	theInfo.nZconstraints = nZConstraints;
1936	+
1937	+	zconStamp = globals->getZconStamp();
1938	+	ZConsParaItem tempParaItem;
1939	+
1940	+	ZConsParaData* zconsParaData = new ZConsParaData();
1941	+	zconsParaData->setID(ZCONSPARADATA_ID);
1942	+
1943	+	for (int i = 0; i < nZConstraints; i++){
1944	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1945	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1946	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1947	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1948	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1949	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1950	+	zconsParaData->addItem(tempParaItem);
1951	+	}
1952	+
1953	+	//check the uniqueness of index
1954	+	if(!zconsParaData->isIndexUnique()){
1955	+	sprintf(painCave.errMsg,
1956	+	"ZConstraint Error: molIndex is not unique!\n");
1957	+	painCave.isFatal = 1;
1958	+	simError();
1959	+	}
1960	+
1961	+	//sort the parameters by index of molecules
1962	+	zconsParaData->sortByIndex();
1963	+
1964	+	//push data into siminfo, therefore, we can retrieve later
1965	+	theInfo.addProperty(zconsParaData);
1966	+	}
1967	+
1968	+	void SimSetup::makeMinimizer(){
1969	+
1970	+	OOPSEMinimizer* myOOPSEMinimizer;
1971	+	MinimizerParameterSet* param;
1972	+	char minimizerName[100];
1973	+
1974	+	for (int i = 0; i < nInfo; i++){
1975	+
1976	+	//prepare parameter set for minimizer
1977	+	param = new MinimizerParameterSet();
1978	+	param->setDefaultParameter();
1979	+
1980	+	if (globals->haveMinimizer()){
1981	+	param->setFTol(globals->getMinFTol());
1982	+	}
1983	+
1984	+	if (globals->haveMinGTol()){
1985	+	param->setGTol(globals->getMinGTol());
1986	+	}
1987	+
1988	+	if (globals->haveMinMaxIter()){
1989	+	param->setMaxIteration(globals->getMinMaxIter());
1990	+	}
1991	+
1992	+	if (globals->haveMinWriteFrq()){
1993	+	param->setMaxIteration(globals->getMinMaxIter());
1994	+	}
1995	+
1996	+	if (globals->haveMinWriteFrq()){
1997	+	param->setWriteFrq(globals->getMinWriteFrq());
1998	+	}
1999	+
2000	+	if (globals->haveMinStepSize()){
2001	+	param->setStepSize(globals->getMinStepSize());
2002	+	}
2003	+
2004	+	if (globals->haveMinLSMaxIter()){
2005	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2006	+	}
2007	+
2008	+	if (globals->haveMinLSTol()){
2009	+	param->setLineSearchTol(globals->getMinLSTol());
2010	+	}
2011	+
2012	+	strcpy(minimizerName, globals->getMinimizer());
2013	+
2014	+	if (!strcasecmp(minimizerName, "CG")){
2015	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2016	+	}
2017	+	else if (!strcasecmp(minimizerName, "SD")){
2018	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2019	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2020	+	}
2021	+	else{
2022	+	sprintf(painCave.errMsg,
2023	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2024	+	painCave.isFatal = 0;
2025	+	simError();
2026	+
2027	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2028	+	}
2029	+	info[i].the_integrator = myOOPSEMinimizer;
2030	+
2031	+	//store the minimizer into simInfo
2032	+	info[i].the_minimizer = myOOPSEMinimizer;
2033	+	info[i].has_minimizer = true;
2034	+	}
2035	+
2036	+	}

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