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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 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
187	<	// make an array of molecule stamps that match the components used.
188	<	// also extract the used stamps out into a separate linked list
187	>	bond_pair* theBonds;
188	>	bend_set* theBends;
189	>	torsion_set* theTorsions;
190
191	<	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++ ){
191	>	set<int> skipList;
192
193	<	id = the_components[i]->getType();
194	<	comp_stamps[i] = NULL;
195	<
181	<	// check to make sure the component isn't already in the list
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196
197	<	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	<	}
197	>	//init the forceField paramters
198
199	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
199	>	the_ff->readParams();
200
201	+	// init the atoms
202
203	+	int nMembers, nNew, rb1, rb2;
204
205	<	// caclulate the number of atoms, bonds, bends and torsions
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207
208	<	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	<	}
208	>	atomOffset = 0;
209
210	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213
214	<	simnfo->n_atoms = tot_atoms;
215	<	simnfo->n_bonds = tot_bonds;
216	<	simnfo->n_bends = tot_bends;
217	<	simnfo->n_torsions = tot_torsions;
218	<	simnfo->n_SRI = tot_SRI;
219	<	simnfo->n_mol = tot_nmol;
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221
222	<
223	<	#ifdef IS_MPI
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226
227	<	// divide the molecules among processors here.
228	<
229	<	mpiSim = new mpiSimulation( simnfo );
230	<
241	<
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231
232	<	globalIndex = mpiSim->divideLabor();
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236
237	<
238	<
239	<	// set up the local variables
248	<
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++ ){
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	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	<
241	>	// make the Atoms
242
243	<	simnfo->n_atoms = mpiSim->getMyNlocal();
244	<
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	<	}
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245
246	<	simnfo->n_bonds = local_bonds;
247	<	simnfo->n_bends = local_bends;
248	<	simnfo->n_torsions = local_torsions;
249	<	simnfo->n_SRI = local_SRI;
250	<	simnfo->n_mol = localMol;
246	>	if (currentAtom->haveOrientation()){
247	>	dAtom = new DirectionalAtom((j + atomOffset),
248	>	info[k].getConfiguration());
249	>	info[k].n_oriented++;
250	>	molInfo.myAtoms[j] = dAtom;
251
252	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
253	<	MPIcheckPoint();
254	<
298	<
299	<	#endif // is_mpi
300	<
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255
256	<	// create the atom and short range interaction arrays
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	Atom::createArrays(simnfo->n_atoms);
261	<	the_atoms = new Atom*[simnfo->n_atoms];
262	<	the_molecules = new Molecule[simnfo->n_mol];
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
267	<	if( simnfo->n_SRI ){
310	<	Exclude::createArray(simnfo->n_SRI);
311	<	the_excludes = new Exclude*[simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	Exclude::createArray( 1 );
318	<	the_excludes = new Exclude*;
319	<	the_excludes[0] = new Exclude(0);
320	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
324	<	}
267	>	}
268
269	<	// set the arrays into the SimInfo object
269	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
270	>	#ifdef IS_MPI
271
272	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274	+	#endif // is_mpi
275	+	}
276
277	<	// get some of the tricky things that may still be in the globals
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<
284	<	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() ){
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
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	–
286		#ifdef IS_MPI
287	<	strcpy( checkPointMsg, "Box size set up" );
288	<	MPIcheckPoint();
289	<	#endif // is_mpi
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	+	info[k].excludes->addPair(exI, exJ);
295	+	}
296
297	<	// initialize the arrays
297	>	//make the bends
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303
304	<	the_ff->setSimInfo( simnfo );
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<	makeAtoms();
309	<	simnfo->identArray = new int[simnfo->n_atoms];
310	<	for(i=0; i<simnfo->n_atoms; i++){
311	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
312	<	}
313	<
314	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315
316	<	if( tot_bends ){
317	<	makeBends();
318	<	}
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	if( tot_torsions ){
323	<	makeTorsions();
324	<	}
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340
341	+	current_extra = current_extra->getNext();
342	+	}
343	+	}
344
345	<	if (the_globals->getUseRF() ) {
346	<	simnfo->useReactionField = 1;
347	<
348	<	if( !the_globals->haveECR() ){
349	<	sprintf( painCave.errMsg,
350	<	"SimSetup Warning: using default value of 1/2 the smallest "
351	<	"box length for the electrostaticCutoffRadius.\n"
352	<	"I hope you have a very fast processor!\n");
353	<	painCave.isFatal = 0;
354	<	simError();
355	<	double smallest;
356	<	smallest = simnfo->box_x;
357	<	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	<	}
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350	>	#ifdef IS_MPI
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	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	<	}
359	>	} else {
360
361	+	tempI = theBends[j].a;
362	+	tempJ = theBends[j].b;
363	+	tempK = theBends[j].c;
364	+
365		#ifdef IS_MPI
366	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
367	<	MPIcheckPoint();
368	<	#endif // is_mpi
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379	>	}
380
381	<	if( the_globals->haveInitialConfig() ){
382	<
383	<	InitializeFromFile* fileInit;
384	<	#ifdef IS_MPI // is_mpi
385	<	if( worldRank == 0 ){
386	<	#endif //is_mpi
387	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387	>
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392	>
393		#ifdef IS_MPI
394	<	}else fileInit = new InitializeFromFile( NULL );
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
404
405	<	delete fileInit;
406	<	}
407	<	else{
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	#ifdef IS_MPI
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	<	// no init from bass
419	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420
421	<	initFromBass();
421	>	// Create the Rigid Body:
422
423	+	myRB = new RigidBody();
424
425	<	#endif
426	<	}
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429
430	<	#ifdef IS_MPI
431	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432
433	+	// tempI is atom numbering on local processor
434	+	tempI = molI + atomOffset;
435
436	<
437	<
438	<
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439
440	<
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446		#ifdef IS_MPI
447	<	if( worldRank == 0 ){
448	<	#endif // is_mpi
449	<
450	<	if( the_globals->haveFinalConfig() ){
451	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
452	<	}
453	<	else{
454	<	strcpy( simnfo->finalName, inFileName );
455	<	char* endTest;
456	<	int nameLength = strlen( simnfo->finalName );
457	<	endTest = &(simnfo->finalName[nameLength - 5]);
458	<	if( !strcmp( endTest, ".bass" ) ){
459	<	strcpy( endTest, ".eor" );
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478	>
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481		}
482	<	else if( !strcmp( endTest, ".BASS" ) ){
483	<	strcpy( endTest, ".eor" );
484	<	}
485	<	else{
486	<	endTest = &(simnfo->finalName[nameLength - 4]);
487	<	if( !strcmp( endTest, ".bss" ) ){
488	<	strcpy( endTest, ".eor" );
489	<	}
490	<	else if( !strcmp( endTest, ".mdl" ) ){
491	<	strcpy( endTest, ".eor" );
492	<	}
493	<	else{
494	<	strcat( simnfo->finalName, ".eor" );
495	<	}
482	>
483	>
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486	>
487	>	molInfo.myIntegrableObjects.clear();
488	>
489	>
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491	>
492	>	#ifdef IS_MPI
493	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	>	#else
495	>	slJ = j+atomOffset;
496	>	#endif
497	>
498	>	// if they aren't on the skip list, then they can be integrated
499	>
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505		}
506	<	}
507	<
508	<	// make the sample and status out names
509	<
510	<	strcpy( simnfo->sampleName, inFileName );
511	<	char* endTest;
512	<	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" );
506	>
507	>	// all rigid bodies are integrated:
508	>
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513		}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
583	–	}
514
515	<	strcpy( simnfo->statusName, inFileName );
516	<	nameLength = strlen( simnfo->statusName );
517	<	endTest = &(simnfo->statusName[nameLength - 5]);
518	<	if( !strcmp( endTest, ".bass" ) ){
519	<	strcpy( endTest, ".stat" );
520	<	}
521	<	else if( !strcmp( endTest, ".BASS" ) ){
522	<	strcpy( endTest, ".stat" );
523	<	}
524	<	else{
525	<	endTest = &(simnfo->statusName[nameLength - 4]);
526	<	if( !strcmp( endTest, ".bss" ) ){
527	<	strcpy( endTest, ".stat" );
528	<	}
529	<	else if( !strcmp( endTest, ".mdl" ) ){
530	<	strcpy( endTest, ".stat" );
531	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
515	>
516	>	// send the arrays off to the forceField for init.
517	>
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523	>
524	>	info[k].molecules[i].initialize(molInfo);
525	>
526	>
527	>	atomOffset += molInfo.nAtoms;
528	>	delete[] theBonds;
529	>	delete[] theBends;
530	>	delete[] theTorsions;
531	>	}
532		}
533	+
534	+	#ifdef IS_MPI
535	+	sprintf(checkPointMsg, "all molecules initialized succesfully");
536	+	MPIcheckPoint();
537		#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	–	}
538
539	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
539	>	// clean up the forcefield
540
541	<	if( the_globals->haveThermalTime() ){
629	<	simnfo->thermalTime = the_globals->getThermalTime();
630	<	}
541	>	if (!globals->haveRcut()){
542
543	<	// check for the temperature set flag
543	>	the_ff->calcRcut();
544
545	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getRcut() );
548	>	}
549
550	+	the_ff->cleanMe();
551	+	}
552
553	<	//   // make the longe range forces and the integrator
553	>	void SimSetup::initFromBass(void){
554	>	int i, j, k;
555	>	int n_cells;
556	>	double cellx, celly, cellz;
557	>	double temp1, temp2, temp3;
558	>	int n_per_extra;
559	>	int n_extra;
560	>	int have_extra, done;
561
562	<	//   new AllLong( simnfo );
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
568	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
569	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	+	have_extra = 0;
572	+	if (temp2 < temp3){
573	+	// we have a non-complete lattice
574	+	have_extra = 1;
575
576	+	n_cells = (int) temp3 - 1;
577	+	cellx = info[0].boxL[0] / temp3;
578	+	celly = info[0].boxL[1] / temp3;
579	+	cellz = info[0].boxL[2] / temp3;
580	+	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	+	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	+	n_per_extra = (int) ceil(temp1);
583
584	<	// initialize the Fortran
585	<
586	<	simnfo->refreshSim();
587	<
588	<	if( !strcmp( simnfo->mixingRule, "standard") ){
589	<	the_ff->initForceField( LB_MIXING_RULE );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588	>	painCave.isFatal = 1;
589	>	simError();
590	>	}
591		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
592		else{
593	<	sprintf( painCave.errMsg,
594	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
595	<	simnfo->mixingRule );
596	<	painCave.isFatal = 1;
663	<	simError();
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597		}
598
599	+	current_mol = 0;
600	+	current_comp_mol = 0;
601	+	current_comp = 0;
602	+	current_atom_ndx = 0;
603
604	<	#ifdef IS_MPI
605	<	strcpy( checkPointMsg,
606	<	"Successfully intialized the mixingRule for Fortran." );
607	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	+	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	void SimSetup::makeMolecules( void ){
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
614	<	molInit info;
615	<	DirectionalAtom* dAtom;
616	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614	>	}
615	>	}
616	>	}
617
618	<	the_ff->readParams();
618	>	if (have_extra){
619	>	done = 0;
620
621	<
622	<	// init the molecules
623	<
624	<	atomOffset = 0;
625	<	excludeOffset = 0;
626	<	for(i=0; i<simnfo->n_mol; i++){
627	<
628	<	stampID = the_molecules[i].getStampID();
629	<
630	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
631	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
632	<	info.nBends    = comp_stamps[stampID]->getNBends();
703	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
621	>	int start_ndx;
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	info.myAtoms = &the_atoms[atomOffset];
635	<	info.myExcludes = &the_excludes[excludeOffset];
636	<	info.myBonds = new Bond*[info.nBonds];
709	<	info.myBends = new Bend*[info.nBends];
710	<	info.myTorsions = new Torsions*[info.nTorsions];
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	theBonds = new bond_pair[info.nBonds];
639	<	theBends = new bend_set[info.nBends];
640	<	theTorsions = new torsion_set[info.nTorsions];
641	<
642	<	// make the Atoms
717	<
718	<	for(j=0; j<info.nAtoms; j++){
719	<
720	<	currentAtom = theComponents[stampID]->getAtom( j );
721	<	if( currentAtom->haveOrientation() ){
722	<
723	<	dAtom = new DirectionalAtom(j + atomOffset);
724	<	simnfo->n_oriented++;
725	<	info.myAtoms[j] = dAtom;
726	<
727	<	ux = currentAtom->getOrntX();
728	<	uy = currentAtom->getOrntY();
729	<	uz = currentAtom->getOrntZ();
730	<
731	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
732	<
733	<	u = sqrt( uSqr );
734	<	ux = ux / u;
735	<	uy = uy / u;
736	<	uz = uz / u;
737	<
738	<	dAtom->setSUx( ux );
739	<	dAtom->setSUy( uy );
740	<	dAtom->setSUz( uz );
741	<	}
742	<	else{
743	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	<	}
745	<	info.myAtoms[j]->setType( currentAtom->getType() );
746	<
747	<	#ifdef IS_MPI
748	<
749	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
750	<
751	<	#endif // is_mpi
752	<	}
753	<
754	<	// make the bonds
755	<	for(j=0; j<info.nBonds; j++){
756	<
757	<	currentBond = comp_stamps[stampID]->getBond( j );
758	<	theBonds[j].a = currentBond->getA() + atomOffset;
759	<	theBonds[j].b = currentBond->getB() + atomOffset;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	exI = theBonds[i].a;
645	<	exJ = theBonds[i].b;
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	// exclude_I must always be the smaller of the pair
651	<	if( exI > exJ ){
652	<	tempEx = exI;
653	<	exI = exJ;
654	<	exJ = tempEx;
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
770	–	#ifdef IS_MPI
771	–	tempEx = exI;
772	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773	–	tempEx = exJ;
774	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
775	–
776	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
777	–	#else  // isn't MPI
778	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779	–	#endif  //is_mpi
657		}
658	<	excludeOffset += info.nBonds;
658	>	}
659
660	<	//make the bends
661	<	for(j=0; j<info.nBends; j++){
662	<
663	<	currentBend = comp_stamps[stampID]->getBend( j );
787	<	theBends[j].a = currentBend->getA() + atomOffset;
788	<	theBends[j].b = currentBend->getB() + atomOffset;
789	<	theBends[j].c = currentBend->getC() + atomOffset;
790	<
791	<	if( currentBend->haveExtras() ){
792	<
793	<	extras = current_bend->getExtras();
794	<	current_extra = extras;
795	<
796	<	while( current_extra != NULL ){
797	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798	<
799	<	switch( current_extra->getType() ){
800	<
801	<	case 0:
802	<	theBends[j].ghost =
803	<	current_extra->getInt() + atomOffset;
804	<	theBends[j].isGhost = 1;
805	<	break;
806	<
807	<	case 1:
808	<	theBends[j].ghost =
809	<	(int)current_extra->getDouble() + atomOffset;
810	<	theBends[j].isGhost = 1;
811	<	break;
812	<
813	<	default:
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Error: ghostVectorSource was neiter a "
816	<	"double nor an int.\n"
817	<	"-->Bend[%d] in %s\n",
818	<	j, comp_stamps[stampID]->getID() );
819	<	painCave.isFatal = 1;
820	<	simError();
821	<	}
822	<	}
823	<
824	<	else{
825	<
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup Error: unhandled bend assignment:\n"
828	<	"    -->%s in Bend[%d] in %s\n",
829	<	current_extra->getlhs(),
830	<	j, comp_stamps[stampID]->getID() );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
834	<
835	<	current_extra = current_extra->getNext();
836	<	}
837	<	}
838	<
839	<	if( !theBends[j].isGhost ){
840	<
841	<	exI = theBends[j].a;
842	<	exJ = theBends[j].c;
843	<	}
844	<	else{
845	<
846	<	exI = theBends[j].a;
847	<	exJ = theBends[j].b;
848	<	}
849	<
850	<	// exclude_I must always be the smaller of the pair
851	<	if( exI > exJ ){
852	<	tempEx = exI;
853	<	exI = exJ;
854	<	exJ = tempEx;
855	<	}
856	<	#ifdef IS_MPI
857	<	tempEx = exI;
858	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861	<
862	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
863	<	#else  // isn't MPI
864	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865	<	#endif  //is_mpi
866	<	}
867	<	excludeOffset += info.nBends;
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662	>	}
663	>	}
664
665	<	for(j=0; j<info.nTorsions; j++){
666	<
667	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
668	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
669	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
670	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
876	<
877	<	exI = theTorsions[j].a;
878	<	exJ = theTorsions[j].d;
665	>	void SimSetup::makeElement(double x, double y, double z){
666	>	int k;
667	>	AtomStamp* current_atom;
668	>	DirectionalAtom* dAtom;
669	>	double rotMat[3][3];
670	>	double pos[3];
671
672	<	// exclude_I must always be the smaller of the pair
673	<	if( exI > exJ ){
674	<	tempEx = exI;
675	<	exI = exJ;
676	<	exJ = tempEx;
677	<	}
678	<	#ifdef IS_MPI
679	<	tempEx = exI;
680	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
681	<	tempEx = exJ;
682	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
894	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
895	<	#endif  //is_mpi
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681	>	painCave.isFatal = 1;
682	>	simError();
683		}
897	–	excludeOffset += info.nTorsions;
684
685	<
686	<	// send the arrays off to the forceField for init.
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
903	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
904	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
905	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	+	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	+	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694	<	the_molecules[i].initialize( info );
695	<	atomOffset += info.nAtoms;
696	<	}
694	>	rotMat[0][0] = 1.0;
695	>	rotMat[0][1] = 0.0;
696	>	rotMat[0][2] = 0.0;
697
698	<	// clean up the forcefield
698	>	rotMat[1][0] = 0.0;
699	>	rotMat[1][1] = 1.0;
700	>	rotMat[1][2] = 0.0;
701
702	<	the_ff->cleanMe();
703	<	}
702	>	rotMat[2][0] = 0.0;
703	>	rotMat[2][1] = 0.0;
704	>	rotMat[2][2] = 1.0;
705
706	+	dAtom->setA(rotMat);
707	+	}
708
709	+	current_atom_ndx++;
710	+	}
711
712	<	void SimSetup::makeAtoms( void ){
712	>	current_mol++;
713	>	current_comp_mol++;
714
715	<	int i, j, k, index;
716	<	double ux, uy, uz, uSqr, u;
717	<	AtomStamp* current_atom;
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716	>	current_comp_mol = 0;
717	>	current_comp++;
718	>	}
719	>	}
720
925	–	DirectionalAtom* dAtom;
926	–	int molIndex, molStart, molEnd, nMemb, lMolIndex;
721
722	<	lMolIndex = 0;
723	<	molIndex = 0;
930	<	index = 0;
931	<	for( i=0; i<n_components; i++ ){
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725	<	for( j=0; j<components_nmol[i]; j++ ){
725	>	ensembleCase = -1;
726	>	ffCase = -1;
727
728	<	#ifdef IS_MPI
936	<	if( mpiSim->getMyMolStart() <= molIndex &&
937	<	molIndex <= mpiSim->getMyMolEnd() ){
938	<	#endif // is_mpi
728	>	// set the easy ones first
729
730	<	molStart = index;
731	<	nMemb = comp_stamps[i]->getNAtoms();
732	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
733	<
944	<	current_atom = comp_stamps[i]->getAtom( k );
945	<	if( current_atom->haveOrientation() ){
946	<
947	<	dAtom = new DirectionalAtom(index);
948	<	simnfo->n_oriented++;
949	<	the_atoms[index] = dAtom;
950	<
951	<	ux = current_atom->getOrntX();
952	<	uy = current_atom->getOrntY();
953	<	uz = current_atom->getOrntZ();
954	<
955	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956	<
957	<	u = sqrt( uSqr );
958	<	ux = ux / u;
959	<	uy = uy / u;
960	<	uz = uz / u;
961	<
962	<	dAtom->setSUx( ux );
963	<	dAtom->setSUy( uy );
964	<	dAtom->setSUz( uz );
965	<	}
966	<	else{
967	<	the_atoms[index] = new GeneralAtom(index);
968	<	}
969	<	the_atoms[index]->setType( current_atom->getType() );
970	<	the_atoms[index]->setIndex( index );
971	<
972	<	// increment the index and repeat;
973	<	index++;
974	<	}
975	<
976	<	molEnd = index -1;
977	<	the_molecules[lMolIndex].setNMembers( nMemb );
978	<	the_molecules[lMolIndex].setStartAtom( molStart );
979	<	the_molecules[lMolIndex].setEndAtom( molEnd );
980	<	the_molecules[lMolIndex].setStampID( i );
981	<	lMolIndex++;
982	<
983	<	#ifdef IS_MPI
984	<	}
985	<	#endif //is_mpi
986	<
987	<	molIndex++;
988	<	}
730	>	for (i = 0; i < nInfo; i++){
731	>	info[i].target_temp = globals->getTargetTemp();
732	>	info[i].dt = globals->getDt();
733	>	info[i].run_time = globals->getRunTime();
734		}
735	+	n_components = globals->getNComponents();
736
991	–	#ifdef IS_MPI
992	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
993	–
994	–	delete[] globalIndex;
737
738	<	mpiSim->mpiRefresh();
997	<	#endif //IS_MPI
998	<
999	<	the_ff->initializeAtoms();
1000	<	}
738	>	// get the forceField
739
740	<	void SimSetup::makeBonds( void ){
740	>	strcpy(force_field, globals->getForceField());
741
742	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
743	<	bond_pair* the_bonds;
744	<	BondStamp* current_bond;
742	>	if (!strcasecmp(force_field, "DUFF")){
743	>	ffCase = FF_DUFF;
744	>	}
745	>	else if (!strcasecmp(force_field, "LJ")){
746	>	ffCase = FF_LJ;
747	>	}
748	>	else if (!strcasecmp(force_field, "EAM")){
749	>	ffCase = FF_EAM;
750	>	}
751	>	else if (!strcasecmp(force_field, "WATER")){
752	>	ffCase = FF_H2O;
753	>	}
754	>	else{
755	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	>	force_field);
757	>	painCave.isFatal = 1;
758	>	simError();
759	>	}
760
761	<	the_bonds = new bond_pair[tot_bonds];
1009	<	index = 0;
1010	<	offset = 0;
1011	<	molIndex = 0;
761	>	// get the ensemble
762
763	<	for( i=0; i<n_components; i++ ){
763	>	strcpy(ensemble, globals->getEnsemble());
764
765	<	for( j=0; j<components_nmol[i]; j++ ){
765	>	if (!strcasecmp(ensemble, "NVE")){
766	>	ensembleCase = NVE_ENS;
767	>	}
768	>	else if (!strcasecmp(ensemble, "NVT")){
769	>	ensembleCase = NVT_ENS;
770	>	}
771	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772	>	ensembleCase = NPTi_ENS;
773	>	}
774	>	else if (!strcasecmp(ensemble, "NPTf")){
775	>	ensembleCase = NPTf_ENS;
776	>	}
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779	>	}
780	>	else{
781	>	sprintf(painCave.errMsg,
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784	>	ensemble);
785	>	painCave.isFatal = 0;
786	>	simError();
787	>	strcpy(ensemble, "NVE");
788	>	ensembleCase = NVE_ENS;
789	>	}
790
791	<	#ifdef IS_MPI
792	<	if( mpiSim->getMyMolStart() <= molIndex &&
1019	<	molIndex <= mpiSim->getMyMolEnd() ){
1020	<	#endif // is_mpi
1021	<
1022	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023	<
1024	<	current_bond = comp_stamps[i]->getBond( k );
1025	<	the_bonds[index].a = current_bond->getA() + offset;
1026	<	the_bonds[index].b = current_bond->getB() + offset;
791	>	for (i = 0; i < nInfo; i++){
792	>	strcpy(info[i].ensemble, ensemble);
793
794	<	exI = the_bonds[index].a;
1029	<	exJ = the_bonds[index].b;
794	>	// get the mixing rule
795
796	<	// exclude_I must always be the smaller of the pair
797	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1037	<
1038	<
1039	<	#ifdef IS_MPI
1040	<
1041	<	the_excludes[index*2] =
1042	<	the_atoms[exI]->getGlobalIndex() + 1;
1043	<	the_excludes[index*2 + 1] =
1044	<	the_atoms[exJ]->getGlobalIndex() + 1;
1045	<
1046	<	#else  // isn't MPI
1047	<
1048	<	the_excludes[index*2] =     exI + 1;
1049	<	the_excludes[index*2 + 1] = exJ + 1;
1050	<	// fortran index from 1 (hence the +1 in the indexing)
1051	<	#endif  //is_mpi
1052	<
1053	<	// increment the index and repeat;
1054	<	index++;
1055	<	}
1056	<	offset += comp_stamps[i]->getNAtoms();
1057	<
1058	<	#ifdef IS_MPI
1059	<	}
1060	<	#endif //is_mpi
1061	<
1062	<	molIndex++;
1063	<	}
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797	>	info[i].usePBC = globals->getPBC();
798		}
799
800	<	the_ff->initializeBonds( the_bonds );
1067	<	}
800	>	// get the components and calculate the tot_nMol and indvidual n_mol
801
802	<	void SimSetup::makeBends( void ){
802	>	the_components = globals->getComponents();
803	>	components_nmol = new int[n_components];
804
1071	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1072	–	bend_set* the_bends;
1073	–	BendStamp* current_bend;
1074	–	LinkedAssign* extras;
1075	–	LinkedAssign* current_extra;
1076	–
805
806	<	the_bends = new bend_set[tot_bends];
807	<	index = 0;
808	<	offset = 0;
1081	<	molIndex = 0;
1082	<	for( i=0; i<n_components; i++ ){
806	>	if (!globals->haveNMol()){
807	>	// we don't have the total number of molecules, so we assume it is
808	>	// given in each component
809
810	<	for( j=0; j<components_nmol[i]; j++ ){
811	<
812	<	#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
816	<
817	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
818	<
1093	<	current_bend = comp_stamps[i]->getBend( k );
1094	<	the_bends[index].a = current_bend->getA() + offset;
1095	<	the_bends[index].b = current_bend->getB() + offset;
1096	<	the_bends[index].c = current_bend->getC() + offset;
1097	<
1098	<	if( current_bend->haveExtras() ){
1099	<
1100	<	extras = current_bend->getExtras();
1101	<	current_extra = extras;
1102	<
1103	<	while( current_extra != NULL ){
1104	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105	<
1106	<	switch( current_extra->getType() ){
1107	<
1108	<	case 0:
1109	<	the_bends[index].ghost =
1110	<	current_extra->getInt() + offset;
1111	<	the_bends[index].isGhost = 1;
1112	<	break;
1113	<
1114	<	case 1:
1115	<	the_bends[index].ghost =
1116	<	(int)current_extra->getDouble() + offset;
1117	<	the_bends[index].isGhost = 1;
1118	<	break;
1119	<
1120	<	default:
1121	<	sprintf( painCave.errMsg,
1122	<	"SimSetup Error: ghostVectorSource was neiter a "
1123	<	"double nor an int.\n"
1124	<	"-->Bend[%d] in %s\n",
1125	<	k, comp_stamps[i]->getID() );
1126	<	painCave.isFatal = 1;
1127	<	simError();
1128	<	}
1129	<	}
1130	<
1131	<	else{
1132	<
1133	<	sprintf( painCave.errMsg,
1134	<	"SimSetup Error: unhandled bend assignment:\n"
1135	<	"    -->%s in Bend[%d] in %s\n",
1136	<	current_extra->getlhs(),
1137	<	k, comp_stamps[i]->getID() );
1138	<	painCave.isFatal = 1;
1139	<	simError();
1140	<	}
1141	<
1142	<	current_extra = current_extra->getNext();
1143	<	}
1144	<	}
1145	<
1146	<	if( !the_bends[index].isGhost ){
1147	<
1148	<	exI = the_bends[index].a;
1149	<	exJ = the_bends[index].c;
1150	<	}
1151	<	else{
1152	<
1153	<	exI = the_bends[index].a;
1154	<	exJ = the_bends[index].b;
1155	<	}
1156	<
1157	<	// exclude_I must always be the smaller of the pair
1158	<	if( exI > exJ ){
1159	<	tempEx = exI;
1160	<	exI = exJ;
1161	<	exJ = tempEx;
1162	<	}
1163	<
1164	<
1165	<	#ifdef IS_MPI
1166	<
1167	<	the_excludes[(index + tot_bonds)*2] =
1168	<	the_atoms[exI]->getGlobalIndex() + 1;
1169	<	the_excludes[(index + tot_bonds)*2 + 1] =
1170	<	the_atoms[exJ]->getGlobalIndex() + 1;
1171	<
1172	<	#else  // isn't MPI
1173	<
1174	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176	<	// fortran index from 1 (hence the +1 in the indexing)
1177	<	#endif  //is_mpi
1178	<
1179	<
1180	<	// increment the index and repeat;
1181	<	index++;
1182	<	}
1183	<	offset += comp_stamps[i]->getNAtoms();
1184	<
1185	<	#ifdef IS_MPI
810	>	tot_nmol = 0;
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819		}
1187	–	#endif //is_mpi
820
821	<	molIndex++;
821	>	tot_nmol += the_components[i]->getNMol();
822	>	components_nmol[i] = the_components[i]->getNMol();
823		}
824		}
825	+	else{
826	+	sprintf(painCave.errMsg,
827	+	"SimSetup error.\n"
828	+	"\tSorry, the ability to specify total"
829	+	" nMols and then give molfractions in the components\n"
830	+	"\tis not currently supported."
831	+	" Please give nMol in the components.\n");
832	+	painCave.isFatal = 1;
833	+	simError();
834	+	}
835
836	<	#ifdef IS_MPI
837	<	sprintf( checkPointMsg,
838	<	"Successfully created the bends list.\n" );
839	<	MPIcheckPoint();
840	<	#endif // is_mpi
841	<
836	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	>	sprintf(painCave.errMsg,
839	>	"Sample time is not divisible by dt.\n"
840	>	"\tThis will result in samples that are not uniformly\n"
841	>	"\tdistributed in time.  If this is a problem, change\n"
842	>	"\tyour sampleTime variable.\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	}
846
847	<	the_ff->initializeBends( the_bends );
848	<	}
847	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	>	sprintf(painCave.errMsg,
849	>	"Status time is not divisible by dt.\n"
850	>	"\tThis will result in status reports that are not uniformly\n"
851	>	"\tdistributed in time.  If this is a problem, change \n"
852	>	"\tyour statusTime variable.\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	}
856
857	<	void SimSetup::makeTorsions( void ){
857	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	>	sprintf(painCave.errMsg,
859	>	"Thermal time is not divisible by dt.\n"
860	>	"\tThis will result in thermalizations that are not uniformly\n"
861	>	"\tdistributed in time.  If this is a problem, change \n"
862	>	"\tyour thermalTime variable.\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	}
866
867	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
868	<	torsion_set* the_torsions;
869	<	TorsionStamp* current_torsion;
867	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	>	sprintf(painCave.errMsg,
869	>	"Reset time is not divisible by dt.\n"
870	>	"\tThis will result in integrator resets that are not uniformly\n"
871	>	"\tdistributed in time.  If this is a problem, change\n"
872	>	"\tyour resetTime variable.\n");
873	>	painCave.isFatal = 0;
874	>	simError();
875	>	}
876
877	<	the_torsions = new torsion_set[tot_torsions];
1210	<	index = 0;
1211	<	offset = 0;
1212	<	molIndex = 0;
1213	<	for( i=0; i<n_components; i++ ){
877	>	// set the status, sample, and thermal kick times
878
879	<	for( j=0; j<components_nmol[i]; j++ ){
879	>	for (i = 0; i < nInfo; i++){
880	>	if (globals->haveSampleTime()){
881	>	info[i].sampleTime = globals->getSampleTime();
882	>	info[i].statusTime = info[i].sampleTime;
883	>	}
884	>	else{
885	>	info[i].sampleTime = globals->getRunTime();
886	>	info[i].statusTime = info[i].sampleTime;
887	>	}
888
889	<	#ifdef IS_MPI
890	<	if( mpiSim->getMyMolStart() <= molIndex &&
891	<	molIndex <= mpiSim->getMyMolEnd() ){
1220	<	#endif // is_mpi
889	>	if (globals->haveStatusTime()){
890	>	info[i].statusTime = globals->getStatusTime();
891	>	}
892
893	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
893	>	if (globals->haveThermalTime()){
894	>	info[i].thermalTime = globals->getThermalTime();
895	>	} else {
896	>	info[i].thermalTime = globals->getRunTime();
897	>	}
898
899	<	current_torsion = comp_stamps[i]->getTorsion( k );
900	<	the_torsions[index].a = current_torsion->getA() + offset;
901	<	the_torsions[index].b = current_torsion->getB() + offset;
902	<	the_torsions[index].c = current_torsion->getC() + offset;
903	<	the_torsions[index].d = current_torsion->getD() + offset;
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903	>	}
904
905	<	exI = the_torsions[index].a;
906	<	exJ = the_torsions[index].d;
905	>	// check for the temperature set flag
906	>
907	>	if (globals->haveTempSet())
908	>	info[i].setTemp = globals->getTempSet();
909
910	<
911	<	// exclude_I must always be the smaller of the pair
912	<	if( exI > exJ ){
913	<	tempEx = exI;
914	<	exI = exJ;
915	<	exJ = tempEx;
916	<	}
910	>	// check for the extended State init
911	>
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	>
915	>	}
916	>
917	>	//setup seed for random number generator
918	>	int seedValue;
919
920	+	if (globals->haveSeed()){
921	+	seedValue = globals->getSeed();
922
923	<	#ifdef IS_MPI
924	<
925	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
926	<	the_atoms[exI]->getGlobalIndex() + 1;
927	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
928	<	the_atoms[exJ]->getGlobalIndex() + 1;
1248	<
1249	<	#else  // isn't MPI
1250	<
1251	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253	<	// fortran indexes from 1 (hence the +1 in the indexing)
1254	<	#endif  //is_mpi
1255	<
923	>	if(seedValue / 1E9 == 0){
924	>	sprintf(painCave.errMsg,
925	>	"Seed for sprng library should contain at least 9 digits\n"
926	>	"OOPSE will generate a seed for user\n");
927	>	painCave.isFatal = 0;
928	>	simError();
929
930	<	// increment the index and repeat;
931	<	index++;
930	>	//using seed generated by system instead of invalid seed set by user
931	>	#ifndef IS_MPI
932	>	seedValue = make_sprng_seed();
933	>	#else
934	>	if (worldRank == 0){
935	>	seedValue = make_sprng_seed();
936		}
937	<	offset += comp_stamps[i]->getNAtoms();
937	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
938	>	#endif
939	>	}
940	>	}//end of if branch of globals->haveSeed()
941	>	else{
942	>
943	>	#ifndef IS_MPI
944	>	seedValue = make_sprng_seed();
945	>	#else
946	>	if (worldRank == 0){
947	>	seedValue = make_sprng_seed();
948	>	}
949	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
950	>	#endif
951	>	}//end of globals->haveSeed()
952
953	+	for (int i = 0; i < nInfo; i++){
954	+	info[i].setSeed(seedValue);
955	+	}
956	+
957		#ifdef IS_MPI
958	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959	+	MPIcheckPoint();
960	+	#endif // is_mpi
961	+	}
962	+
963	+
964	+	void SimSetup::finalInfoCheck(void){
965	+	int index;
966	+	int usesDipoles;
967	+	int usesCharges;
968	+	int i;
969	+
970	+	for (i = 0; i < nInfo; i++){
971	+	// check electrostatic parameters
972	+
973	+	index = 0;
974	+	usesDipoles = 0;
975	+	while ((index < info[i].n_atoms) && !usesDipoles){
976	+	usesDipoles = (info[i].atoms[index])->hasDipole();
977	+	index++;
978	+	}
979	+	index = 0;
980	+	usesCharges = 0;
981	+	while ((index < info[i].n_atoms) && !usesCharges){
982	+	usesCharges= (info[i].atoms[index])->hasCharge();
983	+	index++;
984	+	}
985	+	#ifdef IS_MPI
986	+	int myUse = usesDipoles;
987	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988	+	#endif //is_mpi
989	+
990	+	double theRcut, theRsw;
991	+
992	+	if (globals->getUseRF()){
993	+	info[i].useReactionField = 1;
994	+
995	+	if (!globals->haveRcut()){
996	+	sprintf(painCave.errMsg,
997	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
998	+	"\tOOPSE will use a default value of 15.0 angstroms"
999	+	"\tfor the cutoffRadius.\n");
1000	+	painCave.isFatal = 0;
1001	+	simError();
1002	+	theRcut = 15.0;
1003		}
1004	<	#endif //is_mpi
1004	>	else{
1005	>	theRcut = globals->getRcut();
1006	>	}
1007
1008	<	molIndex++;
1008	>	if (!globals->haveRsw()){
1009	>	sprintf(painCave.errMsg,
1010	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	theRsw = 0.95 * theRcut;
1016	>	}
1017	>	else{
1018	>	theRsw = globals->getRsw();
1019	>	}
1020	>
1021	>	info[i].setDefaultRcut(theRcut, theRsw);
1022	>
1023	>	if (!globals->haveDielectric()){
1024	>	sprintf(painCave.errMsg,
1025	>	"SimSetup Error: No Dielectric constant was set.\n"
1026	>	"\tYou are trying to use Reaction Field without"
1027	>	"\tsetting a dielectric constant!\n");
1028	>	painCave.isFatal = 1;
1029	>	simError();
1030	>	}
1031	>	info[i].dielectric = globals->getDielectric();
1032		}
1033	<	}
1033	>	else{
1034	>	if (usesDipoles || usesCharges){
1035
1036	<	the_ff->initializeTorsions( the_torsions );
1036	>	if (!globals->haveRcut()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1039	>	"\tOOPSE will use a default value of 15.0 angstroms"
1040	>	"\tfor the cutoffRadius.\n");
1041	>	painCave.isFatal = 0;
1042	>	simError();
1043	>	theRcut = 15.0;
1044	>	}
1045	>	else{
1046	>	theRcut = globals->getRcut();
1047	>	}
1048	>
1049	>	if (!globals->haveRsw()){
1050	>	sprintf(painCave.errMsg,
1051	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1052	>	"\tOOPSE will use a default value of\n"
1053	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1054	>	painCave.isFatal = 0;
1055	>	simError();
1056	>	theRsw = 0.95 * theRcut;
1057	>	}
1058	>	else{
1059	>	theRsw = globals->getRsw();
1060	>	}
1061	>
1062	>	info[i].setDefaultRcut(theRcut, theRsw);
1063	>
1064	>	}
1065	>	}
1066	>	}
1067	>	#ifdef IS_MPI
1068	>	strcpy(checkPointMsg, "post processing checks out");
1069	>	MPIcheckPoint();
1070	>	#endif // is_mpi
1071		}
1072	+
1073	+	void SimSetup::initSystemCoords(void){
1074	+	int i;
1075
1076	<	void SimSetup::initFromBass( void ){
1076	>	char* inName;
1077
1078	<	int i, j, k;
1276	<	int n_cells;
1277	<	double cellx, celly, cellz;
1278	<	double temp1, temp2, temp3;
1279	<	int n_per_extra;
1280	<	int n_extra;
1281	<	int have_extra, done;
1078	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079
1080	<	temp1 = (double)tot_nmol / 4.0;
1081	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1285	<	temp3 = ceil( temp2 );
1080	>	for (i = 0; i < info[0].n_atoms; i++)
1081	>	info[0].atoms[i]->setCoords();
1082
1083	<	have_extra =0;
1084	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1085	<	have_extra =1;
1083	>	if (globals->haveInitialConfig()){
1084	>	InitializeFromFile* fileInit;
1085	>	#ifdef IS_MPI // is_mpi
1086	>	if (worldRank == 0){
1087	>	#endif //is_mpi
1088	>	inName = globals->getInitialConfig();
1089	>	fileInit = new InitializeFromFile(inName);
1090	>	#ifdef IS_MPI
1091	>	}
1092	>	else
1093	>	fileInit = new InitializeFromFile(NULL);
1094	>	#endif
1095	>	fileInit->readInit(info); // default velocities on
1096
1097	<	n_cells = (int)temp3 - 1;
1098	<	cellx = simnfo->box_x / temp3;
1099	<	celly = simnfo->box_y / temp3;
1100	<	cellz = simnfo->box_z / temp3;
1101	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1102	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1103	<	n_per_extra = (int)ceil( temp1 );
1097	>	delete fileInit;
1098	>	}
1099	>	else{
1100	>
1101	>	// no init from bass
1102	>
1103	>	sprintf(painCave.errMsg,
1104	>	"Cannot intialize a simulation without an initial configuration file.\n");
1105	>	painCave.isFatal = 1;;
1106	>	simError();
1107	>
1108	>	}
1109
1110	<	if( n_per_extra > 4){
1111	<	sprintf( painCave.errMsg,
1112	<	"SimSetup error. There has been an error in constructing"
1113	<	" the non-complete lattice.\n" );
1114	<	painCave.isFatal = 1;
1304	<	simError();
1305	<	}
1306	<	}
1307	<	else{
1308	<	n_cells = (int)temp3;
1309	<	cellx = simnfo->box_x / temp3;
1310	<	celly = simnfo->box_y / temp3;
1311	<	cellz = simnfo->box_z / temp3;
1312	<	}
1110	>	#ifdef IS_MPI
1111	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112	>	MPIcheckPoint();
1113	>	#endif // is_mpi
1114	>	}
1115
1314	–	current_mol = 0;
1315	–	current_comp_mol = 0;
1316	–	current_comp = 0;
1317	–	current_atom_ndx = 0;
1116
1117	<	for( i=0; i < n_cells ; i++ ){
1118	<	for( j=0; j < n_cells; j++ ){
1321	<	for( k=0; k < n_cells; k++ ){
1117	>	void SimSetup::makeOutNames(void){
1118	>	int k;
1119
1323	–	makeElement( i * cellx,
1324	–	j * celly,
1325	–	k * cellz );
1120
1121	<	makeElement( i * cellx + 0.5 * cellx,
1122	<	j * celly + 0.5 * celly,
1123	<	k * cellz );
1121	>	for (k = 0; k < nInfo; k++){
1122	>	#ifdef IS_MPI
1123	>	if (worldRank == 0){
1124	>	#endif // is_mpi
1125
1126	<	makeElement( i * cellx,
1127	<	j * celly + 0.5 * celly,
1128	<	k * cellz + 0.5 * cellz );
1126	>	if (globals->haveFinalConfig()){
1127	>	strcpy(info[k].finalName, globals->getFinalConfig());
1128	>	}
1129	>	else{
1130	>	strcpy(info[k].finalName, inFileName);
1131	>	char* endTest;
1132	>	int nameLength = strlen(info[k].finalName);
1133	>	endTest = &(info[k].finalName[nameLength - 5]);
1134	>	if (!strcmp(endTest, ".bass")){
1135	>	strcpy(endTest, ".eor");
1136	>	}
1137	>	else if (!strcmp(endTest, ".BASS")){
1138	>	strcpy(endTest, ".eor");
1139	>	}
1140	>	else{
1141	>	endTest = &(info[k].finalName[nameLength - 4]);
1142	>	if (!strcmp(endTest, ".bss")){
1143	>	strcpy(endTest, ".eor");
1144	>	}
1145	>	else if (!strcmp(endTest, ".mdl")){
1146	>	strcpy(endTest, ".eor");
1147	>	}
1148	>	else{
1149	>	strcat(info[k].finalName, ".eor");
1150	>	}
1151	>	}
1152	>	}
1153
1154	<	makeElement( i * cellx + 0.5 * cellx,
1155	<	j * celly,
1156	<	k * cellz + 0.5 * cellz );
1154	>	// make the sample and status out names
1155	>
1156	>	strcpy(info[k].sampleName, inFileName);
1157	>	char* endTest;
1158	>	int nameLength = strlen(info[k].sampleName);
1159	>	endTest = &(info[k].sampleName[nameLength - 5]);
1160	>	if (!strcmp(endTest, ".bass")){
1161	>	strcpy(endTest, ".dump");
1162		}
1163	+	else if (!strcmp(endTest, ".BASS")){
1164	+	strcpy(endTest, ".dump");
1165	+	}
1166	+	else{
1167	+	endTest = &(info[k].sampleName[nameLength - 4]);
1168	+	if (!strcmp(endTest, ".bss")){
1169	+	strcpy(endTest, ".dump");
1170	+	}
1171	+	else if (!strcmp(endTest, ".mdl")){
1172	+	strcpy(endTest, ".dump");
1173	+	}
1174	+	else{
1175	+	strcat(info[k].sampleName, ".dump");
1176	+	}
1177	+	}
1178	+
1179	+	strcpy(info[k].statusName, inFileName);
1180	+	nameLength = strlen(info[k].statusName);
1181	+	endTest = &(info[k].statusName[nameLength - 5]);
1182	+	if (!strcmp(endTest, ".bass")){
1183	+	strcpy(endTest, ".stat");
1184	+	}
1185	+	else if (!strcmp(endTest, ".BASS")){
1186	+	strcpy(endTest, ".stat");
1187	+	}
1188	+	else{
1189	+	endTest = &(info[k].statusName[nameLength - 4]);
1190	+	if (!strcmp(endTest, ".bss")){
1191	+	strcpy(endTest, ".stat");
1192	+	}
1193	+	else if (!strcmp(endTest, ".mdl")){
1194	+	strcpy(endTest, ".stat");
1195	+	}
1196	+	else{
1197	+	strcat(info[k].statusName, ".stat");
1198	+	}
1199	+	}
1200	+
1201	+	#ifdef IS_MPI
1202	+
1203		}
1204	+	#endif // is_mpi
1205		}
1206	+	}
1207
1342	–	if( have_extra ){
1343	–	done = 0;
1208
1209	<	int start_ndx;
1210	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1347	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1209	>	void SimSetup::sysObjectsCreation(void){
1210	>	int i, k;
1211
1212	<	if( i < n_cells ){
1212	>	// create the forceField
1213
1214	<	if( j < n_cells ){
1352	<	start_ndx = n_cells;
1353	<	}
1354	<	else start_ndx = 0;
1355	<	}
1356	<	else start_ndx = 0;
1214	>	createFF();
1215
1216	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1216	>	// extract componentList
1217
1218	<	makeElement( i * cellx,
1361	<	j * celly,
1362	<	k * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1218	>	compList();
1219
1220	<	if( !done && n_per_extra > 1 ){
1366	<	makeElement( i * cellx + 0.5 * cellx,
1367	<	j * celly + 0.5 * celly,
1368	<	k * cellz );
1369	<	done = ( current_mol >= tot_nmol );
1370	<	}
1220	>	// calc the number of atoms, bond, bends, and torsions
1221
1222	<	if( !done && n_per_extra > 2){
1373	<	makeElement( i * cellx,
1374	<	j * celly + 0.5 * celly,
1375	<	k * cellz + 0.5 * cellz );
1376	<	done = ( current_mol >= tot_nmol );
1377	<	}
1222	>	calcSysValues();
1223
1224	<	if( !done && n_per_extra > 3){
1225	<	makeElement( i * cellx + 0.5 * cellx,
1381	<	j * celly,
1382	<	k * cellz + 0.5 * cellz );
1383	<	done = ( current_mol >= tot_nmol );
1384	<	}
1385	<	}
1386	<	}
1387	<	}
1388	<	}
1224	>	#ifdef IS_MPI
1225	>	// divide the molecules among the processors
1226
1227	+	mpiMolDivide();
1228	+	#endif //is_mpi
1229
1230	<	for( i=0; i<simnfo->n_atoms; i++ ){
1392	<	simnfo->atoms[i]->set_vx( 0.0 );
1393	<	simnfo->atoms[i]->set_vy( 0.0 );
1394	<	simnfo->atoms[i]->set_vz( 0.0 );
1395	<	}
1396	<	}
1230	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231
1232	<	void SimSetup::makeElement( double x, double y, double z ){
1232	>	makeSysArrays();
1233
1234	<	int k;
1401	<	AtomStamp* current_atom;
1402	<	DirectionalAtom* dAtom;
1403	<	double rotMat[3][3];
1234	>	// make and initialize the molecules (all but atomic coordinates)
1235
1236	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1236	>	makeMolecules();
1237
1238	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1239	<	if( !current_atom->havePosition() ){
1240	<	sprintf( painCave.errMsg,
1241	<	"SimSetup:initFromBass error.\n"
1411	<	"\tComponent %s, atom %s does not have a position specified.\n"
1412	<	"\tThe initialization routine is unable to give a start"
1413	<	" position.\n",
1414	<	comp_stamps[current_comp]->getID(),
1415	<	current_atom->getType() );
1416	<	painCave.isFatal = 1;
1417	<	simError();
1238	>	for (k = 0; k < nInfo; k++){
1239	>	info[k].identArray = new int[info[k].n_atoms];
1240	>	for (i = 0; i < info[k].n_atoms; i++){
1241	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1242		}
1243	+	}
1244	+	}
1245
1420	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1421	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1422	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1246
1247	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1247	>	void SimSetup::createFF(void){
1248	>	switch (ffCase){
1249	>	case FF_DUFF:
1250	>	the_ff = new DUFF();
1251	>	break;
1252
1253	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1254	<
1255	<	rotMat[0][0] = 1.0;
1429	<	rotMat[0][1] = 0.0;
1430	<	rotMat[0][2] = 0.0;
1431	<
1432	<	rotMat[1][0] = 0.0;
1433	<	rotMat[1][1] = 1.0;
1434	<	rotMat[1][2] = 0.0;
1435	<
1436	<	rotMat[2][0] = 0.0;
1437	<	rotMat[2][1] = 0.0;
1438	<	rotMat[2][2] = 1.0;
1253	>	case FF_LJ:
1254	>	the_ff = new LJFF();
1255	>	break;
1256
1257	<	dAtom->setA( rotMat );
1257	>	case FF_EAM:
1258	>	the_ff = new EAM_FF();
1259	>	break;
1260	>
1261	>	case FF_H2O:
1262	>	the_ff = new WATER();
1263	>	break;
1264	>
1265	>	default:
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1268	>	painCave.isFatal = 1;
1269	>	simError();
1270	>	}
1271	>
1272	>	#ifdef IS_MPI
1273	>	strcpy(checkPointMsg, "ForceField creation successful");
1274	>	MPIcheckPoint();
1275	>	#endif // is_mpi
1276	>	}
1277	>
1278	>
1279	>	void SimSetup::compList(void){
1280	>	int i;
1281	>	char* id;
1282	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1283	>	LinkedMolStamp* currentStamp = NULL;
1284	>	comp_stamps = new MoleculeStamp * [n_components];
1285	>
1286	>	// make an array of molecule stamps that match the components used.
1287	>	// also extract the used stamps out into a separate linked list
1288	>
1289	>	for (i = 0; i < nInfo; i++){
1290	>	info[i].nComponents = n_components;
1291	>	info[i].componentsNmol = components_nmol;
1292	>	info[i].compStamps = comp_stamps;
1293	>	info[i].headStamp = headStamp;
1294	>	}
1295	>
1296	>
1297	>	for (i = 0; i < n_components; i++){
1298	>	id = the_components[i]->getType();
1299	>	comp_stamps[i] = NULL;
1300	>
1301	>	// check to make sure the component isn't already in the list
1302	>
1303	>	comp_stamps[i] = headStamp->match(id);
1304	>	if (comp_stamps[i] == NULL){
1305	>	// extract the component from the list;
1306	>
1307	>	currentStamp = stamps->extractMolStamp(id);
1308	>	if (currentStamp == NULL){
1309	>	sprintf(painCave.errMsg,
1310	>	"SimSetup error: Component \"%s\" was not found in the "
1311	>	"list of declared molecules\n",
1312	>	id);
1313	>	painCave.isFatal = 1;
1314	>	simError();
1315	>	}
1316	>
1317	>	headStamp->add(currentStamp);
1318	>	comp_stamps[i] = headStamp->match(id);
1319		}
1320	+	}
1321
1322	<	current_atom_ndx++;
1322	>	#ifdef IS_MPI
1323	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1324	>	MPIcheckPoint();
1325	>	#endif // is_mpi
1326	>	}
1327	>
1328	>	void SimSetup::calcSysValues(void){
1329	>	int i;
1330	>
1331	>	int* molMembershipArray;
1332	>
1333	>	tot_atoms = 0;
1334	>	tot_bonds = 0;
1335	>	tot_bends = 0;
1336	>	tot_torsions = 0;
1337	>	tot_rigid = 0;
1338	>	for (i = 0; i < n_components; i++){
1339	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344		}
1345	+
1346	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347	+	molMembershipArray = new int[tot_atoms];
1348
1349	<	current_mol++;
1350	<	current_comp_mol++;
1349	>	for (i = 0; i < nInfo; i++){
1350	>	info[i].n_atoms = tot_atoms;
1351	>	info[i].n_bonds = tot_bonds;
1352	>	info[i].n_bends = tot_bends;
1353	>	info[i].n_torsions = tot_torsions;
1354	>	info[i].n_SRI = tot_SRI;
1355	>	info[i].n_mol = tot_nmol;
1356
1357	<	if( current_comp_mol >= components_nmol[current_comp] ){
1357	>	info[i].molMembershipArray = molMembershipArray;
1358	>	}
1359	>	}
1360
1361	<	current_comp_mol = 0;
1362	<	current_comp++;
1361	>	#ifdef IS_MPI
1362	>
1363	>	void SimSetup::mpiMolDivide(void){
1364	>	int i, j, k;
1365	>	int localMol, allMol;
1366	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	>	int local_rigid;
1368	>	vector<int> globalMolIndex;
1369	>
1370	>	mpiSim = new mpiSimulation(info);
1371	>
1372	>	mpiSim->divideLabor();
1373	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1374	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1375	>
1376	>	// set up the local variables
1377	>
1378	>	mol2proc = mpiSim->getMolToProcMap();
1379	>	molCompType = mpiSim->getMolComponentType();
1380	>
1381	>	allMol = 0;
1382	>	localMol = 0;
1383	>	local_atoms = 0;
1384	>	local_bonds = 0;
1385	>	local_bends = 0;
1386	>	local_torsions = 0;
1387	>	local_rigid = 0;
1388	>	globalAtomCounter = 0;
1389	>
1390	>	for (i = 0; i < n_components; i++){
1391	>	for (j = 0; j < components_nmol[i]; j++){
1392	>	if (mol2proc[allMol] == worldRank){
1393	>	local_atoms += comp_stamps[i]->getNAtoms();
1394	>	local_bonds += comp_stamps[i]->getNBonds();
1395	>	local_bends += comp_stamps[i]->getNBends();
1396	>	local_torsions += comp_stamps[i]->getNTorsions();
1397	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1398	>	localMol++;
1399	>	}
1400	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1401	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1402	>	globalAtomCounter++;
1403	>	}
1404	>
1405	>	allMol++;
1406	>	}
1407	>	}
1408	>	local_SRI = local_bonds + local_bends + local_torsions;
1409	>
1410	>	info[0].n_atoms = mpiSim->getMyNlocal();
1411	>
1412	>
1413	>	if (local_atoms != info[0].n_atoms){
1414	>	sprintf(painCave.errMsg,
1415	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1416	>	"\tlocalAtom (%d) are not equal.\n",
1417	>	info[0].n_atoms, local_atoms);
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	info[0].n_bonds = local_bonds;
1423	>	info[0].n_bends = local_bends;
1424	>	info[0].n_torsions = local_torsions;
1425	>	info[0].n_SRI = local_SRI;
1426	>	info[0].n_mol = localMol;
1427	>
1428	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1429	>	MPIcheckPoint();
1430	>	}
1431	>
1432	>	#endif // is_mpi
1433	>
1434	>
1435	>	void SimSetup::makeSysArrays(void){
1436	>
1437	>	#ifndef IS_MPI
1438	>	int k, j;
1439	>	#endif // is_mpi
1440	>	int i, l;
1441	>
1442	>	Atom** the_atoms;
1443	>	Molecule* the_molecules;
1444	>
1445	>	for (l = 0; l < nInfo; l++){
1446	>	// create the atom and short range interaction arrays
1447	>
1448	>	the_atoms = new Atom * [info[l].n_atoms];
1449	>	the_molecules = new Molecule[info[l].n_mol];
1450	>	int molIndex;
1451	>
1452	>	// initialize the molecule's stampID's
1453	>
1454	>	#ifdef IS_MPI
1455	>
1456	>
1457	>	molIndex = 0;
1458	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1459	>	if (mol2proc[i] == worldRank){
1460	>	the_molecules[molIndex].setStampID(molCompType[i]);
1461	>	the_molecules[molIndex].setMyIndex(molIndex);
1462	>	the_molecules[molIndex].setGlobalIndex(i);
1463	>	molIndex++;
1464	>	}
1465	>	}
1466	>
1467	>	#else // is_mpi
1468	>
1469	>	molIndex = 0;
1470	>	globalAtomCounter = 0;
1471	>	for (i = 0; i < n_components; i++){
1472	>	for (j = 0; j < components_nmol[i]; j++){
1473	>	the_molecules[molIndex].setStampID(i);
1474	>	the_molecules[molIndex].setMyIndex(molIndex);
1475	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1476	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1477	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1478	>	globalAtomCounter++;
1479	>	}
1480	>	molIndex++;
1481	>	}
1482	>	}
1483	>
1484	>
1485	>	#endif // is_mpi
1486	>
1487	>	info[l].globalExcludes = new int;
1488	>	info[l].globalExcludes[0] = 0;
1489	>
1490	>	// set the arrays into the SimInfo object
1491	>
1492	>	info[l].atoms = the_atoms;
1493	>	info[l].molecules = the_molecules;
1494	>	info[l].nGlobalExcludes = 0;
1495	>
1496	>	the_ff->setSimInfo(info);
1497		}
1498		}
1499	+
1500	+	void SimSetup::makeIntegrator(void){
1501	+	int k;
1502	+
1503	+	NVE<RealIntegrator>* myNVE = NULL;
1504	+	NVT<RealIntegrator>* myNVT = NULL;
1505	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1506	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1507	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1508	+
1509	+	for (k = 0; k < nInfo; k++){
1510	+	switch (ensembleCase){
1511	+	case NVE_ENS:
1512	+	if (globals->haveZconstraints()){
1513	+	setupZConstraint(info[k]);
1514	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1515	+	}
1516	+	else{
1517	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1518	+	}
1519	+
1520	+	info->the_integrator = myNVE;
1521	+	break;
1522	+
1523	+	case NVT_ENS:
1524	+	if (globals->haveZconstraints()){
1525	+	setupZConstraint(info[k]);
1526	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1527	+	}
1528	+	else
1529	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1530	+
1531	+	myNVT->setTargetTemp(globals->getTargetTemp());
1532	+
1533	+	if (globals->haveTauThermostat())
1534	+	myNVT->setTauThermostat(globals->getTauThermostat());
1535	+	else{
1536	+	sprintf(painCave.errMsg,
1537	+	"SimSetup error: If you use the NVT\n"
1538	+	"\tensemble, you must set tauThermostat.\n");
1539	+	painCave.isFatal = 1;
1540	+	simError();
1541	+	}
1542	+
1543	+	info->the_integrator = myNVT;
1544	+	break;
1545	+
1546	+	case NPTi_ENS:
1547	+	if (globals->haveZconstraints()){
1548	+	setupZConstraint(info[k]);
1549	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1550	+	}
1551	+	else
1552	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1553	+
1554	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1555	+
1556	+	if (globals->haveTargetPressure())
1557	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1558	+	else{
1559	+	sprintf(painCave.errMsg,
1560	+	"SimSetup error: If you use a constant pressure\n"
1561	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1562	+	painCave.isFatal = 1;
1563	+	simError();
1564	+	}
1565	+
1566	+	if (globals->haveTauThermostat())
1567	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1568	+	else{
1569	+	sprintf(painCave.errMsg,
1570	+	"SimSetup error: If you use an NPT\n"
1571	+	"\tensemble, you must set tauThermostat.\n");
1572	+	painCave.isFatal = 1;
1573	+	simError();
1574	+	}
1575	+
1576	+	if (globals->haveTauBarostat())
1577	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1578	+	else{
1579	+	sprintf(painCave.errMsg,
1580	+	"SimSetup error: If you use an NPT\n"
1581	+	"\tensemble, you must set tauBarostat.\n");
1582	+	painCave.isFatal = 1;
1583	+	simError();
1584	+	}
1585	+
1586	+	info->the_integrator = myNPTi;
1587	+	break;
1588	+
1589	+	case NPTf_ENS:
1590	+	if (globals->haveZconstraints()){
1591	+	setupZConstraint(info[k]);
1592	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1593	+	}
1594	+	else
1595	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1596	+
1597	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1598	+
1599	+	if (globals->haveTargetPressure())
1600	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1601	+	else{
1602	+	sprintf(painCave.errMsg,
1603	+	"SimSetup error: If you use a constant pressure\n"
1604	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1605	+	painCave.isFatal = 1;
1606	+	simError();
1607	+	}
1608	+
1609	+	if (globals->haveTauThermostat())
1610	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1611	+
1612	+	else{
1613	+	sprintf(painCave.errMsg,
1614	+	"SimSetup error: If you use an NPT\n"
1615	+	"\tensemble, you must set tauThermostat.\n");
1616	+	painCave.isFatal = 1;
1617	+	simError();
1618	+	}
1619	+
1620	+	if (globals->haveTauBarostat())
1621	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1622	+
1623	+	else{
1624	+	sprintf(painCave.errMsg,
1625	+	"SimSetup error: If you use an NPT\n"
1626	+	"\tensemble, you must set tauBarostat.\n");
1627	+	painCave.isFatal = 1;
1628	+	simError();
1629	+	}
1630	+
1631	+	info->the_integrator = myNPTf;
1632	+	break;
1633	+
1634	+	case NPTxyz_ENS:
1635	+	if (globals->haveZconstraints()){
1636	+	setupZConstraint(info[k]);
1637	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1638	+	}
1639	+	else
1640	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1641	+
1642	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1643	+
1644	+	if (globals->haveTargetPressure())
1645	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1646	+	else{
1647	+	sprintf(painCave.errMsg,
1648	+	"SimSetup error: If you use a constant pressure\n"
1649	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1650	+	painCave.isFatal = 1;
1651	+	simError();
1652	+	}
1653	+
1654	+	if (globals->haveTauThermostat())
1655	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1656	+	else{
1657	+	sprintf(painCave.errMsg,
1658	+	"SimSetup error: If you use an NPT\n"
1659	+	"\tensemble, you must set tauThermostat.\n");
1660	+	painCave.isFatal = 1;
1661	+	simError();
1662	+	}
1663	+
1664	+	if (globals->haveTauBarostat())
1665	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1666	+	else{
1667	+	sprintf(painCave.errMsg,
1668	+	"SimSetup error: If you use an NPT\n"
1669	+	"\tensemble, you must set tauBarostat.\n");
1670	+	painCave.isFatal = 1;
1671	+	simError();
1672	+	}
1673	+
1674	+	info->the_integrator = myNPTxyz;
1675	+	break;
1676	+
1677	+	default:
1678	+	sprintf(painCave.errMsg,
1679	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1680	+	painCave.isFatal = 1;
1681	+	simError();
1682	+	}
1683	+	}
1684	+	}
1685	+
1686	+	void SimSetup::initFortran(void){
1687	+	info[0].refreshSim();
1688	+
1689	+	if (!strcmp(info[0].mixingRule, "standard")){
1690	+	the_ff->initForceField(LB_MIXING_RULE);
1691	+	}
1692	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1693	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1694	+	}
1695	+	else{
1696	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1697	+	info[0].mixingRule);
1698	+	painCave.isFatal = 1;
1699	+	simError();
1700	+	}
1701	+
1702	+
1703	+	#ifdef IS_MPI
1704	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1705	+	MPIcheckPoint();
1706	+	#endif // is_mpi
1707	+	}
1708	+
1709	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1710	+	int nZConstraints;
1711	+	ZconStamp** zconStamp;
1712	+
1713	+	if (globals->haveZconstraintTime()){
1714	+	//add sample time of z-constraint  into SimInfo's property list
1715	+	DoubleData* zconsTimeProp = new DoubleData();
1716	+	zconsTimeProp->setID(ZCONSTIME_ID);
1717	+	zconsTimeProp->setData(globals->getZconsTime());
1718	+	theInfo.addProperty(zconsTimeProp);
1719	+	}
1720	+	else{
1721	+	sprintf(painCave.errMsg,
1722	+	"ZConstraint error: If you use a ZConstraint,\n"
1723	+	"\tyou must set zconsTime.\n");
1724	+	painCave.isFatal = 1;
1725	+	simError();
1726	+	}
1727	+
1728	+	//push zconsTol into siminfo, if user does not specify
1729	+	//value for zconsTol, a default value will be used
1730	+	DoubleData* zconsTol = new DoubleData();
1731	+	zconsTol->setID(ZCONSTOL_ID);
1732	+	if (globals->haveZconsTol()){
1733	+	zconsTol->setData(globals->getZconsTol());
1734	+	}
1735	+	else{
1736	+	double defaultZConsTol = 0.01;
1737	+	sprintf(painCave.errMsg,
1738	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1739	+	"\tOOPSE will use a default value of %f.\n"
1740	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1741	+	defaultZConsTol);
1742	+	painCave.isFatal = 0;
1743	+	simError();
1744	+
1745	+	zconsTol->setData(defaultZConsTol);
1746	+	}
1747	+	theInfo.addProperty(zconsTol);
1748	+
1749	+	//set Force Subtraction Policy
1750	+	StringData* zconsForcePolicy = new StringData();
1751	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1752	+
1753	+	if (globals->haveZconsForcePolicy()){
1754	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1755	+	}
1756	+	else{
1757	+	sprintf(painCave.errMsg,
1758	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1759	+	"\tOOPSE will use PolicyByMass.\n"
1760	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1761	+	painCave.isFatal = 0;
1762	+	simError();
1763	+	zconsForcePolicy->setData("BYMASS");
1764	+	}
1765	+
1766	+	theInfo.addProperty(zconsForcePolicy);
1767	+
1768	+	//set zcons gap
1769	+	DoubleData* zconsGap = new DoubleData();
1770	+	zconsGap->setID(ZCONSGAP_ID);
1771	+
1772	+	if (globals->haveZConsGap()){
1773	+	zconsGap->setData(globals->getZconsGap());
1774	+	theInfo.addProperty(zconsGap);
1775	+	}
1776	+
1777	+	//set zcons fixtime
1778	+	DoubleData* zconsFixtime = new DoubleData();
1779	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1780	+
1781	+	if (globals->haveZConsFixTime()){
1782	+	zconsFixtime->setData(globals->getZconsFixtime());
1783	+	theInfo.addProperty(zconsFixtime);
1784	+	}
1785	+
1786	+	//set zconsUsingSMD
1787	+	IntData* zconsUsingSMD = new IntData();
1788	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1789	+
1790	+	if (globals->haveZConsUsingSMD()){
1791	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1792	+	theInfo.addProperty(zconsUsingSMD);
1793	+	}
1794	+
1795	+	//Determine the name of ouput file and add it into SimInfo's property list
1796	+	//Be careful, do not use inFileName, since it is a pointer which
1797	+	//point to a string at master node, and slave nodes do not contain that string
1798	+
1799	+	string zconsOutput(theInfo.finalName);
1800	+
1801	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1802	+
1803	+	StringData* zconsFilename = new StringData();
1804	+	zconsFilename->setID(ZCONSFILENAME_ID);
1805	+	zconsFilename->setData(zconsOutput);
1806	+
1807	+	theInfo.addProperty(zconsFilename);
1808	+
1809	+	//setup index, pos and other parameters of z-constraint molecules
1810	+	nZConstraints = globals->getNzConstraints();
1811	+	theInfo.nZconstraints = nZConstraints;
1812	+
1813	+	zconStamp = globals->getZconStamp();
1814	+	ZConsParaItem tempParaItem;
1815	+
1816	+	ZConsParaData* zconsParaData = new ZConsParaData();
1817	+	zconsParaData->setID(ZCONSPARADATA_ID);
1818	+
1819	+	for (int i = 0; i < nZConstraints; i++){
1820	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1821	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1822	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1823	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1824	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1825	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1826	+	zconsParaData->addItem(tempParaItem);
1827	+	}
1828	+
1829	+	//check the uniqueness of index
1830	+	if(!zconsParaData->isIndexUnique()){
1831	+	sprintf(painCave.errMsg,
1832	+	"ZConstraint Error: molIndex is not unique!\n");
1833	+	painCave.isFatal = 1;
1834	+	simError();
1835	+	}
1836	+
1837	+	//sort the parameters by index of molecules
1838	+	zconsParaData->sortByIndex();
1839	+
1840	+	//push data into siminfo, therefore, we can retrieve later
1841	+	theInfo.addProperty(zconsParaData);
1842	+	}
1843	+
1844	+	void SimSetup::makeMinimizer(){
1845	+
1846	+	OOPSEMinimizer* myOOPSEMinimizer;
1847	+	MinimizerParameterSet* param;
1848	+	char minimizerName[100];
1849	+
1850	+	for (int i = 0; i < nInfo; i++){
1851	+
1852	+	//prepare parameter set for minimizer
1853	+	param = new MinimizerParameterSet();
1854	+	param->setDefaultParameter();
1855	+
1856	+	if (globals->haveMinimizer()){
1857	+	param->setFTol(globals->getMinFTol());
1858	+	}
1859	+
1860	+	if (globals->haveMinGTol()){
1861	+	param->setGTol(globals->getMinGTol());
1862	+	}
1863	+
1864	+	if (globals->haveMinMaxIter()){
1865	+	param->setMaxIteration(globals->getMinMaxIter());
1866	+	}
1867	+
1868	+	if (globals->haveMinWriteFrq()){
1869	+	param->setMaxIteration(globals->getMinMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinWriteFrq()){
1873	+	param->setWriteFrq(globals->getMinWriteFrq());
1874	+	}
1875	+
1876	+	if (globals->haveMinStepSize()){
1877	+	param->setStepSize(globals->getMinStepSize());
1878	+	}
1879	+
1880	+	if (globals->haveMinLSMaxIter()){
1881	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1882	+	}
1883	+
1884	+	if (globals->haveMinLSTol()){
1885	+	param->setLineSearchTol(globals->getMinLSTol());
1886	+	}
1887	+
1888	+	strcpy(minimizerName, globals->getMinimizer());
1889	+
1890	+	if (!strcasecmp(minimizerName, "CG")){
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	else if (!strcasecmp(minimizerName, "SD")){
1894	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1895	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1896	+	}
1897	+	else{
1898	+	sprintf(painCave.errMsg,
1899	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1900	+	painCave.isFatal = 0;
1901	+	simError();
1902	+
1903	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1904	+	}
1905	+	info[i].the_integrator = myOOPSEMinimizer;
1906	+
1907	+	//store the minimizer into simInfo
1908	+	info[i].the_minimizer = myOOPSEMinimizer;
1909	+	info[i].has_minimizer = true;
1910	+	}
1911	+
1912	+	}

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