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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 429 by mmeineke, Thu Mar 27 21:52:21 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 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_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
138	>	// initialize the system coordinates
139
140	<	#ifdef IS_MPI
141	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#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
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
155	>	// initialize the Fortran
156
157	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// 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() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
166	>	}
167
129	–	tot_nmol += the_components[i]->getNMol();
130	–	components_nmol[i] = the_components[i]->getNMol();
131	–	}
132	–	}
133	–	else{
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error.\n"
136	–	"\tSorry, the ability to specify total"
137	–	" nMols and then give molfractions in the components\n"
138	–	"\tis not currently supported."
139	–	" Please give nMol in the components.\n" );
140	–	painCave.isFatal = 1;
141	–	simError();
142	–
143	–
144	–	//     tot_nmol = the_globals->getNMol();
145	–
146	–	//   //we have the total number of molecules, now we check for molfractions
147	–	//     for( i=0; i<n_components; i++ ){
148	–
149	–	//       if( !the_components[i]->haveMolFraction() ){
150	–
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
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;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
191	>	set<int> skipList;
192
193	<	id = the_components[i]->getType();
194	<	comp_stamps[i] = NULL;
195	<
179	<	// 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 );
182	<	if( comp_stamps[i] == NULL ){
183	<
184	<	// extract the component from the list;
185	<
186	<	currentStamp = the_stamps->extractMolStamp( id );
187	<	if( currentStamp == NULL ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: Component \"%s\" was not found in the "
190	<	"list of declared molecules\n",
191	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
197	>	//init the forceField paramters
198
199	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
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;
212	<	tot_bonds = 0;
213	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
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	<
239	<
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
246	<
247	<	int localMol, allMol;
248	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
249	<
250	<	int* mol2proc = mpiSim->getMolToProcMap();
251	<	int* molCompType = mpiSim->getMolComponentType();
252	<
253	<	allMol = 0;
254	<	localMol = 0;
255	<	local_atoms = 0;
256	<	local_bonds = 0;
257	<	local_bends = 0;
258	<	local_torsions = 0;
259	<	for( i=0; i<n_components; i++ ){
260	<
261	<	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( mol2proc[j] == worldRank ){
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 not 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];
263	<	int molIndex;
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	<	// initialize the molecule's stampID's
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
267	+	}
268	+
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
312	–
271
272	<	molIndex = 0;
315	<	for(i=0; i<mpiSim->getTotNmol(); i++){
316	<
317	<	if(mol2proc[i] == worldRank ){
318	<	the_molecules[molIndex].setStampID( molCompType[i] );
319	<	molIndex++;
320	<	}
321	<	}
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
323	–	#else // is_mpi
324	–
325	–	molIndex = 0;
326	–	for(i=0; i<n_components; i++){
327	–	for(j=0; j<components_nmol[i]; j++ ){
328	–	the_molecules[molIndex].setStampID( i );
329	–	molIndex++;
330	–	}
331	–	}
332	–
333	–
274		#endif // is_mpi
275	+	}
276
277	+	// make the bonds
278	+	for (j = 0; j < molInfo.nBonds; j++){
279	+	currentBond = comp_stamps[stampID]->getBond(j);
280	+	theBonds[j].a = currentBond->getA() + atomOffset;
281	+	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<	if( simnfo->n_SRI ){
284	<	Exclude::createArray(simnfo->n_SRI);
339	<	the_excludes = new Exclude*[simnfo->n_SRI];
340	<	simnfo->globalExcludes = new int;
341	<	simnfo->n_exclude = tot_SRI;
342	<	}
343	<	else{
344	<
345	<	Exclude::createArray( 1 );
346	<	the_excludes = new Exclude*;
347	<	the_excludes[0] = new Exclude(0);
348	<	the_excludes[0]->setPair( 0,0 );
349	<	simnfo->globalExcludes = new int;
350	<	simnfo->globalExcludes[0] = 0;
351	<	simnfo->n_exclude = 0;
352	<	}
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
286	<	// set the arrays into the SimInfo object
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	simnfo->atoms = the_atoms;
295	<	simnfo->molecules = the_molecules;
358	<	simnfo->nGlobalExcludes = 0;
359	<	simnfo->excludes = the_excludes;
294	>	info[k].excludes->addPair(exI, exJ);
295	>	}
296
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	<	// get some of the tricky things that may still be in the globals
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<
309	<	if( the_globals->haveBox() ){
310	<	simnfo->box_x = the_globals->getBox();
311	<	simnfo->box_y = the_globals->getBox();
312	<	simnfo->box_z = the_globals->getBox();
313	<	}
314	<	else if( the_globals->haveDensity() ){
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	<	double vol;
317	<	vol = (double)tot_nmol / the_globals->getDensity();
318	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
319	<	simnfo->box_y = simnfo->box_x;
320	<	simnfo->box_z = simnfo->box_x;
377	<	}
378	<	else{
379	<	if( !the_globals->haveBoxX() ){
380	<	sprintf( painCave.errMsg,
381	<	"SimSetup error, no periodic BoxX size given.\n" );
382	<	painCave.isFatal = 1;
383	<	simError();
384	<	}
385	<	simnfo->box_x = the_globals->getBoxX();
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	if( !the_globals->haveBoxY() ){
323	<	sprintf( painCave.errMsg,
324	<	"SimSetup error, no periodic BoxY size given.\n" );
325	<	painCave.isFatal = 1;
326	<	simError();
327	<	}
328	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
342	<	sprintf( painCave.errMsg,
343	<	"SimSetup error, no periodic BoxZ size given.\n" );
398	<	painCave.isFatal = 1;
399	<	simError();
400	<	}
401	<	simnfo->box_z = the_globals->getBoxZ();
402	<	}
341	>	current_extra = current_extra->getNext();
342	>	}
343	>	}
344
345	+	if (theBends[j].isGhost) {
346	+
347	+	tempI = theBends[j].a;
348	+	tempJ = theBends[j].b;
349	+
350		#ifdef IS_MPI
351	<	strcpy( checkPointMsg, "Box size set up" );
352	<	MPIcheckPoint();
353	<	#endif // is_mpi
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	+	} else {
360
361	<	// initialize the arrays
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379	>	}
380
381	<	the_ff->setSimInfo( simnfo );
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	<	makeMolecules();
389	<	simnfo->identArray = new int[simnfo->n_atoms];
390	<	for(i=0; i<simnfo->n_atoms; i++){
391	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
418	<	}
419	<
420	<	if (the_globals->getUseRF() ) {
421	<	simnfo->useReactionField = 1;
422	<
423	<	if( !the_globals->haveECR() ){
424	<	sprintf( painCave.errMsg,
425	<	"SimSetup Warning: using default value of 1/2 the smallest "
426	<	"box length for the electrostaticCutoffRadius.\n"
427	<	"I hope you have a very fast processor!\n");
428	<	painCave.isFatal = 0;
429	<	simError();
430	<	double smallest;
431	<	smallest = simnfo->box_x;
432	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
433	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
434	<	simnfo->ecr = 0.5 * smallest;
435	<	} else {
436	<	simnfo->ecr        = the_globals->getECR();
437	<	}
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392
393	<	if( !the_globals->haveEST() ){
394	<	sprintf( painCave.errMsg,
395	<	"SimSetup Warning: using default value of 0.05 * the "
396	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
397	<	);
398	<	painCave.isFatal = 0;
399	<	simError();
400	<	simnfo->est = 0.05 * simnfo->ecr;
401	<	} else {
402	<	simnfo->est        = the_globals->getEST();
403	<	}
404	<
405	<	if(!the_globals->haveDielectric() ){
406	<	sprintf( painCave.errMsg,
407	<	"SimSetup Error: You are trying to use Reaction Field without"
408	<	"setting a dielectric constant!\n"
409	<	);
410	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
459	<	simnfo->dielectric = the_globals->getDielectric();
460	<	} else {
461	<	if (simnfo->n_dipoles) {
462	<
463	<	if( !the_globals->haveECR() ){
464	<	sprintf( painCave.errMsg,
465	<	"SimSetup Warning: using default value of 1/2 the smallest"
466	<	"box length for the electrostaticCutoffRadius.\n"
467	<	"I hope you have a very fast processor!\n");
468	<	painCave.isFatal = 0;
469	<	simError();
470	<	double smallest;
471	<	smallest = simnfo->box_x;
472	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
473	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
474	<	simnfo->ecr = 0.5 * smallest;
475	<	} else {
476	<	simnfo->ecr        = the_globals->getECR();
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404	>
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411		}
412	+
413
414	<	if( !the_globals->haveEST() ){
415	<	sprintf( painCave.errMsg,
416	<	"SimSetup Warning: using default value of 5% of the"
482	<	"electrostaticCutoffRadius for the "
483	<	"electrostaticSkinThickness\n"
484	<	);
485	<	painCave.isFatal = 0;
486	<	simError();
487	<	simnfo->est = 0.05 * simnfo->ecr;
488	<	} else {
489	<	simnfo->est        = the_globals->getEST();
490	<	}
491	<	}
492	<	}
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	<	#ifdef IS_MPI
419	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
496	<	MPIcheckPoint();
497	<	#endif // is_mpi
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420
421	<	if( the_globals->haveInitialConfig() ){
500	<
501	<	InitializeFromFile* fileInit;
502	<	#ifdef IS_MPI // is_mpi
503	<	if( worldRank == 0 ){
504	<	#endif //is_mpi
505	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
506	<	#ifdef IS_MPI
507	<	}else fileInit = new InitializeFromFile( NULL );
508	<	#endif
509	<	fileInit->read_xyz( simnfo ); // default velocities on
421	>	// Create the Rigid Body:
422
423	<	delete fileInit;
512	<	}
513	<	else{
423	>	myRB = new RigidBody();
424
425	<	#ifdef IS_MPI
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429
430	<	// no init from bass
431	<
519	<	sprintf( painCave.errMsg,
520	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
521	<	painCave.isFatal;
522	<	simError();
523	<
524	<	#else
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432
433	<	initFromBass();
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435
436	+	// currentAtom is the AtomStamp (which we need for
437	+	// rigid body reference positions)
438	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
439
440	<	#endif
441	<	}
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	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
448	<	MPIcheckPoint();
449	<	#endif // is_mpi
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	+	molInfo.myRigidBodies.push_back(myRB);
480	+	info[k].rigidBodies.push_back(myRB);
481	+	}
482	+
483
484	<
485	<
540	<
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486
487	<
487	>	molInfo.myIntegrableObjects.clear();
488	>
489	>
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491	>
492		#ifdef IS_MPI
493	<	if( worldRank == 0 ){
494	<	#endif // is_mpi
495	<
496	<	if( the_globals->haveFinalConfig() ){
497	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
498	<	}
499	<	else{
500	<	strcpy( simnfo->finalName, inFileName );
501	<	char* endTest;
502	<	int nameLength = strlen( simnfo->finalName );
503	<	endTest = &(simnfo->finalName[nameLength - 5]);
504	<	if( !strcmp( endTest, ".bass" ) ){
556	<	strcpy( endTest, ".eor" );
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	<	else if( !strcmp( endTest, ".BASS" ) ){
507	<	strcpy( endTest, ".eor" );
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		}
561	–	else{
562	–	endTest = &(simnfo->finalName[nameLength - 4]);
563	–	if( !strcmp( endTest, ".bss" ) ){
564	–	strcpy( endTest, ".eor" );
565	–	}
566	–	else if( !strcmp( endTest, ".mdl" ) ){
567	–	strcpy( endTest, ".eor" );
568	–	}
569	–	else{
570	–	strcat( simnfo->finalName, ".eor" );
571	–	}
572	–	}
573	–	}
514
515	<	// make the sample and status out names
516	<
517	<	strcpy( simnfo->sampleName, inFileName );
518	<	char* endTest;
519	<	int nameLength = strlen( simnfo->sampleName );
520	<	endTest = &(simnfo->sampleName[nameLength - 5]);
521	<	if( !strcmp( endTest, ".bass" ) ){
522	<	strcpy( endTest, ".dump" );
523	<	}
524	<	else if( !strcmp( endTest, ".BASS" ) ){
525	<	strcpy( endTest, ".dump" );
526	<	}
527	<	else{
528	<	endTest = &(simnfo->sampleName[nameLength - 4]);
529	<	if( !strcmp( endTest, ".bss" ) ){
530	<	strcpy( endTest, ".dump" );
531	<	}
592	<	else if( !strcmp( endTest, ".mdl" ) ){
593	<	strcpy( endTest, ".dump" );
594	<	}
595	<	else{
596	<	strcat( simnfo->sampleName, ".dump" );
597	<	}
598	<	}
599	<
600	<	strcpy( simnfo->statusName, inFileName );
601	<	nameLength = strlen( simnfo->statusName );
602	<	endTest = &(simnfo->statusName[nameLength - 5]);
603	<	if( !strcmp( endTest, ".bass" ) ){
604	<	strcpy( endTest, ".stat" );
605	<	}
606	<	else if( !strcmp( endTest, ".BASS" ) ){
607	<	strcpy( endTest, ".stat" );
608	<	}
609	<	else{
610	<	endTest = &(simnfo->statusName[nameLength - 4]);
611	<	if( !strcmp( endTest, ".bss" ) ){
612	<	strcpy( endTest, ".stat" );
613	<	}
614	<	else if( !strcmp( endTest, ".mdl" ) ){
615	<	strcpy( endTest, ".stat" );
616	<	}
617	<	else{
618	<	strcat( simnfo->statusName, ".stat" );
619	<	}
620	<	}
621	<
622	<	#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
625	–
626	–	// set the status, sample, and themal kick times
627	–
628	–	if( the_globals->haveSampleTime() ){
629	–	simnfo->sampleTime = the_globals->getSampleTime();
630	–	simnfo->statusTime = simnfo->sampleTime;
631	–	simnfo->thermalTime = simnfo->sampleTime;
632	–	}
633	–	else{
634	–	simnfo->sampleTime = the_globals->getRunTime();
635	–	simnfo->statusTime = simnfo->sampleTime;
636	–	simnfo->thermalTime = simnfo->sampleTime;
637	–	}
538
539	<	if( the_globals->haveStatusTime() ){
640	<	simnfo->statusTime = the_globals->getStatusTime();
641	<	}
539	>	// clean up the forcefield
540
541	<	if( the_globals->haveThermalTime() ){
644	<	simnfo->thermalTime = the_globals->getThermalTime();
645	<	}
541	>	if (!globals->haveLJrcut()){
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->getLJrcut() );
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_Ex" ) ) new Symplectic( simnfo, the_ff );
568	<	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		}
668	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
669	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
670	–	}
592		else{
593	<	sprintf( painCave.errMsg,
594	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
595	<	simnfo->mixingRule );
596	<	painCave.isFatal = 1;
676	<	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();
684	<	#endif // is_mpi
685	<	}
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;
694	<	LinkedAssign* current_extra;
695	<	AtomStamp* currentAtom;
696	<	BondStamp* currentBond;
697	<	BendStamp* currentBend;
698	<	TorsionStamp* currentTorsion;
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614	>	}
615	>	}
616	>	}
617
618	<	bond_pair* theBonds;
619	<	bend_set* theBends;
702	<	torsion_set* theTorsions;
618	>	if (have_extra){
619	>	done = 0;
620
621	<
622	<	//init the forceField paramters
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	<	the_ff->readParams();
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	<
639	<	// init the atoms
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	<	double ux, uy, uz, u, uSqr;
645	<
646	<	atomOffset = 0;
647	<	excludeOffset = 0;
648	<	for(i=0; i<simnfo->n_mol; i++){
717	<
718	<	stampID = the_molecules[i].getStampID();
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	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
651	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
652	<	info.nBends    = comp_stamps[stampID]->getNBends();
653	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
654	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
655	<
726	<	info.myAtoms = &the_atoms[atomOffset];
727	<	info.myExcludes = &the_excludes[excludeOffset];
728	<	info.myBonds = new Bond*[info.nBonds];
729	<	info.myBends = new Bend*[info.nBends];
730	<	info.myTorsions = new Torsion*[info.nTorsions];
731	<
732	<	theBonds = new bond_pair[info.nBonds];
733	<	theBends = new bend_set[info.nBends];
734	<	theTorsions = new torsion_set[info.nTorsions];
735	<
736	<	// make the Atoms
737	<
738	<	for(j=0; j<info.nAtoms; j++){
739	<
740	<	currentAtom = comp_stamps[stampID]->getAtom( j );
741	<	if( currentAtom->haveOrientation() ){
742	<
743	<	dAtom = new DirectionalAtom(j + atomOffset);
744	<	simnfo->n_oriented++;
745	<	info.myAtoms[j] = dAtom;
746	<
747	<	ux = currentAtom->getOrntX();
748	<	uy = currentAtom->getOrntY();
749	<	uz = currentAtom->getOrntZ();
750	<
751	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
752	<
753	<	u = sqrt( uSqr );
754	<	ux = ux / u;
755	<	uy = uy / u;
756	<	uz = uz / u;
757	<
758	<	dAtom->setSUx( ux );
759	<	dAtom->setSUy( uy );
760	<	dAtom->setSUz( uz );
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657	<	else{
658	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
764	<	}
765	<	info.myAtoms[j]->setType( currentAtom->getType() );
766	<
767	<	#ifdef IS_MPI
768	<
769	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
770	<
771	<	#endif // is_mpi
772	<	}
773	<
774	<	// make the bonds
775	<	for(j=0; j<info.nBonds; j++){
776	<
777	<	currentBond = comp_stamps[stampID]->getBond( j );
778	<	theBonds[j].a = currentBond->getA() + atomOffset;
779	<	theBonds[j].b = currentBond->getB() + atomOffset;
657	>	}
658	>	}
659
660	<	exI = theBonds[i].a;
661	<	exJ = theBonds[i].b;
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662	>	}
663	>	}
664
665	<	// exclude_I must always be the smaller of the pair
666	<	if( exI > exJ ){
667	<	tempEx = exI;
668	<	exI = exJ;
669	<	exJ = tempEx;
670	<	}
790	<	#ifdef IS_MPI
791	<	tempEx = exI;
792	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
793	<	tempEx = exJ;
794	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
795	<
796	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
797	<	#else  // isn't MPI
798	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
799	<	#endif  //is_mpi
800	<	}
801	<	excludeOffset += info.nBonds;
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	<	//make the bends
673	<	for(j=0; j<info.nBends; j++){
674	<
675	<	currentBend = comp_stamps[stampID]->getBend( j );
676	<	theBends[j].a = currentBend->getA() + atomOffset;
677	<	theBends[j].b = currentBend->getB() + atomOffset;
678	<	theBends[j].c = currentBend->getC() + atomOffset;
679	<
680	<	if( currentBend->haveExtras() ){
681	<
682	<	extras = currentBend->getExtras();
814	<	current_extra = extras;
815	<
816	<	while( current_extra != NULL ){
817	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
818	<
819	<	switch( current_extra->getType() ){
820	<
821	<	case 0:
822	<	theBends[j].ghost =
823	<	current_extra->getInt() + atomOffset;
824	<	theBends[j].isGhost = 1;
825	<	break;
826	<
827	<	case 1:
828	<	theBends[j].ghost =
829	<	(int)current_extra->getDouble() + atomOffset;
830	<	theBends[j].isGhost = 1;
831	<	break;
832	<
833	<	default:
834	<	sprintf( painCave.errMsg,
835	<	"SimSetup Error: ghostVectorSource was neiter a "
836	<	"double nor an int.\n"
837	<	"-->Bend[%d] in %s\n",
838	<	j, comp_stamps[stampID]->getID() );
839	<	painCave.isFatal = 1;
840	<	simError();
841	<	}
842	<	}
843	<
844	<	else{
845	<
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Error: unhandled bend assignment:\n"
848	<	"    -->%s in Bend[%d] in %s\n",
849	<	current_extra->getlhs(),
850	<	j, comp_stamps[stampID]->getID() );
851	<	painCave.isFatal = 1;
852	<	simError();
853	<	}
854	<
855	<	current_extra = current_extra->getNext();
856	<	}
857	<	}
858	<
859	<	if( !theBends[j].isGhost ){
860	<
861	<	exI = theBends[j].a;
862	<	exJ = theBends[j].c;
863	<	}
864	<	else{
865	<
866	<	exI = theBends[j].a;
867	<	exJ = theBends[j].b;
868	<	}
869	<
870	<	// exclude_I must always be the smaller of the pair
871	<	if( exI > exJ ){
872	<	tempEx = exI;
873	<	exI = exJ;
874	<	exJ = tempEx;
875	<	}
876	<	#ifdef IS_MPI
877	<	tempEx = exI;
878	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
879	<	tempEx = exJ;
880	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
881	<
882	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
883	<	#else  // isn't MPI
884	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
885	<	#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		}
887	–	excludeOffset += info.nBends;
684
685	<	for(j=0; j<info.nTorsions; j++){
686	<
687	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
892	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
893	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
894	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
895	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
896	<
897	<	exI = theTorsions[j].a;
898	<	exJ = theTorsions[j].d;
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	// exclude_I must always be the smaller of the pair
901	<	if( exI > exJ ){
902	<	tempEx = exI;
903	<	exI = exJ;
904	<	exJ = tempEx;
905	<	}
906	<	#ifdef IS_MPI
907	<	tempEx = exI;
908	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
909	<	tempEx = exJ;
910	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
911	<
912	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
913	<	#else  // isn't MPI
914	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
915	<	#endif  //is_mpi
916	<	}
917	<	excludeOffset += info.nTorsions;
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<
692	<	// send the arrays off to the forceField for init.
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
695	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
696	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
925	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
694	>	rotMat[0][0] = 1.0;
695	>	rotMat[0][1] = 0.0;
696	>	rotMat[0][2] = 0.0;
697
698	+	rotMat[1][0] = 0.0;
699	+	rotMat[1][1] = 1.0;
700	+	rotMat[1][2] = 0.0;
701
702	<	the_molecules[i].initialize( info );
703	<	atomOffset += info.nAtoms;
704	<	delete[] theBonds;
705	<	delete[] theBends;
706	<	delete[] theTorsions;
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	<	// clean up the forcefield
713	<	the_ff->calcRcut();
714	<	the_ff->cleanMe();
712	>	current_mol++;
713	>	current_comp_mol++;
714	>
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716	>	current_comp_mol = 0;
717	>	current_comp++;
718	>	}
719		}
720
940	–	void SimSetup::initFromBass( void ){
721
722	<	int i, j, k;
723	<	int n_cells;
944	<	double cellx, celly, cellz;
945	<	double temp1, temp2, temp3;
946	<	int n_per_extra;
947	<	int n_extra;
948	<	int have_extra, done;
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725	<	temp1 = (double)tot_nmol / 4.0;
726	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
952	<	temp3 = ceil( temp2 );
725	>	ensembleCase = -1;
726	>	ffCase = -1;
727
728	<	have_extra =0;
955	<	if( temp2 < temp3 ){ // we have a non-complete lattice
956	<	have_extra =1;
728	>	// set the easy ones first
729
730	<	n_cells = (int)temp3 - 1;
731	<	cellx = simnfo->box_x / temp3;
732	<	celly = simnfo->box_y / temp3;
733	<	cellz = simnfo->box_z / temp3;
734	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
735	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
964	<	n_per_extra = (int)ceil( temp1 );
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
737	<	if( n_per_extra > 4){
738	<	sprintf( painCave.errMsg,
739	<	"SimSetup error. There has been an error in constructing"
740	<	" the non-complete lattice.\n" );
741	<	painCave.isFatal = 1;
742	<	simError();
743	<	}
737	>
738	>	// get the forceField
739	>
740	>	strcpy(force_field, globals->getForceField());
741	>
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	<	n_cells = (int)temp3;
756	<	cellx = simnfo->box_x / temp3;
757	<	celly = simnfo->box_y / temp3;
758	<	cellz = simnfo->box_z / temp3;
755	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	>	force_field);
757	>	painCave.isFatal = 1;
758	>	simError();
759		}
760
761	<	current_mol = 0;
982	<	current_comp_mol = 0;
983	<	current_comp = 0;
984	<	current_atom_ndx = 0;
761	>	// get the ensemble
762
763	<	for( i=0; i < n_cells ; i++ ){
987	<	for( j=0; j < n_cells; j++ ){
988	<	for( k=0; k < n_cells; k++ ){
763	>	strcpy(ensemble, globals->getEnsemble());
764
765	<	makeElement( i * cellx,
766	<	j * celly,
767	<	k * cellz );
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	<	makeElement( i * cellx + 0.5 * cellx,
792	<	j * celly + 0.5 * celly,
996	<	k * cellz );
791	>	for (i = 0; i < nInfo; i++){
792	>	strcpy(info[i].ensemble, ensemble);
793
794	<	makeElement( i * cellx,
999	<	j * celly + 0.5 * celly,
1000	<	k * cellz + 0.5 * cellz );
794	>	// get the mixing rule
795
796	<	makeElement( i * cellx + 0.5 * cellx,
797	<	j * celly,
798	<	k * cellz + 0.5 * cellz );
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797	>	info[i].usePBC = globals->getPBC();
798	>	}
799	>
800	>	// get the components and calculate the tot_nMol and indvidual n_mol
801	>
802	>	the_components = globals->getComponents();
803	>	components_nmol = new int[n_components];
804	>
805	>
806	>	if (!globals->haveNMol()){
807	>	// we don't have the total number of molecules, so we assume it is
808	>	// given in each component
809	>
810	>	tot_nmol = 0;
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819		}
820	+
821	+	tot_nmol += the_components[i]->getNMol();
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	<	if( have_extra ){
837	<	done = 0;
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	<	int start_ndx;
848	<	for( i=0; i < (n_cells+1) && !done; i++ ){
849	<	for( j=0; j < (n_cells+1) && !done; j++ ){
847	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	>	sprintf(painCave.errMsg,
849	>	"Status time is not divisible by dt.\n"
850	>	"\tThis will result in status reports that are not uniformly\n"
851	>	"\tdistributed in time.  If this is a problem, change \n"
852	>	"\tyour statusTime variable.\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	}
856
857	<	if( i < n_cells ){
857	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	>	sprintf(painCave.errMsg,
859	>	"Thermal time is not divisible by dt.\n"
860	>	"\tThis will result in thermalizations that are not uniformly\n"
861	>	"\tdistributed in time.  If this is a problem, change \n"
862	>	"\tyour thermalTime variable.\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	}
866
867	<	if( j < n_cells ){
868	<	start_ndx = n_cells;
869	<	}
870	<	else start_ndx = 0;
871	<	}
872	<	else start_ndx = 0;
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	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
877	>	// set the status, sample, and thermal kick times
878
879	<	makeElement( i * cellx,
880	<	j * celly,
881	<	k * cellz );
882	<	done = ( current_mol >= tot_nmol );
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	<	if( !done && n_per_extra > 1 ){
890	<	makeElement( i * cellx + 0.5 * cellx,
891	<	j * celly + 0.5 * celly,
1035	<	k * cellz );
1036	<	done = ( current_mol >= tot_nmol );
1037	<	}
889	>	if (globals->haveStatusTime()){
890	>	info[i].statusTime = globals->getStatusTime();
891	>	}
892
893	<	if( !done && n_per_extra > 2){
894	<	makeElement( i * cellx,
895	<	j * celly + 0.5 * celly,
896	<	k * cellz + 0.5 * cellz );
897	<	done = ( current_mol >= tot_nmol );
1044	<	}
893	>	if (globals->haveThermalTime()){
894	>	info[i].thermalTime = globals->getThermalTime();
895	>	} else {
896	>	info[i].thermalTime = globals->getRunTime();
897	>	}
898
899	<	if( !done && n_per_extra > 3){
900	<	makeElement( i * cellx + 0.5 * cellx,
901	<	j * celly,
902	<	k * cellz + 0.5 * cellz );
1050	<	done = ( current_mol >= tot_nmol );
1051	<	}
1052	<	}
1053	<	}
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903		}
904	+
905	+	// check for the temperature set flag
906	+
907	+	if (globals->haveTempSet())
908	+	info[i].setTemp = globals->getTempSet();
909	+
910	+	// 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	<	for( i=0; i<simnfo->n_atoms; i++ ){
924	<	simnfo->atoms[i]->set_vx( 0.0 );
925	<	simnfo->atoms[i]->set_vy( 0.0 );
926	<	simnfo->atoms[i]->set_vz( 0.0 );
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	>	//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	>	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
1065	–	void SimSetup::makeElement( double x, double y, double z ){
963
964	<	int k;
965	<	AtomStamp* current_atom;
966	<	DirectionalAtom* dAtom;
967	<	double rotMat[3][3];
964	>	void SimSetup::finalInfoCheck(void){
965	>	int index;
966	>	int usesDipoles;
967	>	int usesCharges;
968	>	int i;
969
970	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
970	>	for (i = 0; i < nInfo; i++){
971	>	// check electrostatic parameters
972
973	<	current_atom = comp_stamps[current_comp]->getAtom( k );
974	<	if( !current_atom->havePosition() ){
975	<	sprintf( painCave.errMsg,
976	<	"SimSetup:initFromBass error.\n"
977	<	"\tComponent %s, atom %s does not have a position specified.\n"
1079	<	"\tThe initialization routine is unable to give a start"
1080	<	" position.\n",
1081	<	comp_stamps[current_comp]->getID(),
1082	<	current_atom->getType() );
1083	<	painCave.isFatal = 1;
1084	<	simError();
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	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1088	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1089	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
990	>	double theEcr, theEst;
991
992	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
992	>	if (globals->getUseRF()){
993	>	info[i].useReactionField = 1;
994
995	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
995	>	if (!globals->haveECR()){
996	>	sprintf(painCave.errMsg,
997	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
998	>	"\tOOPSE will use a default value of 15.0 angstroms"
999	>	"\tfor the electrostaticCutoffRadius.\n");
1000	>	painCave.isFatal = 0;
1001	>	simError();
1002	>	theEcr = 15.0;
1003	>	}
1004	>	else{
1005	>	theEcr = globals->getECR();
1006	>	}
1007
1008	<	rotMat[0][0] = 1.0;
1009	<	rotMat[0][1] = 0.0;
1010	<	rotMat[0][2] = 0.0;
1008	>	if (!globals->haveEST()){
1009	>	sprintf(painCave.errMsg,
1010	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.05 * electrostaticCutoffRadius\n"
1013	>	"\tfor the electrostaticSkinThickness\n");
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	theEst = 0.05 * theEcr;
1017	>	}
1018	>	else{
1019	>	theEst = globals->getEST();
1020	>	}
1021
1022	<	rotMat[1][0] = 0.0;
1100	<	rotMat[1][1] = 1.0;
1101	<	rotMat[1][2] = 0.0;
1022	>	info[i].setDefaultEcr(theEcr, theEst);
1023
1024	<	rotMat[2][0] = 0.0;
1025	<	rotMat[2][1] = 0.0;
1026	<	rotMat[2][2] = 1.0;
1024	>	if (!globals->haveDielectric()){
1025	>	sprintf(painCave.errMsg,
1026	>	"SimSetup Error: No Dielectric constant was set.\n"
1027	>	"\tYou are trying to use Reaction Field without"
1028	>	"\tsetting a dielectric constant!\n");
1029	>	painCave.isFatal = 1;
1030	>	simError();
1031	>	}
1032	>	info[i].dielectric = globals->getDielectric();
1033	>	}
1034	>	else{
1035	>	if (usesDipoles || usesCharges){
1036	>	if (!globals->haveECR()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1039	>	"\tOOPSE will use a default value of 15.0 angstroms"
1040	>	"\tfor the electrostaticCutoffRadius.\n");
1041	>	painCave.isFatal = 0;
1042	>	simError();
1043	>	theEcr = 15.0;
1044	>	}
1045	>	else{
1046	>	theEcr = globals->getECR();
1047	>	}
1048	>
1049	>	if (!globals->haveEST()){
1050	>	sprintf(painCave.errMsg,
1051	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1052	>	"\tOOPSE will use a default value of\n"
1053	>	"\t0.05 * electrostaticCutoffRadius\n"
1054	>	"\tfor the electrostaticSkinThickness\n");
1055	>	painCave.isFatal = 0;
1056	>	simError();
1057	>	theEst = 0.05 * theEcr;
1058	>	}
1059	>	else{
1060	>	theEst = globals->getEST();
1061	>	}
1062	>
1063	>	info[i].setDefaultEcr(theEcr, theEst);
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	<	dAtom->setA( rotMat );
1076	>	char* inName;
1077	>
1078	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079	>
1080	>	for (i = 0; i < info[0].n_atoms; i++)
1081	>	info[0].atoms[i]->setCoords();
1082	>
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	<	current_atom_ndx++;
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	<	current_mol++;
1111	<	current_comp_mol++;
1110	>	#ifdef IS_MPI
1111	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112	>	MPIcheckPoint();
1113	>	#endif // is_mpi
1114	>	}
1115
1116	–	if( current_comp_mol >= components_nmol[current_comp] ){
1116
1117	<	current_comp_mol = 0;
1118	<	current_comp++;
1117	>	void SimSetup::makeOutNames(void){
1118	>	int k;
1119	>
1120	>
1121	>	for (k = 0; k < nInfo; k++){
1122	>	#ifdef IS_MPI
1123	>	if (worldRank == 0){
1124	>	#endif // is_mpi
1125	>
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	>	// 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	+
1208	+
1209	+	void SimSetup::sysObjectsCreation(void){
1210	+	int i, k;
1211	+
1212	+	// create the forceField
1213	+
1214	+	createFF();
1215	+
1216	+	// extract componentList
1217	+
1218	+	compList();
1219	+
1220	+	// calc the number of atoms, bond, bends, and torsions
1221	+
1222	+	calcSysValues();
1223	+
1224	+	#ifdef IS_MPI
1225	+	// divide the molecules among the processors
1226	+
1227	+	mpiMolDivide();
1228	+	#endif //is_mpi
1229	+
1230	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231	+
1232	+	makeSysArrays();
1233	+
1234	+	// make and initialize the molecules (all but atomic coordinates)
1235	+
1236	+	makeMolecules();
1237	+
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	+
1246	+
1247	+	void SimSetup::createFF(void){
1248	+	switch (ffCase){
1249	+	case FF_DUFF:
1250	+	the_ff = new DUFF();
1251	+	break;
1252	+
1253	+	case FF_LJ:
1254	+	the_ff = new LJFF();
1255	+	break;
1256	+
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	+	#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	+	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	+	info[i].molMembershipArray = molMembershipArray;
1358	+	}
1359	+	}
1360	+
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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