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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 984 by gezelter, Mon Jan 26 21:52:56 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"
#	Line 12 | Line 15
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 27 | Line 75 | SimSetup::~SimSetup(){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
122	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
122	>	// gather all of the information from the Bass file
123
124	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
124	>	gatherInfo();
125
126	<	// 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();
126	>	// creation of complex system objects
127
128	<	// 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 );
128	>	sysObjectsCreation();
129
130	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
130	>	// check on the post processing info
131
132	+	finalInfoCheck();
133
134	<	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	<	}
134	>	// initialize the system coordinates
135
136	<	#ifdef IS_MPI
137	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	<
139	>	if( !(globals->getUseInitTime()) )
140	>	info[0].currentTime = 0.0;
141	>	}
142
143	<	// 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];
143	>	// make the output filenames
144
145	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
145	>	makeOutNames();
146
147	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
147	>	// make the integrator
148
149	<	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	<	}
149	>	makeIntegrator();
150
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	–	}
159	–
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "Have the number of components" );
153	<	MPIcheckPoint();
163	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
155	>	// initialize the Fortran
156
157	<	simnfo->nComponents = n_components;
158	<	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++ ){
157	>	initFortran();
158	>	}
159
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
160
161	<	comp_stamps[i] = headStamp->match( id );
162	<	if( comp_stamps[i] == NULL ){
163	<
164	<	// extract the component from the list;
165	<
166	<	currentStamp = the_stamps->extractMolStamp( id );
167	<	if( currentStamp == NULL ){
168	<	sprintf( painCave.errMsg,
169	<	"SimSetup error: Component \"%s\" was not found in the "
170	<	"list of declared molecules\n",
171	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164	>	molInit molInfo;
165	>	DirectionalAtom* dAtom;
166	>	LinkedAssign* extras;
167	>	LinkedAssign* current_extra;
168	>	AtomStamp* currentAtom;
169	>	BondStamp* currentBond;
170	>	BendStamp* currentBend;
171	>	TorsionStamp* currentTorsion;
172
173	<	#ifdef IS_MPI
174	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
175	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
173	>	bond_pair* theBonds;
174	>	bend_set* theBends;
175	>	torsion_set* theTorsions;
176
177	+	//init the forceField paramters
178
179	+	the_ff->readParams();
180
211	–	// caclulate the number of atoms, bonds, bends and torsions
181
182	<	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	<	}
182	>	// init the atoms
183
184	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
184	>	double phi, theta, psi;
185	>	double sux, suy, suz;
186	>	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
187	>	double ux, uy, uz, u, uSqr;
188
189	<	simnfo->n_atoms = tot_atoms;
190	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
189	>	for (k = 0; k < nInfo; k++){
190	>	the_ff->setSimInfo(&(info[k]));
191
192	<
193	<	#ifdef IS_MPI
192	>	atomOffset = 0;
193	>	excludeOffset = 0;
194	>	for (i = 0; i < info[k].n_mol; i++){
195	>	stampID = info[k].molecules[i].getStampID();
196
197	<	// divide the molecules among processors here.
198	<
199	<	mpiSim = new mpiSimulation( simnfo );
200	<
201	<
242	<
243	<	globalIndex = mpiSim->divideLabor();
197	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
198	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
199	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
200	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
201	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
202
203	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
204	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
205	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
206	+	molInfo.myBends = new Bend * [molInfo.nBends];
207	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
208
209	+	theBonds = new bond_pair[molInfo.nBonds];
210	+	theBends = new bend_set[molInfo.nBends];
211	+	theTorsions = new torsion_set[molInfo.nTorsions];
212
213	<	// 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++ ){
213	>	// make the Atoms
214
215	<	for( j=0; j<components_nmol[i]; j++ ){
216	<
217	<	if( mpiSim->getMyMolStart() <= allMol &&
218	<	allMol <= mpiSim->getMyMolEnd() ){
219	<
220	<	local_atoms +=    comp_stamps[i]->getNAtoms();
221	<	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	<
215	>	for (j = 0; j < molInfo.nAtoms; j++){
216	>	currentAtom = comp_stamps[stampID]->getAtom(j);
217	>	if (currentAtom->haveOrientation()){
218	>	dAtom = new DirectionalAtom((j + atomOffset),
219	>	info[k].getConfiguration());
220	>	info[k].n_oriented++;
221	>	molInfo.myAtoms[j] = dAtom;
222
223	<	simnfo->n_atoms = mpiSim->getMyNlocal();
224	<
225	<	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	<	}
223	>	// Directional Atoms have standard unit vectors which are oriented
224	>	// in space using the three Euler angles.  We assume the standard
225	>	// unit vector was originally along the z axis below.
226
227	<	simnfo->n_bonds = local_bonds;
228	<	simnfo->n_bends = local_bends;
229	<	simnfo->n_torsions = local_torsions;
230	<	simnfo->n_SRI = local_SRI;
231	<	simnfo->n_mol = localMol;
227	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
228	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
229	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
230	>
231	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
232	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
233	>	Axz = sin(theta) * sin(psi);
234	>
235	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
236	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
237	>	Ayz = sin(theta) * cos(psi);
238	>
239	>	Azx = sin(phi) * sin(theta);
240	>	Azy = -cos(phi) * sin(theta);
241	>	Azz = cos(theta);
242
243	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
244	<	MPIcheckPoint();
245	<
298	<
299	<	#endif // is_mpi
300	<
243	>	sux = 0.0;
244	>	suy = 0.0;
245	>	suz = 1.0;
246
247	<	// create the atom and short range interaction arrays
247	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
248	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
249	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
250
251	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
251	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
252
253	+	u = sqrt(uSqr);
254	+	ux = ux / u;
255	+	uy = uy / u;
256	+	uz = uz / u;
257
258	<	if( simnfo->n_SRI ){
259	<	Exclude::createArray(simnfo->n_SRI);
260	<	the_excludes = new Exclude*[simnfo->n_SRI];
261	<	simnfo->globalExcludes = new int;
262	<	simnfo->n_exclude = tot_SRI;
263	<	}
264	<	else{
265	<
266	<	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	<	}
258	>	dAtom->setSUx(ux);
259	>	dAtom->setSUy(uy);
260	>	dAtom->setSUz(uz);
261	>	}
262	>	else{
263	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	>	info[k].getConfiguration());
265	>	}
266	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
267
268	<	// set the arrays into the SimInfo object
268	>	#ifdef IS_MPI
269
270	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
270	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
271
272	+	#endif // is_mpi
273	+	}
274
275	<	// get some of the tricky things that may still be in the globals
275	>	// make the bonds
276	>	for (j = 0; j < molInfo.nBonds; j++){
277	>	currentBond = comp_stamps[stampID]->getBond(j);
278	>	theBonds[j].a = currentBond->getA() + atomOffset;
279	>	theBonds[j].b = currentBond->getB() + atomOffset;
280
281	<
282	<	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() ){
281	>	exI = theBonds[j].a;
282	>	exJ = theBonds[j].b;
283
284	<	double vol;
285	<	vol = (double)tot_nmol / the_globals->getDensity();
286	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
287	<	simnfo->box_y = simnfo->box_x;
288	<	simnfo->box_z = simnfo->box_x;
289	<	}
290	<	else{
291	<	if( !the_globals->haveBoxX() ){
292	<	sprintf( painCave.errMsg,
293	<	"SimSetup error, no periodic BoxX size given.\n" );
294	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
284	>	// exclude_I must always be the smaller of the pair
285	>	if (exI > exJ){
286	>	tempEx = exI;
287	>	exI = exJ;
288	>	exJ = tempEx;
289	>	}
290	>	#ifdef IS_MPI
291	>	tempEx = exI;
292	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	tempEx = exJ;
294	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295
296	<	if( !the_globals->haveBoxY() ){
297	<	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();
296	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
297	>	#else  // isn't MPI
298
299	<	if( !the_globals->haveBoxZ() ){
300	<	sprintf( painCave.errMsg,
301	<	"SimSetup error, no periodic BoxZ size given.\n" );
302	<	painCave.isFatal = 1;
371	<	simError();
372	<	}
373	<	simnfo->box_z = the_globals->getBoxZ();
374	<	}
299	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
300	>	#endif  //is_mpi
301	>	}
302	>	excludeOffset += molInfo.nBonds;
303
304	<	#ifdef IS_MPI
305	<	strcpy( checkPointMsg, "Box size set up" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
304	>	//make the bends
305	>	for (j = 0; j < molInfo.nBends; j++){
306	>	currentBend = comp_stamps[stampID]->getBend(j);
307	>	theBends[j].a = currentBend->getA() + atomOffset;
308	>	theBends[j].b = currentBend->getB() + atomOffset;
309	>	theBends[j].c = currentBend->getC() + atomOffset;
310
311	+	if (currentBend->haveExtras()){
312	+	extras = currentBend->getExtras();
313	+	current_extra = extras;
314
315	<	// initialize the arrays
315	>	while (current_extra != NULL){
316	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
317	>	switch (current_extra->getType()){
318	>	case 0:
319	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
320	>	theBends[j].isGhost = 1;
321	>	break;
322
323	<	the_ff->setSimInfo( simnfo );
323	>	case 1:
324	>	theBends[j].ghost = (int) current_extra->getDouble() +
325	>	atomOffset;
326	>	theBends[j].isGhost = 1;
327	>	break;
328
329	<	makeAtoms();
330	<	simnfo->identArray = new int[simnfo->n_atoms];
331	<	for(i=0; i<simnfo->n_atoms; i++){
332	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
333	<	}
334	<
335	<	if( tot_bonds ){
336	<	makeBonds();
337	<	}
329	>	default:
330	>	sprintf(painCave.errMsg,
331	>	"SimSetup Error: ghostVectorSource was neither a "
332	>	"double nor an int.\n"
333	>	"-->Bend[%d] in %s\n",
334	>	j, comp_stamps[stampID]->getID());
335	>	painCave.isFatal = 1;
336	>	simError();
337	>	}
338	>	}
339	>	else{
340	>	sprintf(painCave.errMsg,
341	>	"SimSetup Error: unhandled bend assignment:\n"
342	>	"    -->%s in Bend[%d] in %s\n",
343	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
344	>	painCave.isFatal = 1;
345	>	simError();
346	>	}
347	>
348	>	current_extra = current_extra->getNext();
349	>	}
350	>	}
351	>
352	>	if (!theBends[j].isGhost){
353	>	exI = theBends[j].a;
354	>	exJ = theBends[j].c;
355	>	}
356	>	else{
357	>	exI = theBends[j].a;
358	>	exJ = theBends[j].b;
359	>	}
360
361	<	if( tot_bends ){
362	<	makeBends();
363	<	}
361	>	// exclude_I must always be the smaller of the pair
362	>	if (exI > exJ){
363	>	tempEx = exI;
364	>	exI = exJ;
365	>	exJ = tempEx;
366	>	}
367	>	#ifdef IS_MPI
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372
373	<	if( tot_torsions ){
374	<	makeTorsions();
375	<	}
373	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
374	>	#else  // isn't MPI
375	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
376	>	#endif  //is_mpi
377	>	}
378	>	excludeOffset += molInfo.nBends;
379
380	+	for (j = 0; j < molInfo.nTorsions; j++){
381	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
382	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
383	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
384	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
385	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
386
387	<	if (the_globals->getUseRF() ) {
388	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	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	<	}
387	>	exI = theTorsions[j].a;
388	>	exJ = theTorsions[j].d;
389
390	<	if( !the_globals->haveEST() ){
391	<	sprintf( painCave.errMsg,
392	<	"SimSetup Warning: using default value of 0.05 * the "
393	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
394	<	);
395	<	painCave.isFatal = 0;
396	<	simError();
397	<	simnfo->est = 0.05 * simnfo->ecr;
398	<	} else {
399	<	simnfo->est        = the_globals->getEST();
400	<	}
401	<
402	<	if(!the_globals->haveDielectric() ){
403	<	sprintf( painCave.errMsg,
404	<	"SimSetup Error: You are trying to use Reaction Field without"
405	<	"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();
390	>	// exclude_I must always be the smaller of the pair
391	>	if (exI > exJ){
392	>	tempEx = exI;
393	>	exI = exJ;
394	>	exJ = tempEx;
395	>	}
396	>	#ifdef IS_MPI
397	>	tempEx = exI;
398	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	>	tempEx = exJ;
400	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
401	>
402	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
403	>	#else  // isn't MPI
404	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
405	>	#endif  //is_mpi
406		}
407	<
408	<	if( !the_globals->haveEST() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 5% of the"
411	<	"electrostaticCutoffRadius for the "
412	<	"electrostaticSkinThickness\n"
413	<	);
414	<	painCave.isFatal = 0;
415	<	simError();
416	<	simnfo->est = 0.05 * simnfo->ecr;
417	<	} else {
418	<	simnfo->est        = the_globals->getEST();
419	<	}
407	>	excludeOffset += molInfo.nTorsions;
408	>
409	>
410	>	// send the arrays off to the forceField for init.
411	>
412	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
413	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
414	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
415	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
416	>	theTorsions);
417	>
418	>
419	>	info[k].molecules[i].initialize(molInfo);
420	>
421	>
422	>	atomOffset += molInfo.nAtoms;
423	>	delete[] theBonds;
424	>	delete[] theBends;
425	>	delete[] theTorsions;
426		}
427	<	}
427	>	}
428
429		#ifdef IS_MPI
430	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
430	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
431		MPIcheckPoint();
432		#endif // is_mpi
433
434	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
434	>	// clean up the forcefield
435
436	<	delete fileInit;
437	<	}
438	<	else{
436	>	the_ff->calcRcut();
437	>	the_ff->cleanMe();
438	>	}
439
440	<	#ifdef IS_MPI
440	>	void SimSetup::initFromBass(void){
441	>	int i, j, k;
442	>	int n_cells;
443	>	double cellx, celly, cellz;
444	>	double temp1, temp2, temp3;
445	>	int n_per_extra;
446	>	int n_extra;
447	>	int have_extra, done;
448
449	<	// no init from bass
450	<
451	<	sprintf( painCave.errMsg,
452	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
449	>	double vel[3];
450	>	vel[0] = 0.0;
451	>	vel[1] = 0.0;
452	>	vel[2] = 0.0;
453
454	<	initFromBass();
454	>	temp1 = (double) tot_nmol / 4.0;
455	>	temp2 = pow(temp1, (1.0 / 3.0));
456	>	temp3 = ceil(temp2);
457
458	+	have_extra = 0;
459	+	if (temp2 < temp3){
460	+	// we have a non-complete lattice
461	+	have_extra = 1;
462
463	<	#endif
464	<	}
463	>	n_cells = (int) temp3 - 1;
464	>	cellx = info[0].boxL[0] / temp3;
465	>	celly = info[0].boxL[1] / temp3;
466	>	cellz = info[0].boxL[2] / temp3;
467	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
468	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
469	>	n_per_extra = (int) ceil(temp1);
470
471	<	#ifdef IS_MPI
472	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
473	<	MPIcheckPoint();
474	<	#endif // is_mpi
471	>	if (n_per_extra > 4){
472	>	sprintf(painCave.errMsg,
473	>	"SimSetup error. There has been an error in constructing"
474	>	" the non-complete lattice.\n");
475	>	painCave.isFatal = 1;
476	>	simError();
477	>	}
478	>	}
479	>	else{
480	>	n_cells = (int) temp3;
481	>	cellx = info[0].boxL[0] / temp3;
482	>	celly = info[0].boxL[1] / temp3;
483	>	cellz = info[0].boxL[2] / temp3;
484	>	}
485
486	+	current_mol = 0;
487	+	current_comp_mol = 0;
488	+	current_comp = 0;
489	+	current_atom_ndx = 0;
490
491	<
492	<
493	<
491	>	for (i = 0; i < n_cells ; i++){
492	>	for (j = 0; j < n_cells; j++){
493	>	for (k = 0; k < n_cells; k++){
494	>	makeElement(i * cellx, j * celly, k * cellz);
495
496	<
497	<	#ifdef IS_MPI
498	<	if( worldRank == 0 ){
499	<	#endif // is_mpi
500	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
496	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
497	>
498	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
499	>
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
501		}
543	–	else if( !strcmp( endTest, ".BASS" ) ){
544	–	strcpy( endTest, ".eor" );
545	–	}
546	–	else{
547	–	endTest = &(simnfo->finalName[nameLength - 4]);
548	–	if( !strcmp( endTest, ".bss" ) ){
549	–	strcpy( endTest, ".eor" );
550	–	}
551	–	else if( !strcmp( endTest, ".mdl" ) ){
552	–	strcpy( endTest, ".eor" );
553	–	}
554	–	else{
555	–	strcat( simnfo->finalName, ".eor" );
556	–	}
557	–	}
502		}
503	<
504	<	// make the sample and status out names
505	<
506	<	strcpy( simnfo->sampleName, inFileName );
507	<	char* endTest;
508	<	int nameLength = strlen( simnfo->sampleName );
509	<	endTest = &(simnfo->sampleName[nameLength - 5]);
510	<	if( !strcmp( endTest, ".bass" ) ){
511	<	strcpy( endTest, ".dump" );
512	<	}
513	<	else if( !strcmp( endTest, ".BASS" ) ){
514	<	strcpy( endTest, ".dump" );
515	<	}
516	<	else{
517	<	endTest = &(simnfo->sampleName[nameLength - 4]);
518	<	if( !strcmp( endTest, ".bss" ) ){
519	<	strcpy( endTest, ".dump" );
503	>	}
504	>
505	>	if (have_extra){
506	>	done = 0;
507	>
508	>	int start_ndx;
509	>	for (i = 0; i < (n_cells + 1) && !done; i++){
510	>	for (j = 0; j < (n_cells + 1) && !done; j++){
511	>	if (i < n_cells){
512	>	if (j < n_cells){
513	>	start_ndx = n_cells;
514	>	}
515	>	else
516	>	start_ndx = 0;
517	>	}
518	>	else
519	>	start_ndx = 0;
520	>
521	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
522	>	makeElement(i * cellx, j * celly, k * cellz);
523	>	done = (current_mol >= tot_nmol);
524	>
525	>	if (!done && n_per_extra > 1){
526	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
527	>	k * cellz);
528	>	done = (current_mol >= tot_nmol);
529	>	}
530	>
531	>	if (!done && n_per_extra > 2){
532	>	makeElement(i * cellx, j * celly + 0.5 * celly,
533	>	k * cellz + 0.5 * cellz);
534	>	done = (current_mol >= tot_nmol);
535	>	}
536	>
537	>	if (!done && n_per_extra > 3){
538	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
539	>	k * cellz + 0.5 * cellz);
540	>	done = (current_mol >= tot_nmol);
541	>	}
542	>	}
543		}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
544		}
584	–
585	–	strcpy( simnfo->statusName, inFileName );
586	–	nameLength = strlen( simnfo->statusName );
587	–	endTest = &(simnfo->statusName[nameLength - 5]);
588	–	if( !strcmp( endTest, ".bass" ) ){
589	–	strcpy( endTest, ".stat" );
590	–	}
591	–	else if( !strcmp( endTest, ".BASS" ) ){
592	–	strcpy( endTest, ".stat" );
593	–	}
594	–	else{
595	–	endTest = &(simnfo->statusName[nameLength - 4]);
596	–	if( !strcmp( endTest, ".bss" ) ){
597	–	strcpy( endTest, ".stat" );
598	–	}
599	–	else if( !strcmp( endTest, ".mdl" ) ){
600	–	strcpy( endTest, ".stat" );
601	–	}
602	–	else{
603	–	strcat( simnfo->statusName, ".stat" );
604	–	}
605	–	}
606	–
607	–	#ifdef IS_MPI
545		}
609	–	#endif // is_mpi
610	–
611	–	// set the status, sample, and themal kick times
612	–
613	–	if( the_globals->haveSampleTime() ){
614	–	simnfo->sampleTime = the_globals->getSampleTime();
615	–	simnfo->statusTime = simnfo->sampleTime;
616	–	simnfo->thermalTime = simnfo->sampleTime;
617	–	}
618	–	else{
619	–	simnfo->sampleTime = the_globals->getRunTime();
620	–	simnfo->statusTime = simnfo->sampleTime;
621	–	simnfo->thermalTime = simnfo->sampleTime;
622	–	}
546
547	<	if( the_globals->haveStatusTime() ){
548	<	simnfo->statusTime = the_globals->getStatusTime();
547	>	for (i = 0; i < info[0].n_atoms; i++){
548	>	info[0].atoms[i]->setVel(vel);
549		}
550	+	}
551
552	<	if( the_globals->haveThermalTime() ){
553	<	simnfo->thermalTime = the_globals->getThermalTime();
554	<	}
552	>	void SimSetup::makeElement(double x, double y, double z){
553	>	int k;
554	>	AtomStamp* current_atom;
555	>	DirectionalAtom* dAtom;
556	>	double rotMat[3][3];
557	>	double pos[3];
558
559	<	// check for the temperature set flag
559	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
560	>	current_atom = comp_stamps[current_comp]->getAtom(k);
561	>	if (!current_atom->havePosition()){
562	>	sprintf(painCave.errMsg,
563	>	"SimSetup:initFromBass error.\n"
564	>	"\tComponent %s, atom %s does not have a position specified.\n"
565	>	"\tThe initialization routine is unable to give a start"
566	>	" position.\n",
567	>	comp_stamps[current_comp]->getID(), current_atom->getType());
568	>	painCave.isFatal = 1;
569	>	simError();
570	>	}
571
572	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
572	>	pos[0] = x + current_atom->getPosX();
573	>	pos[1] = y + current_atom->getPosY();
574	>	pos[2] = z + current_atom->getPosZ();
575
576	+	info[0].atoms[current_atom_ndx]->setPos(pos);
577
578	<	//   // make the longe range forces and the integrator
578	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
579	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
580
581	<	//   new AllLong( simnfo );
581	>	rotMat[0][0] = 1.0;
582	>	rotMat[0][1] = 0.0;
583	>	rotMat[0][2] = 0.0;
584
585	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
586	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
587	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
585	>	rotMat[1][0] = 0.0;
586	>	rotMat[1][1] = 1.0;
587	>	rotMat[1][2] = 0.0;
588
589	+	rotMat[2][0] = 0.0;
590	+	rotMat[2][1] = 0.0;
591	+	rotMat[2][2] = 1.0;
592
593	+	dAtom->setA(rotMat);
594	+	}
595
596	<	// initialize the Fortran
649	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
596	>	current_atom_ndx++;
597		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
598
599	+	current_mol++;
600	+	current_comp_mol++;
601
602	<	#ifdef IS_MPI
603	<	strcpy( checkPointMsg,
604	<	"Successfully intialized the mixingRule for Fortran." );
605	<	MPIcheckPoint();
671	<	#endif // is_mpi
602	>	if (current_comp_mol >= components_nmol[current_comp]){
603	>	current_comp_mol = 0;
604	>	current_comp++;
605	>	}
606		}
607
608
609	<	void SimSetup::makeMolecules( void ){
609	>	void SimSetup::gatherInfo(void){
610	>	int i;
611
612	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
613	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
612	>	ensembleCase = -1;
613	>	ffCase = -1;
614
615	<	the_ff->readParams();
615	>	// set the easy ones first
616
617	<
618	<	// init the molecules
617	>	for (i = 0; i < nInfo; i++){
618	>	info[i].target_temp = globals->getTargetTemp();
619	>	info[i].dt = globals->getDt();
620	>	info[i].run_time = globals->getRunTime();
621	>	}
622	>	n_components = globals->getNComponents();
623
694	–	atomOffset = 0;
695	–	excludeOffset = 0;
696	–	for(i=0; i<simnfo->n_mol; i++){
697	–
698	–	stampID = the_molecules[i].getStampID();
624
625	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
701	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	<	info.nBends    = comp_stamps[stampID]->getNBends();
703	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
625	>	// get the forceField
626
627	<	info.myAtoms = &the_atoms[atomOffset];
707	<	info.myExcludes = &the_excludes[excludeOffset];
708	<	info.myBonds = new Bond*[info.nBonds];
709	<	info.myBends = new Bend*[info.nBends];
710	<	info.myTorsions = new Torsions*[info.nTorsions];
627	>	strcpy(force_field, globals->getForceField());
628
629	<	theBonds = new bond_pair[info.nBonds];
630	<	theBends = new bend_set[info.nBends];
631	<	theTorsions = new torsion_set[info.nTorsions];
632	<
633	<	// make the Atoms
634	<
635	<	for(j=0; j<info.nAtoms; j++){
636	<
637	<	currentAtom = theComponents[stampID]->getAtom( j );
638	<	if( currentAtom->haveOrientation() ){
639	<
640	<	dAtom = new DirectionalAtom(j + atomOffset);
641	<	simnfo->n_oriented++;
642	<	info.myAtoms[j] = dAtom;
643	<
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;
629	>	if (!strcasecmp(force_field, "DUFF")){
630	>	ffCase = FF_DUFF;
631	>	}
632	>	else if (!strcasecmp(force_field, "LJ")){
633	>	ffCase = FF_LJ;
634	>	}
635	>	else if (!strcasecmp(force_field, "EAM")){
636	>	ffCase = FF_EAM;
637	>	}
638	>	else{
639	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
640	>	force_field);
641	>	painCave.isFatal = 1;
642	>	simError();
643	>	}
644
645	<	exI = theBonds[i].a;
762	<	exJ = theBonds[i].b;
645	>	// get the ensemble
646
647	<	// exclude_I must always be the smaller of the pair
765	<	if( exI > exJ ){
766	<	tempEx = exI;
767	<	exI = exJ;
768	<	exJ = tempEx;
769	<	}
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
780	<	}
781	<	excludeOffset += info.nBonds;
647	>	strcpy(ensemble, globals->getEnsemble());
648
649	<	//make the bends
650	<	for(j=0; j<info.nBends; j++){
651	<
652	<	currentBend = comp_stamps[stampID]->getBend( j );
653	<	theBends[j].a = currentBend->getA() + atomOffset;
654	<	theBends[j].b = currentBend->getB() + atomOffset;
655	<	theBends[j].c = currentBend->getC() + atomOffset;
656	<
657	<	if( currentBend->haveExtras() ){
658	<
659	<	extras = current_bend->getExtras();
660	<	current_extra = extras;
661	<
662	<	while( current_extra != NULL ){
663	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
664	<
665	<	switch( current_extra->getType() ){
666	<
667	<	case 0:
668	<	theBends[j].ghost =
669	<	current_extra->getInt() + atomOffset;
670	<	theBends[j].isGhost = 1;
671	<	break;
672	<
673	<	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;
649	>	if (!strcasecmp(ensemble, "NVE")){
650	>	ensembleCase = NVE_ENS;
651	>	}
652	>	else if (!strcasecmp(ensemble, "NVT")){
653	>	ensembleCase = NVT_ENS;
654	>	}
655	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
656	>	ensembleCase = NPTi_ENS;
657	>	}
658	>	else if (!strcasecmp(ensemble, "NPTf")){
659	>	ensembleCase = NPTf_ENS;
660	>	}
661	>	else if (!strcasecmp(ensemble, "NPTxyz")){
662	>	ensembleCase = NPTxyz_ENS;
663	>	}
664	>	else{
665	>	sprintf(painCave.errMsg,
666	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
667	>	"\treverting to NVE for this simulation.\n",
668	>	ensemble);
669	>	painCave.isFatal = 0;
670	>	simError();
671	>	strcpy(ensemble, "NVE");
672	>	ensembleCase = NVE_ENS;
673	>	}
674
675	<	for(j=0; j<info.nTorsions; j++){
676	<
871	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
872	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
873	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
874	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
876	<
877	<	exI = theTorsions[j].a;
878	<	exJ = theTorsions[j].d;
675	>	for (i = 0; i < nInfo; i++){
676	>	strcpy(info[i].ensemble, ensemble);
677
678	<	// exclude_I must always be the smaller of the pair
881	<	if( exI > exJ ){
882	<	tempEx = exI;
883	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	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
896	<	}
897	<	excludeOffset += info.nTorsions;
678	>	// get the mixing rule
679
680	<
681	<	// send the arrays off to the forceField for init.
680	>	strcpy(info[i].mixingRule, globals->getMixingRule());
681	>	info[i].usePBC = globals->getPBC();
682	>	}
683
684	<	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 );
684	>	// get the components and calculate the tot_nMol and indvidual n_mol
685
686	+	the_components = globals->getComponents();
687	+	components_nmol = new int[n_components];
688
908	–	the_molecules[i].initialize( info );
909	–	atomOffset += info.nAtoms;
910	–	}
689
690	<	// clean up the forcefield
690	>	if (!globals->haveNMol()){
691	>	// we don't have the total number of molecules, so we assume it is
692	>	// given in each component
693
694	<	the_ff->cleanMe();
695	<	}
694	>	tot_nmol = 0;
695	>	for (i = 0; i < n_components; i++){
696	>	if (!the_components[i]->haveNMol()){
697	>	// we have a problem
698	>	sprintf(painCave.errMsg,
699	>	"SimSetup Error. No global NMol or component NMol given.\n"
700	>	"\tCannot calculate the number of atoms.\n");
701	>	painCave.isFatal = 1;
702	>	simError();
703	>	}
704
705	+	tot_nmol += the_components[i]->getNMol();
706	+	components_nmol[i] = the_components[i]->getNMol();
707	+	}
708	+	}
709	+	else{
710	+	sprintf(painCave.errMsg,
711	+	"SimSetup error.\n"
712	+	"\tSorry, the ability to specify total"
713	+	" nMols and then give molfractions in the components\n"
714	+	"\tis not currently supported."
715	+	" Please give nMol in the components.\n");
716	+	painCave.isFatal = 1;
717	+	simError();
718	+	}
719
720	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
721	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
722	+	sprintf(painCave.errMsg,
723	+	"Sample time is not divisible by dt.\n"
724	+	"\tThis will result in samples that are not uniformly\n"
725	+	"\tdistributed in time.  If this is a problem, change\n"
726	+	"\tyour sampleTime variable.\n");
727	+	painCave.isFatal = 0;
728	+	simError();
729	+	}
730
731	<	void SimSetup::makeAtoms( void ){
731	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
732	>	sprintf(painCave.errMsg,
733	>	"Status time is not divisible by dt.\n"
734	>	"\tThis will result in status reports that are not uniformly\n"
735	>	"\tdistributed in time.  If this is a problem, change \n"
736	>	"\tyour statusTime variable.\n");
737	>	painCave.isFatal = 0;
738	>	simError();
739	>	}
740
741	<	int i, j, k, index;
742	<	double ux, uy, uz, uSqr, u;
743	<	AtomStamp* current_atom;
741	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
742	>	sprintf(painCave.errMsg,
743	>	"Thermal time is not divisible by dt.\n"
744	>	"\tThis will result in thermalizations that are not uniformly\n"
745	>	"\tdistributed in time.  If this is a problem, change \n"
746	>	"\tyour thermalTime variable.\n");
747	>	painCave.isFatal = 0;
748	>	simError();
749	>	}
750
751	<	DirectionalAtom* dAtom;
752	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
751	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
752	>	sprintf(painCave.errMsg,
753	>	"Reset time is not divisible by dt.\n"
754	>	"\tThis will result in integrator resets that are not uniformly\n"
755	>	"\tdistributed in time.  If this is a problem, change\n"
756	>	"\tyour resetTime variable.\n");
757	>	painCave.isFatal = 0;
758	>	simError();
759	>	}
760
761	<	lMolIndex = 0;
929	<	molIndex = 0;
930	<	index = 0;
931	<	for( i=0; i<n_components; i++ ){
761	>	// set the status, sample, and thermal kick times
762
763	<	for( j=0; j<components_nmol[i]; j++ ){
763	>	for (i = 0; i < nInfo; i++){
764	>	if (globals->haveSampleTime()){
765	>	info[i].sampleTime = globals->getSampleTime();
766	>	info[i].statusTime = info[i].sampleTime;
767	>	info[i].thermalTime = info[i].sampleTime;
768	>	}
769	>	else{
770	>	info[i].sampleTime = globals->getRunTime();
771	>	info[i].statusTime = info[i].sampleTime;
772	>	info[i].thermalTime = info[i].sampleTime;
773	>	}
774
775	<	#ifdef IS_MPI
776	<	if( mpiSim->getMyMolStart() <= molIndex &&
777	<	molIndex <= mpiSim->getMyMolEnd() ){
938	<	#endif // is_mpi
775	>	if (globals->haveStatusTime()){
776	>	info[i].statusTime = globals->getStatusTime();
777	>	}
778
779	<	molStart = index;
780	<	nMemb = comp_stamps[i]->getNAtoms();
781	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943	<
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++;
779	>	if (globals->haveThermalTime()){
780	>	info[i].thermalTime = globals->getThermalTime();
781	>	}
782
783	<	#ifdef IS_MPI
784	<	}
785	<	#endif //is_mpi
786	<
987	<	molIndex++;
783	>	info[i].resetIntegrator = 0;
784	>	if( globals->haveResetTime() ){
785	>	info[i].resetTime = globals->getResetTime();
786	>	info[i].resetIntegrator = 1;
787		}
989	–	}
788
789	<	#ifdef IS_MPI
992	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
789	>	// check for the temperature set flag
790
791	<	delete[] globalIndex;
791	>	if (globals->haveTempSet())
792	>	info[i].setTemp = globals->getTempSet();
793
794	<	mpiSim->mpiRefresh();
997	<	#endif //IS_MPI
998	<
999	<	the_ff->initializeAtoms();
1000	<	}
794	>	// check for the extended State init
795
796	<	void SimSetup::makeBonds( void ){
796	>	info[i].useInitXSstate = globals->getUseInitXSstate();
797	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
798	>
799	>	}
800	>
801	>	//setup seed for random number generator
802	>	int seedValue;
803
804	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
805	<	bond_pair* the_bonds;
1006	<	BondStamp* current_bond;
1007	<
1008	<	the_bonds = new bond_pair[tot_bonds];
1009	<	index = 0;
1010	<	offset = 0;
1011	<	molIndex = 0;
1012	<
1013	<	for( i=0; i<n_components; i++ ){
1014	<
1015	<	for( j=0; j<components_nmol[i]; j++ ){
804	>	if (globals->haveSeed()){
805	>	seedValue = globals->getSeed();
806
807	<	#ifdef IS_MPI
808	<	if( mpiSim->getMyMolStart() <= molIndex &&
809	<	molIndex <= mpiSim->getMyMolEnd() ){
810	<	#endif // is_mpi
811	<
812	<	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;
807	>	if(seedValue / 1E9 == 0){
808	>	sprintf(painCave.errMsg,
809	>	"Seed for sprng library should contain at least 9 digits\n"
810	>	"OOPSE will generate a seed for user\n");
811	>	painCave.isFatal = 0;
812	>	simError();
813
814	<	exI = the_bonds[index].a;
815	<	exJ = the_bonds[index].b;
816	<
817	<	// exclude_I must always be the smaller of the pair
818	<	if( exI > exJ ){
819	<	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
814	>	//using seed generated by system instead of invalid seed set by user
815	>	#ifndef IS_MPI
816	>	seedValue = make_sprng_seed();
817	>	#else
818	>	if (worldRank == 0){
819	>	seedValue = make_sprng_seed();
820		}
821	<	#endif //is_mpi
822	<
823	<	molIndex++;
824	<	}
821	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
822	>	#endif
823	>	}
824	>	}//end of if branch of globals->haveSeed()
825	>	else{
826	>
827	>	#ifndef IS_MPI
828	>	seedValue = make_sprng_seed();
829	>	#else
830	>	if (worldRank == 0){
831	>	seedValue = make_sprng_seed();
832	>	}
833	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
834	>	#endif
835	>	}//end of globals->haveSeed()
836	>
837	>	for (int i = 0; i < nInfo; i++){
838	>	info[i].setSeed(seedValue);
839		}
840
841	<	the_ff->initializeBonds( the_bonds );
841	>	#ifdef IS_MPI
842	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
843	>	MPIcheckPoint();
844	>	#endif // is_mpi
845		}
846
1069	–	void SimSetup::makeBends( void ){
847
848	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
849	<	bend_set* the_bends;
850	<	BendStamp* current_bend;
851	<	LinkedAssign* extras;
1075	<	LinkedAssign* current_extra;
1076	<
848	>	void SimSetup::finalInfoCheck(void){
849	>	int index;
850	>	int usesDipoles;
851	>	int i;
852
853	<	the_bends = new bend_set[tot_bends];
854	<	index = 0;
1080	<	offset = 0;
1081	<	molIndex = 0;
1082	<	for( i=0; i<n_components; i++ ){
853	>	for (i = 0; i < nInfo; i++){
854	>	// check electrostatic parameters
855
856	<	for( j=0; j<components_nmol[i]; j++ ){
856	>	index = 0;
857	>	usesDipoles = 0;
858	>	while ((index < info[i].n_atoms) && !usesDipoles){
859	>	usesDipoles = (info[i].atoms[index])->hasDipole();
860	>	index++;
861	>	}
862
863		#ifdef IS_MPI
864	<	if( mpiSim->getMyMolStart() <= molIndex &&
865	<	molIndex <= mpiSim->getMyMolEnd() ){
866	<	#endif // is_mpi
864	>	int myUse = usesDipoles;
865	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	>	#endif //is_mpi
867
868	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092	<
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	<	}
868	>	double theEcr, theEst;
869
870	+	if (globals->getUseRF()){
871	+	info[i].useReactionField = 1;
872
873	<	#ifdef IS_MPI
873	>	if (!globals->haveECR()){
874	>	sprintf(painCave.errMsg,
875	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
876	>	"\tOOPSE will use a default value of 15.0 angstroms"
877	>	"\tfor the electrostaticCutoffRadius.\n");
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEcr = 15.0;
881	>	}
882	>	else{
883	>	theEcr = globals->getECR();
884	>	}
885
886	<	the_excludes[(index + tot_bonds)*2] =
887	<	the_atoms[exI]->getGlobalIndex() + 1;
888	<	the_excludes[(index + tot_bonds)*2 + 1] =
889	<	the_atoms[exJ]->getGlobalIndex() + 1;
890	<
891	<	#else  // isn't MPI
892	<
893	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
894	<	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
886	>	if (!globals->haveEST()){
887	>	sprintf(painCave.errMsg,
888	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
889	>	"\tOOPSE will use a default value of\n"
890	>	"\t0.05 * electrostaticCutoffRadius\n"
891	>	"\tfor the electrostaticSkinThickness\n");
892	>	painCave.isFatal = 0;
893	>	simError();
894	>	theEst = 0.05 * theEcr;
895		}
896	<	#endif //is_mpi
896	>	else{
897	>	theEst = globals->getEST();
898	>	}
899
900	<	molIndex++;
900	>	info[i].setDefaultEcr(theEcr, theEst);
901	>
902	>	if (!globals->haveDielectric()){
903	>	sprintf(painCave.errMsg,
904	>	"SimSetup Error: No Dielectric constant was set.\n"
905	>	"\tYou are trying to use Reaction Field without"
906	>	"\tsetting a dielectric constant!\n");
907	>	painCave.isFatal = 1;
908	>	simError();
909	>	}
910	>	info[i].dielectric = globals->getDielectric();
911		}
912	+	else{
913	+	if (usesDipoles){
914	+	if (!globals->haveECR()){
915	+	sprintf(painCave.errMsg,
916	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
917	+	"\tOOPSE will use a default value of 15.0 angstroms"
918	+	"\tfor the electrostaticCutoffRadius.\n");
919	+	painCave.isFatal = 0;
920	+	simError();
921	+	theEcr = 15.0;
922	+	}
923	+	else{
924	+	theEcr = globals->getECR();
925	+	}
926	+
927	+	if (!globals->haveEST()){
928	+	sprintf(painCave.errMsg,
929	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
930	+	"\tOOPSE will use a default value of\n"
931	+	"\t0.05 * electrostaticCutoffRadius\n"
932	+	"\tfor the electrostaticSkinThickness\n");
933	+	painCave.isFatal = 0;
934	+	simError();
935	+	theEst = 0.05 * theEcr;
936	+	}
937	+	else{
938	+	theEst = globals->getEST();
939	+	}
940	+
941	+	info[i].setDefaultEcr(theEcr, theEst);
942	+	}
943	+	}
944		}
1192	–
945		#ifdef IS_MPI
946	<	sprintf( checkPointMsg,
1195	<	"Successfully created the bends list.\n" );
946	>	strcpy(checkPointMsg, "post processing checks out");
947		MPIcheckPoint();
948		#endif // is_mpi
949	+	}
950
951	+	void SimSetup::initSystemCoords(void){
952	+	int i;
953
954	<	the_ff->initializeBends( the_bends );
1201	<	}
954	>	char* inName;
955
956	<	void SimSetup::makeTorsions( void ){
956	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
957
958	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
959	<	torsion_set* the_torsions;
1207	<	TorsionStamp* current_torsion;
958	>	for (i = 0; i < info[0].n_atoms; i++)
959	>	info[0].atoms[i]->setCoords();
960
961	<	the_torsions = new torsion_set[tot_torsions];
962	<	index = 0;
963	<	offset = 0;
964	<	molIndex = 0;
965	<	for( i=0; i<n_components; i++ ){
961	>	if (globals->haveInitialConfig()){
962	>	InitializeFromFile* fileInit;
963	>	#ifdef IS_MPI // is_mpi
964	>	if (worldRank == 0){
965	>	#endif //is_mpi
966	>	inName = globals->getInitialConfig();
967	>	fileInit = new InitializeFromFile(inName);
968	>	#ifdef IS_MPI
969	>	}
970	>	else
971	>	fileInit = new InitializeFromFile(NULL);
972	>	#endif
973	>	fileInit->readInit(info); // default velocities on
974
975	<	for( j=0; j<components_nmol[i]; j++ ){
975	>	delete fileInit;
976	>	}
977	>	else{
978	>
979	>	// no init from bass
980	>
981	>	sprintf(painCave.errMsg,
982	>	"Cannot intialize a simulation without an initial configuration file.\n");
983	>	painCave.isFatal = 1;;
984	>	simError();
985	>
986	>	}
987
988		#ifdef IS_MPI
989	<	if( mpiSim->getMyMolStart() <= molIndex &&
990	<	molIndex <= mpiSim->getMyMolEnd() ){
991	<	#endif // is_mpi
989	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
990	>	MPIcheckPoint();
991	>	#endif // is_mpi
992	>	}
993
1222	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
994
995	<	current_torsion = comp_stamps[i]->getTorsion( k );
996	<	the_torsions[index].a = current_torsion->getA() + offset;
1226	<	the_torsions[index].b = current_torsion->getB() + offset;
1227	<	the_torsions[index].c = current_torsion->getC() + offset;
1228	<	the_torsions[index].d = current_torsion->getD() + offset;
995	>	void SimSetup::makeOutNames(void){
996	>	int k;
997
1230	–	exI = the_torsions[index].a;
1231	–	exJ = the_torsions[index].d;
998
999	<
1234	<	// exclude_I must always be the smaller of the pair
1235	<	if( exI > exJ ){
1236	<	tempEx = exI;
1237	<	exI = exJ;
1238	<	exJ = tempEx;
1239	<	}
1240	<
1241	<
999	>	for (k = 0; k < nInfo; k++){
1000		#ifdef IS_MPI
1001	<
1002	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1245	<	the_atoms[exI]->getGlobalIndex() + 1;
1246	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247	<	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	<
1001	>	if (worldRank == 0){
1002	>	#endif // is_mpi
1003
1004	<	// increment the index and repeat;
1005	<	index++;
1004	>	if (globals->haveFinalConfig()){
1005	>	strcpy(info[k].finalName, globals->getFinalConfig());
1006		}
1007	<	offset += comp_stamps[i]->getNAtoms();
1008	<
1009	<	#ifdef IS_MPI
1007	>	else{
1008	>	strcpy(info[k].finalName, inFileName);
1009	>	char* endTest;
1010	>	int nameLength = strlen(info[k].finalName);
1011	>	endTest = &(info[k].finalName[nameLength - 5]);
1012	>	if (!strcmp(endTest, ".bass")){
1013	>	strcpy(endTest, ".eor");
1014	>	}
1015	>	else if (!strcmp(endTest, ".BASS")){
1016	>	strcpy(endTest, ".eor");
1017	>	}
1018	>	else{
1019	>	endTest = &(info[k].finalName[nameLength - 4]);
1020	>	if (!strcmp(endTest, ".bss")){
1021	>	strcpy(endTest, ".eor");
1022	>	}
1023	>	else if (!strcmp(endTest, ".mdl")){
1024	>	strcpy(endTest, ".eor");
1025	>	}
1026	>	else{
1027	>	strcat(info[k].finalName, ".eor");
1028	>	}
1029	>	}
1030		}
1264	–	#endif //is_mpi
1031
1032	<	molIndex++;
1032	>	// make the sample and status out names
1033	>
1034	>	strcpy(info[k].sampleName, inFileName);
1035	>	char* endTest;
1036	>	int nameLength = strlen(info[k].sampleName);
1037	>	endTest = &(info[k].sampleName[nameLength - 5]);
1038	>	if (!strcmp(endTest, ".bass")){
1039	>	strcpy(endTest, ".dump");
1040	>	}
1041	>	else if (!strcmp(endTest, ".BASS")){
1042	>	strcpy(endTest, ".dump");
1043	>	}
1044	>	else{
1045	>	endTest = &(info[k].sampleName[nameLength - 4]);
1046	>	if (!strcmp(endTest, ".bss")){
1047	>	strcpy(endTest, ".dump");
1048	>	}
1049	>	else if (!strcmp(endTest, ".mdl")){
1050	>	strcpy(endTest, ".dump");
1051	>	}
1052	>	else{
1053	>	strcat(info[k].sampleName, ".dump");
1054	>	}
1055	>	}
1056	>
1057	>	strcpy(info[k].statusName, inFileName);
1058	>	nameLength = strlen(info[k].statusName);
1059	>	endTest = &(info[k].statusName[nameLength - 5]);
1060	>	if (!strcmp(endTest, ".bass")){
1061	>	strcpy(endTest, ".stat");
1062	>	}
1063	>	else if (!strcmp(endTest, ".BASS")){
1064	>	strcpy(endTest, ".stat");
1065	>	}
1066	>	else{
1067	>	endTest = &(info[k].statusName[nameLength - 4]);
1068	>	if (!strcmp(endTest, ".bss")){
1069	>	strcpy(endTest, ".stat");
1070	>	}
1071	>	else if (!strcmp(endTest, ".mdl")){
1072	>	strcpy(endTest, ".stat");
1073	>	}
1074	>	else{
1075	>	strcat(info[k].statusName, ".stat");
1076	>	}
1077	>	}
1078	>
1079	>	#ifdef IS_MPI
1080	>
1081		}
1082	+	#endif // is_mpi
1083		}
1269	–
1270	–	the_ff->initializeTorsions( the_torsions );
1084		}
1085
1273	–	void SimSetup::initFromBass( void ){
1086
1087	<	int i, j, k;
1088	<	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;
1087	>	void SimSetup::sysObjectsCreation(void){
1088	>	int i, k;
1089
1090	<	temp1 = (double)tot_nmol / 4.0;
1284	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1285	<	temp3 = ceil( temp2 );
1090	>	// create the forceField
1091
1092	<	have_extra =0;
1288	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1289	<	have_extra =1;
1092	>	createFF();
1093
1094	<	n_cells = (int)temp3 - 1;
1292	<	cellx = simnfo->box_x / temp3;
1293	<	celly = simnfo->box_y / temp3;
1294	<	cellz = simnfo->box_z / temp3;
1295	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1296	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1297	<	n_per_extra = (int)ceil( temp1 );
1094	>	// extract componentList
1095
1096	<	if( n_per_extra > 4){
1097	<	sprintf( painCave.errMsg,
1098	<	"SimSetup error. There has been an error in constructing"
1099	<	" the non-complete lattice.\n" );
1096	>	compList();
1097	>
1098	>	// calc the number of atoms, bond, bends, and torsions
1099	>
1100	>	calcSysValues();
1101	>
1102	>	#ifdef IS_MPI
1103	>	// divide the molecules among the processors
1104	>
1105	>	mpiMolDivide();
1106	>	#endif //is_mpi
1107	>
1108	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1109	>
1110	>	makeSysArrays();
1111	>
1112	>	// make and initialize the molecules (all but atomic coordinates)
1113	>
1114	>	makeMolecules();
1115	>
1116	>	for (k = 0; k < nInfo; k++){
1117	>	info[k].identArray = new int[info[k].n_atoms];
1118	>	for (i = 0; i < info[k].n_atoms; i++){
1119	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1120	>	}
1121	>	}
1122	>	}
1123	>
1124	>
1125	>	void SimSetup::createFF(void){
1126	>	switch (ffCase){
1127	>	case FF_DUFF:
1128	>	the_ff = new DUFF();
1129	>	break;
1130	>
1131	>	case FF_LJ:
1132	>	the_ff = new LJFF();
1133	>	break;
1134	>
1135	>	case FF_EAM:
1136	>	the_ff = new EAM_FF();
1137	>	break;
1138	>
1139	>	default:
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1142		painCave.isFatal = 1;
1143		simError();
1305	–	}
1144		}
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	–	}
1145
1146	<	current_mol = 0;
1147	<	current_comp_mol = 0;
1148	<	current_comp = 0;
1149	<	current_atom_ndx = 0;
1146	>	#ifdef IS_MPI
1147	>	strcpy(checkPointMsg, "ForceField creation successful");
1148	>	MPIcheckPoint();
1149	>	#endif // is_mpi
1150	>	}
1151
1319	–	for( i=0; i < n_cells ; i++ ){
1320	–	for( j=0; j < n_cells; j++ ){
1321	–	for( k=0; k < n_cells; k++ ){
1152
1153	<	makeElement( i * cellx,
1154	<	j * celly,
1155	<	k * cellz );
1153	>	void SimSetup::compList(void){
1154	>	int i;
1155	>	char* id;
1156	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1157	>	LinkedMolStamp* currentStamp = NULL;
1158	>	comp_stamps = new MoleculeStamp * [n_components];
1159
1160	<	makeElement( i * cellx + 0.5 * cellx,
1161	<	j * celly + 0.5 * celly,
1329	<	k * cellz );
1160	>	// make an array of molecule stamps that match the components used.
1161	>	// also extract the used stamps out into a separate linked list
1162
1163	<	makeElement( i * cellx,
1164	<	j * celly + 0.5 * celly,
1165	<	k * cellz + 0.5 * cellz );
1163	>	for (i = 0; i < nInfo; i++){
1164	>	info[i].nComponents = n_components;
1165	>	info[i].componentsNmol = components_nmol;
1166	>	info[i].compStamps = comp_stamps;
1167	>	info[i].headStamp = headStamp;
1168	>	}
1169
1170	<	makeElement( i * cellx + 0.5 * cellx,
1171	<	j * celly,
1172	<	k * cellz + 0.5 * cellz );
1170	>
1171	>	for (i = 0; i < n_components; i++){
1172	>	id = the_components[i]->getType();
1173	>	comp_stamps[i] = NULL;
1174	>
1175	>	// check to make sure the component isn't already in the list
1176	>
1177	>	comp_stamps[i] = headStamp->match(id);
1178	>	if (comp_stamps[i] == NULL){
1179	>	// extract the component from the list;
1180	>
1181	>	currentStamp = stamps->extractMolStamp(id);
1182	>	if (currentStamp == NULL){
1183	>	sprintf(painCave.errMsg,
1184	>	"SimSetup error: Component \"%s\" was not found in the "
1185	>	"list of declared molecules\n",
1186	>	id);
1187	>	painCave.isFatal = 1;
1188	>	simError();
1189		}
1190	+
1191	+	headStamp->add(currentStamp);
1192	+	comp_stamps[i] = headStamp->match(id);
1193		}
1194		}
1195
1196	<	if( have_extra ){
1197	<	done = 0;
1196	>	#ifdef IS_MPI
1197	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1198	>	MPIcheckPoint();
1199	>	#endif // is_mpi
1200	>	}
1201
1202	<	int start_ndx;
1203	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1347	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1202	>	void SimSetup::calcSysValues(void){
1203	>	int i;
1204
1205	<	if( i < n_cells ){
1205	>	int* molMembershipArray;
1206
1207	<	if( j < n_cells ){
1208	<	start_ndx = n_cells;
1209	<	}
1210	<	else start_ndx = 0;
1211	<	}
1212	<	else start_ndx = 0;
1207	>	tot_atoms = 0;
1208	>	tot_bonds = 0;
1209	>	tot_bends = 0;
1210	>	tot_torsions = 0;
1211	>	for (i = 0; i < n_components; i++){
1212	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1213	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1214	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1215	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1216	>	}
1217
1218	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1218	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1219	>	molMembershipArray = new int[tot_atoms];
1220
1221	<	makeElement( i * cellx,
1222	<	j * celly,
1223	<	k * cellz );
1224	<	done = ( current_mol >= tot_nmol );
1221	>	for (i = 0; i < nInfo; i++){
1222	>	info[i].n_atoms = tot_atoms;
1223	>	info[i].n_bonds = tot_bonds;
1224	>	info[i].n_bends = tot_bends;
1225	>	info[i].n_torsions = tot_torsions;
1226	>	info[i].n_SRI = tot_SRI;
1227	>	info[i].n_mol = tot_nmol;
1228
1229	<	if( !done && n_per_extra > 1 ){
1230	<	makeElement( i * cellx + 0.5 * cellx,
1231	<	j * celly + 0.5 * celly,
1368	<	k * cellz );
1369	<	done = ( current_mol >= tot_nmol );
1370	<	}
1229	>	info[i].molMembershipArray = molMembershipArray;
1230	>	}
1231	>	}
1232
1233	<	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	<	}
1233	>	#ifdef IS_MPI
1234
1235	<	if( !done && n_per_extra > 3){
1236	<	makeElement( i * cellx + 0.5 * cellx,
1237	<	j * celly,
1238	<	k * cellz + 0.5 * cellz );
1239	<	done = ( current_mol >= tot_nmol );
1240	<	}
1241	<	}
1235	>	void SimSetup::mpiMolDivide(void){
1236	>	int i, j, k;
1237	>	int localMol, allMol;
1238	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1239	>
1240	>	mpiSim = new mpiSimulation(info);
1241	>
1242	>	globalIndex = mpiSim->divideLabor();
1243	>
1244	>	// set up the local variables
1245	>
1246	>	mol2proc = mpiSim->getMolToProcMap();
1247	>	molCompType = mpiSim->getMolComponentType();
1248	>
1249	>	allMol = 0;
1250	>	localMol = 0;
1251	>	local_atoms = 0;
1252	>	local_bonds = 0;
1253	>	local_bends = 0;
1254	>	local_torsions = 0;
1255	>	globalAtomIndex = 0;
1256	>
1257	>
1258	>	for (i = 0; i < n_components; i++){
1259	>	for (j = 0; j < components_nmol[i]; j++){
1260	>	if (mol2proc[allMol] == worldRank){
1261	>	local_atoms += comp_stamps[i]->getNAtoms();
1262	>	local_bonds += comp_stamps[i]->getNBonds();
1263	>	local_bends += comp_stamps[i]->getNBends();
1264	>	local_torsions += comp_stamps[i]->getNTorsions();
1265	>	localMol++;
1266	>	}
1267	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1268	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1269	>	globalAtomIndex++;
1270		}
1271	+
1272	+	allMol++;
1273		}
1274		}
1275	+	local_SRI = local_bonds + local_bends + local_torsions;
1276
1277	+	info[0].n_atoms = mpiSim->getMyNlocal();
1278
1279	<	for( i=0; i<simnfo->n_atoms; i++ ){
1280	<	simnfo->atoms[i]->set_vx( 0.0 );
1281	<	simnfo->atoms[i]->set_vy( 0.0 );
1282	<	simnfo->atoms[i]->set_vz( 0.0 );
1279	>	if (local_atoms != info[0].n_atoms){
1280	>	sprintf(painCave.errMsg,
1281	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1282	>	"\tlocalAtom (%d) are not equal.\n",
1283	>	info[0].n_atoms, local_atoms);
1284	>	painCave.isFatal = 1;
1285	>	simError();
1286		}
1287	+
1288	+	info[0].n_bonds = local_bonds;
1289	+	info[0].n_bends = local_bends;
1290	+	info[0].n_torsions = local_torsions;
1291	+	info[0].n_SRI = local_SRI;
1292	+	info[0].n_mol = localMol;
1293	+
1294	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1295	+	MPIcheckPoint();
1296		}
1297
1298	<	void SimSetup::makeElement( double x, double y, double z ){
1298	>	#endif // is_mpi
1299
1400	–	int k;
1401	–	AtomStamp* current_atom;
1402	–	DirectionalAtom* dAtom;
1403	–	double rotMat[3][3];
1300
1301	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1301	>	void SimSetup::makeSysArrays(void){
1302	>
1303	>	#ifndef IS_MPI
1304	>	int k, j;
1305	>	#endif // is_mpi
1306	>	int i, l;
1307
1308	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1309	<	if( !current_atom->havePosition() ){
1310	<	sprintf( painCave.errMsg,
1410	<	"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();
1418	<	}
1308	>	Atom** the_atoms;
1309	>	Molecule* the_molecules;
1310	>	Exclude** the_excludes;
1311
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() );
1312
1313	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1313	>	for (l = 0; l < nInfo; l++){
1314	>	// create the atom and short range interaction arrays
1315
1316	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1316	>	the_atoms = new Atom * [info[l].n_atoms];
1317	>	the_molecules = new Molecule[info[l].n_mol];
1318	>	int molIndex;
1319
1320	<	rotMat[0][0] = 1.0;
1429	<	rotMat[0][1] = 0.0;
1430	<	rotMat[0][2] = 0.0;
1320	>	// initialize the molecule's stampID's
1321
1322	<	rotMat[1][0] = 0.0;
1433	<	rotMat[1][1] = 1.0;
1434	<	rotMat[1][2] = 0.0;
1322	>	#ifdef IS_MPI
1323
1436	–	rotMat[2][0] = 0.0;
1437	–	rotMat[2][1] = 0.0;
1438	–	rotMat[2][2] = 1.0;
1324
1325	<	dAtom->setA( rotMat );
1325	>	molIndex = 0;
1326	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1327	>	if (mol2proc[i] == worldRank){
1328	>	the_molecules[molIndex].setStampID(molCompType[i]);
1329	>	the_molecules[molIndex].setMyIndex(molIndex);
1330	>	the_molecules[molIndex].setGlobalIndex(i);
1331	>	molIndex++;
1332	>	}
1333		}
1334
1335	<	current_atom_ndx++;
1335	>	#else // is_mpi
1336	>
1337	>	molIndex = 0;
1338	>	globalAtomIndex = 0;
1339	>	for (i = 0; i < n_components; i++){
1340	>	for (j = 0; j < components_nmol[i]; j++){
1341	>	the_molecules[molIndex].setStampID(i);
1342	>	the_molecules[molIndex].setMyIndex(molIndex);
1343	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1344	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1345	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1346	>	globalAtomIndex++;
1347	>	}
1348	>	molIndex++;
1349	>	}
1350	>	}
1351	>
1352	>
1353	>	#endif // is_mpi
1354	>
1355	>
1356	>	if (info[l].n_SRI){
1357	>	Exclude::createArray(info[l].n_SRI);
1358	>	the_excludes = new Exclude * [info[l].n_SRI];
1359	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1360	>	the_excludes[ex] = new Exclude(ex);
1361	>	}
1362	>	info[l].globalExcludes = new int;
1363	>	info[l].n_exclude = info[l].n_SRI;
1364	>	}
1365	>	else{
1366	>	Exclude::createArray(1);
1367	>	the_excludes = new Exclude * ;
1368	>	the_excludes[0] = new Exclude(0);
1369	>	the_excludes[0]->setPair(0, 0);
1370	>	info[l].globalExcludes = new int;
1371	>	info[l].globalExcludes[0] = 0;
1372	>	info[l].n_exclude = 0;
1373	>	}
1374	>
1375	>	// set the arrays into the SimInfo object
1376	>
1377	>	info[l].atoms = the_atoms;
1378	>	info[l].molecules = the_molecules;
1379	>	info[l].nGlobalExcludes = 0;
1380	>	info[l].excludes = the_excludes;
1381	>
1382	>	the_ff->setSimInfo(info);
1383		}
1384	+	}
1385
1386	<	current_mol++;
1387	<	current_comp_mol++;
1386	>	void SimSetup::makeIntegrator(void){
1387	>	int k;
1388
1389	<	if( current_comp_mol >= components_nmol[current_comp] ){
1389	>	NVE<RealIntegrator>* myNVE = NULL;
1390	>	NVT<RealIntegrator>* myNVT = NULL;
1391	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1392	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1393	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1394	>
1395	>	for (k = 0; k < nInfo; k++){
1396	>	switch (ensembleCase){
1397	>	case NVE_ENS:
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1401	>	}
1402	>	else{
1403	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1404	>	}
1405	>
1406	>	info->the_integrator = myNVE;
1407	>	break;
1408
1409	<	current_comp_mol = 0;
1410	<	current_comp++;
1409	>	case NVT_ENS:
1410	>	if (globals->haveZconstraints()){
1411	>	setupZConstraint(info[k]);
1412	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1413	>	}
1414	>	else
1415	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1416	>
1417	>	myNVT->setTargetTemp(globals->getTargetTemp());
1418	>
1419	>	if (globals->haveTauThermostat())
1420	>	myNVT->setTauThermostat(globals->getTauThermostat());
1421	>	else{
1422	>	sprintf(painCave.errMsg,
1423	>	"SimSetup error: If you use the NVT\n"
1424	>	"\tensemble, you must set tauThermostat.\n");
1425	>	painCave.isFatal = 1;
1426	>	simError();
1427	>	}
1428	>
1429	>	info->the_integrator = myNVT;
1430	>	break;
1431	>
1432	>	case NPTi_ENS:
1433	>	if (globals->haveZconstraints()){
1434	>	setupZConstraint(info[k]);
1435	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1436	>	}
1437	>	else
1438	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1439	>
1440	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1441	>
1442	>	if (globals->haveTargetPressure())
1443	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1444	>	else{
1445	>	sprintf(painCave.errMsg,
1446	>	"SimSetup error: If you use a constant pressure\n"
1447	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1448	>	painCave.isFatal = 1;
1449	>	simError();
1450	>	}
1451	>
1452	>	if (globals->haveTauThermostat())
1453	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1454	>	else{
1455	>	sprintf(painCave.errMsg,
1456	>	"SimSetup error: If you use an NPT\n"
1457	>	"\tensemble, you must set tauThermostat.\n");
1458	>	painCave.isFatal = 1;
1459	>	simError();
1460	>	}
1461	>
1462	>	if (globals->haveTauBarostat())
1463	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1464	>	else{
1465	>	sprintf(painCave.errMsg,
1466	>	"SimSetup error: If you use an NPT\n"
1467	>	"\tensemble, you must set tauBarostat.\n");
1468	>	painCave.isFatal = 1;
1469	>	simError();
1470	>	}
1471	>
1472	>	info->the_integrator = myNPTi;
1473	>	break;
1474	>
1475	>	case NPTf_ENS:
1476	>	if (globals->haveZconstraints()){
1477	>	setupZConstraint(info[k]);
1478	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1479	>	}
1480	>	else
1481	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1482	>
1483	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1484	>
1485	>	if (globals->haveTargetPressure())
1486	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1487	>	else{
1488	>	sprintf(painCave.errMsg,
1489	>	"SimSetup error: If you use a constant pressure\n"
1490	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494	>
1495	>	if (globals->haveTauThermostat())
1496	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1497	>
1498	>	else{
1499	>	sprintf(painCave.errMsg,
1500	>	"SimSetup error: If you use an NPT\n"
1501	>	"\tensemble, you must set tauThermostat.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if (globals->haveTauBarostat())
1507	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1508	>
1509	>	else{
1510	>	sprintf(painCave.errMsg,
1511	>	"SimSetup error: If you use an NPT\n"
1512	>	"\tensemble, you must set tauBarostat.\n");
1513	>	painCave.isFatal = 1;
1514	>	simError();
1515	>	}
1516	>
1517	>	info->the_integrator = myNPTf;
1518	>	break;
1519	>
1520	>	case NPTxyz_ENS:
1521	>	if (globals->haveZconstraints()){
1522	>	setupZConstraint(info[k]);
1523	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1524	>	}
1525	>	else
1526	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1527	>
1528	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1529	>
1530	>	if (globals->haveTargetPressure())
1531	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1532	>	else{
1533	>	sprintf(painCave.errMsg,
1534	>	"SimSetup error: If you use a constant pressure\n"
1535	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1536	>	painCave.isFatal = 1;
1537	>	simError();
1538	>	}
1539	>
1540	>	if (globals->haveTauThermostat())
1541	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1542	>	else{
1543	>	sprintf(painCave.errMsg,
1544	>	"SimSetup error: If you use an NPT\n"
1545	>	"\tensemble, you must set tauThermostat.\n");
1546	>	painCave.isFatal = 1;
1547	>	simError();
1548	>	}
1549	>
1550	>	if (globals->haveTauBarostat())
1551	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1552	>	else{
1553	>	sprintf(painCave.errMsg,
1554	>	"SimSetup error: If you use an NPT\n"
1555	>	"\tensemble, you must set tauBarostat.\n");
1556	>	painCave.isFatal = 1;
1557	>	simError();
1558	>	}
1559	>
1560	>	info->the_integrator = myNPTxyz;
1561	>	break;
1562	>
1563	>	default:
1564	>	sprintf(painCave.errMsg,
1565	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1566	>	painCave.isFatal = 1;
1567	>	simError();
1568	>	}
1569		}
1570		}
1571	+
1572	+	void SimSetup::initFortran(void){
1573	+	info[0].refreshSim();
1574	+
1575	+	if (!strcmp(info[0].mixingRule, "standard")){
1576	+	the_ff->initForceField(LB_MIXING_RULE);
1577	+	}
1578	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1579	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1580	+	}
1581	+	else{
1582	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1583	+	info[0].mixingRule);
1584	+	painCave.isFatal = 1;
1585	+	simError();
1586	+	}
1587	+
1588	+
1589	+	#ifdef IS_MPI
1590	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1591	+	MPIcheckPoint();
1592	+	#endif // is_mpi
1593	+	}
1594	+
1595	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1596	+	int nZConstraints;
1597	+	ZconStamp** zconStamp;
1598	+
1599	+	if (globals->haveZconstraintTime()){
1600	+	//add sample time of z-constraint  into SimInfo's property list
1601	+	DoubleData* zconsTimeProp = new DoubleData();
1602	+	zconsTimeProp->setID(ZCONSTIME_ID);
1603	+	zconsTimeProp->setData(globals->getZconsTime());
1604	+	theInfo.addProperty(zconsTimeProp);
1605	+	}
1606	+	else{
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint error: If you use a ZConstraint,\n"
1609	+	"\tyou must set zconsTime.\n");
1610	+	painCave.isFatal = 1;
1611	+	simError();
1612	+	}
1613	+
1614	+	//push zconsTol into siminfo, if user does not specify
1615	+	//value for zconsTol, a default value will be used
1616	+	DoubleData* zconsTol = new DoubleData();
1617	+	zconsTol->setID(ZCONSTOL_ID);
1618	+	if (globals->haveZconsTol()){
1619	+	zconsTol->setData(globals->getZconsTol());
1620	+	}
1621	+	else{
1622	+	double defaultZConsTol = 0.01;
1623	+	sprintf(painCave.errMsg,
1624	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1625	+	"\tOOPSE will use a default value of %f.\n"
1626	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1627	+	defaultZConsTol);
1628	+	painCave.isFatal = 0;
1629	+	simError();
1630	+
1631	+	zconsTol->setData(defaultZConsTol);
1632	+	}
1633	+	theInfo.addProperty(zconsTol);
1634	+
1635	+	//set Force Subtraction Policy
1636	+	StringData* zconsForcePolicy = new StringData();
1637	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	+
1639	+	if (globals->haveZconsForcePolicy()){
1640	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	+	}
1642	+	else{
1643	+	sprintf(painCave.errMsg,
1644	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1645	+	"\tOOPSE will use PolicyByMass.\n"
1646	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1647	+	painCave.isFatal = 0;
1648	+	simError();
1649	+	zconsForcePolicy->setData("BYMASS");
1650	+	}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
1677	+
1678	+	for (int i = 0; i < nZConstraints; i++){
1679	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
1684	+	zconsParaData->addItem(tempParaItem);
1685	+	}
1686	+
1687	+	//check the uniqueness of index
1688	+	if(!zconsParaData->isIndexUnique()){
1689	+	sprintf(painCave.errMsg,
1690	+	"ZConstraint Error: molIndex is not unique!\n");
1691	+	painCave.isFatal = 1;
1692	+	simError();
1693	+	}
1694	+
1695	+	//sort the parameters by index of molecules
1696	+	zconsParaData->sortByIndex();
1697	+
1698	+	//push data into siminfo, therefore, we can retrieve later
1699	+	theInfo.addProperty(zconsParaData);
1700	+	}

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