ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 999 by chrisfen, Fri Jan 30 15:01:09 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 | SimSetup::SimSetup(){
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	+	#define FF_H2O 3
31	+
32	+	using namespace std;
33	+
34	+	/**
35	+	* Check whether dividend is divisble by divisor or not
36	+	*/
37	+	bool isDivisible(double dividend, double divisor){
38	+	double tolerance = 0.000001;
39	+	double quotient;
40	+	double diff;
41	+	int intQuotient;
42	+
43	+	quotient = dividend / divisor;
44	+
45	+	if (quotient < 0)
46	+	quotient = -quotient;
47	+
48	+	intQuotient = int (quotient + tolerance);
49	+
50	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
51	+
52	+	if (diff <= tolerance)
53	+	return true;
54	+	else
55	+	return false;
56	+	}
57	+
58		SimSetup::SimSetup(){
59	+
60	+	initSuspend = false;
61	+	isInfoArray = 0;
62	+	nInfo = 1;
63	+
64		stamps = new MakeStamps();
65		globals = new Globals();
66	<
66	>
67	>
68		#ifdef IS_MPI
69	<	strcpy( checkPointMsg, "SimSetup creation successful" );
69	>	strcpy(checkPointMsg, "SimSetup creation successful");
70		MPIcheckPoint();
71		#endif // IS_MPI
72		}
#	Line 27 | Line 76 | void SimSetup::parseFile( char* fileName ){
76		delete globals;
77		}
78
79	<	void SimSetup::parseFile( char* fileName ){
79	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
80	>	info = the_info;
81	>	nInfo = theNinfo;
82	>	isInfoArray = 1;
83	>	initSuspend = true;
84	>	}
85
86	+
87	+	void SimSetup::parseFile(char* fileName){
88		#ifdef IS_MPI
89	<	if( worldRank == 0 ){
89	>	if (worldRank == 0){
90		#endif // is_mpi
91	<
91	>
92		inFileName = fileName;
93	<	set_interface_stamps( stamps, globals );
94	<
93	>	set_interface_stamps(stamps, globals);
94	>
95		#ifdef IS_MPI
96		mpiEventInit();
97		#endif
98
99	<	yacc_BASS( fileName );
99	>	yacc_BASS(fileName);
100
101		#ifdef IS_MPI
102		throwMPIEvent(NULL);
103		}
104	<	else receiveParse();
104	>	else{
105	>	receiveParse();
106	>	}
107		#endif
108
109		}
110
111		#ifdef IS_MPI
112		void SimSetup::receiveParse(void){
113	<
114	<	set_interface_stamps( stamps, globals );
115	<	mpiEventInit();
116	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
113	>	set_interface_stamps(stamps, globals);
114	>	mpiEventInit();
115	>	MPIcheckPoint();
116	>	mpiEventLoop();
117		}
118
119		#endif // is_mpi
120
121	<	void SimSetup::createSim( void ){
121	>	void SimSetup::createSim(void){
122
123	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
123	>	// gather all of the information from the Bass file
124
125	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
125	>	gatherInfo();
126
127	<	// 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();
127	>	// creation of complex system objects
128
129	<	// 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 );
129	>	sysObjectsCreation();
130
131	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
131	>	// check on the post processing info
132
133	+	finalInfoCheck();
134
135	<	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	<	}
135	>	// initialize the system coordinates
136
137	<	#ifdef IS_MPI
138	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
137	>	if ( !initSuspend ){
138	>	initSystemCoords();
139
140	<
140	>	if( !(globals->getUseInitTime()) )
141	>	info[0].currentTime = 0.0;
142	>	}
143
144	<	// 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];
144	>	// make the output filenames
145
146	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
146	>	makeOutNames();
147
148	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
148	>	// make the integrator
149
150	<	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	<	}
150	>	makeIntegrator();
151
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	–
152		#ifdef IS_MPI
153	<	strcpy( checkPointMsg, "Have the number of components" );
154	<	MPIcheckPoint();
163	<	#endif // is_mpi
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
156	>	// initialize the Fortran
157
158	<	simnfo->nComponents = n_components;
159	<	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++ ){
158	>	initFortran();
159	>	}
160
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
161
162	<	comp_stamps[i] = headStamp->match( id );
163	<	if( comp_stamps[i] == NULL ){
164	<
165	<	// extract the component from the list;
166	<
167	<	currentStamp = the_stamps->extractMolStamp( id );
168	<	if( currentStamp == NULL ){
169	<	sprintf( painCave.errMsg,
170	<	"SimSetup error: Component \"%s\" was not found in the "
171	<	"list of declared molecules\n",
172	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
162	>	void SimSetup::makeMolecules(void){
163	>	int k;
164	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
165	>	molInit molInfo;
166	>	DirectionalAtom* dAtom;
167	>	LinkedAssign* extras;
168	>	LinkedAssign* current_extra;
169	>	AtomStamp* currentAtom;
170	>	BondStamp* currentBond;
171	>	BendStamp* currentBend;
172	>	TorsionStamp* currentTorsion;
173
174	<	#ifdef IS_MPI
175	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
176	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
174	>	bond_pair* theBonds;
175	>	bend_set* theBends;
176	>	torsion_set* theTorsions;
177
178	+	//init the forceField paramters
179
180	+	the_ff->readParams();
181
211	–	// caclulate the number of atoms, bonds, bends and torsions
182
183	<	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	<	}
183	>	// init the atoms
184
185	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
185	>	double phi, theta, psi;
186	>	double sux, suy, suz;
187	>	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
188	>	double ux, uy, uz, u, uSqr;
189
190	<	simnfo->n_atoms = tot_atoms;
191	<	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;
190	>	for (k = 0; k < nInfo; k++){
191	>	the_ff->setSimInfo(&(info[k]));
192
193	<
194	<	#ifdef IS_MPI
193	>	atomOffset = 0;
194	>	excludeOffset = 0;
195	>	for (i = 0; i < info[k].n_mol; i++){
196	>	stampID = info[k].molecules[i].getStampID();
197
198	<	// divide the molecules among processors here.
199	<
200	<	mpiSim = new mpiSimulation( simnfo );
201	<
202	<
242	<
243	<	globalIndex = mpiSim->divideLabor();
198	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
199	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
200	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
201	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
202	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
203
204	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
205	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
206	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
207	+	molInfo.myBends = new Bend * [molInfo.nBends];
208	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
209
210	+	theBonds = new bond_pair[molInfo.nBonds];
211	+	theBends = new bend_set[molInfo.nBends];
212	+	theTorsions = new torsion_set[molInfo.nTorsions];
213
214	<	// 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++ ){
214	>	// make the Atoms
215
216	<	for( j=0; j<components_nmol[i]; j++ ){
217	<
218	<	if( mpiSim->getMyMolStart() <= allMol &&
219	<	allMol <= mpiSim->getMyMolEnd() ){
220	<
221	<	local_atoms +=    comp_stamps[i]->getNAtoms();
222	<	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	<
216	>	for (j = 0; j < molInfo.nAtoms; j++){
217	>	currentAtom = comp_stamps[stampID]->getAtom(j);
218	>	if (currentAtom->haveOrientation()){
219	>	dAtom = new DirectionalAtom((j + atomOffset),
220	>	info[k].getConfiguration());
221	>	info[k].n_oriented++;
222	>	molInfo.myAtoms[j] = dAtom;
223
224	<	simnfo->n_atoms = mpiSim->getMyNlocal();
225	<
226	<	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	<	}
224	>	// Directional Atoms have standard unit vectors which are oriented
225	>	// in space using the three Euler angles.  We assume the standard
226	>	// unit vector was originally along the z axis below.
227
228	<	simnfo->n_bonds = local_bonds;
229	<	simnfo->n_bends = local_bends;
230	<	simnfo->n_torsions = local_torsions;
231	<	simnfo->n_SRI = local_SRI;
232	<	simnfo->n_mol = localMol;
228	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
229	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
230	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
231	>
232	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
233	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
234	>	Axz = sin(theta) * sin(psi);
235	>
236	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
237	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
238	>	Ayz = sin(theta) * cos(psi);
239	>
240	>	Azx = sin(phi) * sin(theta);
241	>	Azy = -cos(phi) * sin(theta);
242	>	Azz = cos(theta);
243
244	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
245	<	MPIcheckPoint();
246	<
298	<
299	<	#endif // is_mpi
300	<
244	>	sux = 0.0;
245	>	suy = 0.0;
246	>	suz = 1.0;
247
248	<	// create the atom and short range interaction arrays
248	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
249	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
250	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
251
252	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
252	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
253
254	+	u = sqrt(uSqr);
255	+	ux = ux / u;
256	+	uy = uy / u;
257	+	uz = uz / u;
258
259	<	if( simnfo->n_SRI ){
260	<	Exclude::createArray(simnfo->n_SRI);
261	<	the_excludes = new Exclude*[simnfo->n_SRI];
262	<	simnfo->globalExcludes = new int;
263	<	simnfo->n_exclude = tot_SRI;
264	<	}
265	<	else{
266	<
267	<	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	<	}
259	>	dAtom->setSUx(ux);
260	>	dAtom->setSUy(uy);
261	>	dAtom->setSUz(uz);
262	>	}
263	>	else{
264	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265	>	info[k].getConfiguration());
266	>	}
267	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
268
269	<	// set the arrays into the SimInfo object
269	>	#ifdef IS_MPI
270
271	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
271	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
272
273	+	#endif // is_mpi
274	+	}
275
276	<	// get some of the tricky things that may still be in the globals
276	>	// make the bonds
277	>	for (j = 0; j < molInfo.nBonds; j++){
278	>	currentBond = comp_stamps[stampID]->getBond(j);
279	>	theBonds[j].a = currentBond->getA() + atomOffset;
280	>	theBonds[j].b = currentBond->getB() + atomOffset;
281
282	<
283	<	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() ){
282	>	exI = theBonds[j].a;
283	>	exJ = theBonds[j].b;
284
285	<	double vol;
286	<	vol = (double)tot_nmol / the_globals->getDensity();
287	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
288	<	simnfo->box_y = simnfo->box_x;
289	<	simnfo->box_z = simnfo->box_x;
290	<	}
291	<	else{
292	<	if( !the_globals->haveBoxX() ){
293	<	sprintf( painCave.errMsg,
294	<	"SimSetup error, no periodic BoxX size given.\n" );
295	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
285	>	// exclude_I must always be the smaller of the pair
286	>	if (exI > exJ){
287	>	tempEx = exI;
288	>	exI = exJ;
289	>	exJ = tempEx;
290	>	}
291	>	#ifdef IS_MPI
292	>	tempEx = exI;
293	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
294	>	tempEx = exJ;
295	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
296
297	<	if( !the_globals->haveBoxY() ){
298	<	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();
297	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
298	>	#else  // isn't MPI
299
300	<	if( !the_globals->haveBoxZ() ){
301	<	sprintf( painCave.errMsg,
302	<	"SimSetup error, no periodic BoxZ size given.\n" );
303	<	painCave.isFatal = 1;
371	<	simError();
372	<	}
373	<	simnfo->box_z = the_globals->getBoxZ();
374	<	}
300	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
301	>	#endif  //is_mpi
302	>	}
303	>	excludeOffset += molInfo.nBonds;
304
305	<	#ifdef IS_MPI
306	<	strcpy( checkPointMsg, "Box size set up" );
307	<	MPIcheckPoint();
308	<	#endif // is_mpi
305	>	//make the bends
306	>	for (j = 0; j < molInfo.nBends; j++){
307	>	currentBend = comp_stamps[stampID]->getBend(j);
308	>	theBends[j].a = currentBend->getA() + atomOffset;
309	>	theBends[j].b = currentBend->getB() + atomOffset;
310	>	theBends[j].c = currentBend->getC() + atomOffset;
311
312	+	if (currentBend->haveExtras()){
313	+	extras = currentBend->getExtras();
314	+	current_extra = extras;
315
316	<	// initialize the arrays
316	>	while (current_extra != NULL){
317	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
318	>	switch (current_extra->getType()){
319	>	case 0:
320	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
321	>	theBends[j].isGhost = 1;
322	>	break;
323
324	<	the_ff->setSimInfo( simnfo );
324	>	case 1:
325	>	theBends[j].ghost = (int) current_extra->getDouble() +
326	>	atomOffset;
327	>	theBends[j].isGhost = 1;
328	>	break;
329
330	<	makeAtoms();
331	<	simnfo->identArray = new int[simnfo->n_atoms];
332	<	for(i=0; i<simnfo->n_atoms; i++){
333	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
334	<	}
335	<
336	<	if( tot_bonds ){
337	<	makeBonds();
338	<	}
330	>	default:
331	>	sprintf(painCave.errMsg,
332	>	"SimSetup Error: ghostVectorSource was neither a "
333	>	"double nor an int.\n"
334	>	"-->Bend[%d] in %s\n",
335	>	j, comp_stamps[stampID]->getID());
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>	}
340	>	else{
341	>	sprintf(painCave.errMsg,
342	>	"SimSetup Error: unhandled bend assignment:\n"
343	>	"    -->%s in Bend[%d] in %s\n",
344	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
345	>	painCave.isFatal = 1;
346	>	simError();
347	>	}
348	>
349	>	current_extra = current_extra->getNext();
350	>	}
351	>	}
352	>
353	>	if (!theBends[j].isGhost){
354	>	exI = theBends[j].a;
355	>	exJ = theBends[j].c;
356	>	}
357	>	else{
358	>	exI = theBends[j].a;
359	>	exJ = theBends[j].b;
360	>	}
361
362	<	if( tot_bends ){
363	<	makeBends();
364	<	}
362	>	// exclude_I must always be the smaller of the pair
363	>	if (exI > exJ){
364	>	tempEx = exI;
365	>	exI = exJ;
366	>	exJ = tempEx;
367	>	}
368	>	#ifdef IS_MPI
369	>	tempEx = exI;
370	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
371	>	tempEx = exJ;
372	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373
374	<	if( tot_torsions ){
375	<	makeTorsions();
376	<	}
374	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
375	>	#else  // isn't MPI
376	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
377	>	#endif  //is_mpi
378	>	}
379	>	excludeOffset += molInfo.nBends;
380
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	<	if (the_globals->getUseRF() ) {
389	<	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	<	}
388	>	exI = theTorsions[j].a;
389	>	exJ = theTorsions[j].d;
390
391	<	if( !the_globals->haveEST() ){
392	<	sprintf( painCave.errMsg,
393	<	"SimSetup Warning: using default value of 0.05 * the "
394	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
395	<	);
396	<	painCave.isFatal = 0;
397	<	simError();
398	<	simnfo->est = 0.05 * simnfo->ecr;
399	<	} else {
400	<	simnfo->est        = the_globals->getEST();
401	<	}
402	<
403	<	if(!the_globals->haveDielectric() ){
404	<	sprintf( painCave.errMsg,
405	<	"SimSetup Error: You are trying to use Reaction Field without"
406	<	"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();
391	>	// exclude_I must always be the smaller of the pair
392	>	if (exI > exJ){
393	>	tempEx = exI;
394	>	exI = exJ;
395	>	exJ = tempEx;
396	>	}
397	>	#ifdef IS_MPI
398	>	tempEx = exI;
399	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
400	>	tempEx = exJ;
401	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	>
403	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
404	>	#else  // isn't MPI
405	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
406	>	#endif  //is_mpi
407		}
408	<
409	<	if( !the_globals->haveEST() ){
410	<	sprintf( painCave.errMsg,
411	<	"SimSetup Warning: using default value of 5% of the"
412	<	"electrostaticCutoffRadius for the "
413	<	"electrostaticSkinThickness\n"
414	<	);
415	<	painCave.isFatal = 0;
416	<	simError();
417	<	simnfo->est = 0.05 * simnfo->ecr;
418	<	} else {
419	<	simnfo->est        = the_globals->getEST();
420	<	}
408	>	excludeOffset += molInfo.nTorsions;
409	>
410	>
411	>	// send the arrays off to the forceField for init.
412	>
413	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
414	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
415	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
416	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
417	>	theTorsions);
418	>
419	>
420	>	info[k].molecules[i].initialize(molInfo);
421	>
422	>
423	>	atomOffset += molInfo.nAtoms;
424	>	delete[] theBonds;
425	>	delete[] theBends;
426	>	delete[] theTorsions;
427		}
428	<	}
428	>	}
429
430		#ifdef IS_MPI
431	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
431	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
432		MPIcheckPoint();
433		#endif // is_mpi
434
435	<	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
435	>	// clean up the forcefield
436
437	<	delete fileInit;
438	<	}
439	<	else{
437	>	the_ff->calcRcut();
438	>	the_ff->cleanMe();
439	>	}
440
441	<	#ifdef IS_MPI
441	>	void SimSetup::initFromBass(void){
442	>	int i, j, k;
443	>	int n_cells;
444	>	double cellx, celly, cellz;
445	>	double temp1, temp2, temp3;
446	>	int n_per_extra;
447	>	int n_extra;
448	>	int have_extra, done;
449
450	<	// no init from bass
451	<
452	<	sprintf( painCave.errMsg,
453	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
450	>	double vel[3];
451	>	vel[0] = 0.0;
452	>	vel[1] = 0.0;
453	>	vel[2] = 0.0;
454
455	<	initFromBass();
455	>	temp1 = (double) tot_nmol / 4.0;
456	>	temp2 = pow(temp1, (1.0 / 3.0));
457	>	temp3 = ceil(temp2);
458
459	+	have_extra = 0;
460	+	if (temp2 < temp3){
461	+	// we have a non-complete lattice
462	+	have_extra = 1;
463
464	<	#endif
465	<	}
464	>	n_cells = (int) temp3 - 1;
465	>	cellx = info[0].boxL[0] / temp3;
466	>	celly = info[0].boxL[1] / temp3;
467	>	cellz = info[0].boxL[2] / temp3;
468	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
469	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
470	>	n_per_extra = (int) ceil(temp1);
471
472	<	#ifdef IS_MPI
473	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
474	<	MPIcheckPoint();
475	<	#endif // is_mpi
472	>	if (n_per_extra > 4){
473	>	sprintf(painCave.errMsg,
474	>	"SimSetup error. There has been an error in constructing"
475	>	" the non-complete lattice.\n");
476	>	painCave.isFatal = 1;
477	>	simError();
478	>	}
479	>	}
480	>	else{
481	>	n_cells = (int) temp3;
482	>	cellx = info[0].boxL[0] / temp3;
483	>	celly = info[0].boxL[1] / temp3;
484	>	cellz = info[0].boxL[2] / temp3;
485	>	}
486
487	+	current_mol = 0;
488	+	current_comp_mol = 0;
489	+	current_comp = 0;
490	+	current_atom_ndx = 0;
491
492	<
493	<
494	<
492	>	for (i = 0; i < n_cells ; i++){
493	>	for (j = 0; j < n_cells; j++){
494	>	for (k = 0; k < n_cells; k++){
495	>	makeElement(i * cellx, j * celly, k * cellz);
496
497	<
498	<	#ifdef IS_MPI
499	<	if( worldRank == 0 ){
500	<	#endif // is_mpi
501	<
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" );
497	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
498	>
499	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
500	>
501	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
502		}
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	–	}
503		}
504	<
505	<	// make the sample and status out names
506	<
507	<	strcpy( simnfo->sampleName, inFileName );
508	<	char* endTest;
509	<	int nameLength = strlen( simnfo->sampleName );
510	<	endTest = &(simnfo->sampleName[nameLength - 5]);
511	<	if( !strcmp( endTest, ".bass" ) ){
512	<	strcpy( endTest, ".dump" );
513	<	}
514	<	else if( !strcmp( endTest, ".BASS" ) ){
515	<	strcpy( endTest, ".dump" );
516	<	}
517	<	else{
518	<	endTest = &(simnfo->sampleName[nameLength - 4]);
519	<	if( !strcmp( endTest, ".bss" ) ){
520	<	strcpy( endTest, ".dump" );
504	>	}
505	>
506	>	if (have_extra){
507	>	done = 0;
508	>
509	>	int start_ndx;
510	>	for (i = 0; i < (n_cells + 1) && !done; i++){
511	>	for (j = 0; j < (n_cells + 1) && !done; j++){
512	>	if (i < n_cells){
513	>	if (j < n_cells){
514	>	start_ndx = n_cells;
515	>	}
516	>	else
517	>	start_ndx = 0;
518	>	}
519	>	else
520	>	start_ndx = 0;
521	>
522	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
523	>	makeElement(i * cellx, j * celly, k * cellz);
524	>	done = (current_mol >= tot_nmol);
525	>
526	>	if (!done && n_per_extra > 1){
527	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
528	>	k * cellz);
529	>	done = (current_mol >= tot_nmol);
530	>	}
531	>
532	>	if (!done && n_per_extra > 2){
533	>	makeElement(i * cellx, j * celly + 0.5 * celly,
534	>	k * cellz + 0.5 * cellz);
535	>	done = (current_mol >= tot_nmol);
536	>	}
537	>
538	>	if (!done && n_per_extra > 3){
539	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
540	>	k * cellz + 0.5 * cellz);
541	>	done = (current_mol >= tot_nmol);
542	>	}
543	>	}
544		}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
545		}
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
546		}
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	–	}
547
548	<	if( the_globals->haveStatusTime() ){
549	<	simnfo->statusTime = the_globals->getStatusTime();
548	>	for (i = 0; i < info[0].n_atoms; i++){
549	>	info[0].atoms[i]->setVel(vel);
550		}
551	+	}
552
553	<	if( the_globals->haveThermalTime() ){
554	<	simnfo->thermalTime = the_globals->getThermalTime();
555	<	}
553	>	void SimSetup::makeElement(double x, double y, double z){
554	>	int k;
555	>	AtomStamp* current_atom;
556	>	DirectionalAtom* dAtom;
557	>	double rotMat[3][3];
558	>	double pos[3];
559
560	<	// check for the temperature set flag
560	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
561	>	current_atom = comp_stamps[current_comp]->getAtom(k);
562	>	if (!current_atom->havePosition()){
563	>	sprintf(painCave.errMsg,
564	>	"SimSetup:initFromBass error.\n"
565	>	"\tComponent %s, atom %s does not have a position specified.\n"
566	>	"\tThe initialization routine is unable to give a start"
567	>	" position.\n",
568	>	comp_stamps[current_comp]->getID(), current_atom->getType());
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572
573	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
573	>	pos[0] = x + current_atom->getPosX();
574	>	pos[1] = y + current_atom->getPosY();
575	>	pos[2] = z + current_atom->getPosZ();
576
577	+	info[0].atoms[current_atom_ndx]->setPos(pos);
578
579	<	//   // make the longe range forces and the integrator
579	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
580	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
581
582	<	//   new AllLong( simnfo );
582	>	rotMat[0][0] = 1.0;
583	>	rotMat[0][1] = 0.0;
584	>	rotMat[0][2] = 0.0;
585
586	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
587	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
588	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
586	>	rotMat[1][0] = 0.0;
587	>	rotMat[1][1] = 1.0;
588	>	rotMat[1][2] = 0.0;
589
590	+	rotMat[2][0] = 0.0;
591	+	rotMat[2][1] = 0.0;
592	+	rotMat[2][2] = 1.0;
593
594	+	dAtom->setA(rotMat);
595	+	}
596
597	<	// initialize the Fortran
649	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
597	>	current_atom_ndx++;
598		}
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	–	}
599
600	+	current_mol++;
601	+	current_comp_mol++;
602
603	<	#ifdef IS_MPI
604	<	strcpy( checkPointMsg,
605	<	"Successfully intialized the mixingRule for Fortran." );
606	<	MPIcheckPoint();
671	<	#endif // is_mpi
603	>	if (current_comp_mol >= components_nmol[current_comp]){
604	>	current_comp_mol = 0;
605	>	current_comp++;
606	>	}
607		}
608
609
610	<	void SimSetup::makeMolecules( void ){
610	>	void SimSetup::gatherInfo(void){
611	>	int i;
612
613	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
614	<	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
613	>	ensembleCase = -1;
614	>	ffCase = -1;
615
616	<	the_ff->readParams();
616	>	// set the easy ones first
617
618	<
619	<	// init the molecules
618	>	for (i = 0; i < nInfo; i++){
619	>	info[i].target_temp = globals->getTargetTemp();
620	>	info[i].dt = globals->getDt();
621	>	info[i].run_time = globals->getRunTime();
622	>	}
623	>	n_components = globals->getNComponents();
624
694	–	atomOffset = 0;
695	–	excludeOffset = 0;
696	–	for(i=0; i<simnfo->n_mol; i++){
697	–
698	–	stampID = the_molecules[i].getStampID();
625
626	<	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;
626	>	// get the forceField
627
628	<	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];
628	>	strcpy(force_field, globals->getForceField());
629
630	<	theBonds = new bond_pair[info.nBonds];
631	<	theBends = new bend_set[info.nBends];
632	<	theTorsions = new torsion_set[info.nTorsions];
633	<
634	<	// make the Atoms
635	<
636	<	for(j=0; j<info.nAtoms; j++){
637	<
638	<	currentAtom = theComponents[stampID]->getAtom( j );
639	<	if( currentAtom->haveOrientation() ){
640	<
641	<	dAtom = new DirectionalAtom(j + atomOffset);
642	<	simnfo->n_oriented++;
643	<	info.myAtoms[j] = dAtom;
644	<
645	<	ux = currentAtom->getOrntX();
646	<	uy = currentAtom->getOrntY();
647	<	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;
630	>	if (!strcasecmp(force_field, "DUFF")){
631	>	ffCase = FF_DUFF;
632	>	}
633	>	else if (!strcasecmp(force_field, "LJ")){
634	>	ffCase = FF_LJ;
635	>	}
636	>	else if (!strcasecmp(force_field, "EAM")){
637	>	ffCase = FF_EAM;
638	>	}
639	>	else if (!strcasecmp(force_field, "WATER")){
640	>	ffCase = FF_H2O;
641	>	}
642	>	else{
643	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
644	>	force_field);
645	>	painCave.isFatal = 1;
646	>	simError();
647	>	}
648
649	<	exI = theBonds[i].a;
762	<	exJ = theBonds[i].b;
649	>	// get the ensemble
650
651	<	// 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;
651	>	strcpy(ensemble, globals->getEnsemble());
652
653	<	//make the bends
654	<	for(j=0; j<info.nBends; j++){
655	<
656	<	currentBend = comp_stamps[stampID]->getBend( j );
657	<	theBends[j].a = currentBend->getA() + atomOffset;
658	<	theBends[j].b = currentBend->getB() + atomOffset;
659	<	theBends[j].c = currentBend->getC() + atomOffset;
660	<
661	<	if( currentBend->haveExtras() ){
662	<
663	<	extras = current_bend->getExtras();
664	<	current_extra = extras;
665	<
666	<	while( current_extra != NULL ){
667	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
668	<
669	<	switch( current_extra->getType() ){
670	<
671	<	case 0:
672	<	theBends[j].ghost =
673	<	current_extra->getInt() + atomOffset;
674	<	theBends[j].isGhost = 1;
675	<	break;
676	<
677	<	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;
653	>	if (!strcasecmp(ensemble, "NVE")){
654	>	ensembleCase = NVE_ENS;
655	>	}
656	>	else if (!strcasecmp(ensemble, "NVT")){
657	>	ensembleCase = NVT_ENS;
658	>	}
659	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
660	>	ensembleCase = NPTi_ENS;
661	>	}
662	>	else if (!strcasecmp(ensemble, "NPTf")){
663	>	ensembleCase = NPTf_ENS;
664	>	}
665	>	else if (!strcasecmp(ensemble, "NPTxyz")){
666	>	ensembleCase = NPTxyz_ENS;
667	>	}
668	>	else{
669	>	sprintf(painCave.errMsg,
670	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
671	>	"\treverting to NVE for this simulation.\n",
672	>	ensemble);
673	>	painCave.isFatal = 0;
674	>	simError();
675	>	strcpy(ensemble, "NVE");
676	>	ensembleCase = NVE_ENS;
677	>	}
678
679	<	for(j=0; j<info.nTorsions; j++){
680	<
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;
679	>	for (i = 0; i < nInfo; i++){
680	>	strcpy(info[i].ensemble, ensemble);
681
682	<	// 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;
682	>	// get the mixing rule
683
684	<
684	>	strcpy(info[i].mixingRule, globals->getMixingRule());
685	>	info[i].usePBC = globals->getPBC();
686	>	}
687
688	+	// get the components and calculate the tot_nMol and indvidual n_mol
689
690	+	the_components = globals->getComponents();
691	+	components_nmol = new int[n_components];
692
693
694	+	if (!globals->haveNMol()){
695	+	// we don't have the total number of molecules, so we assume it is
696	+	// given in each component
697
698	+	tot_nmol = 0;
699	+	for (i = 0; i < n_components; i++){
700	+	if (!the_components[i]->haveNMol()){
701	+	// we have a problem
702	+	sprintf(painCave.errMsg,
703	+	"SimSetup Error. No global NMol or component NMol given.\n"
704	+	"\tCannot calculate the number of atoms.\n");
705	+	painCave.isFatal = 1;
706	+	simError();
707	+	}
708
709	<	void SimSetup::makeAtoms( void ){
709	>	tot_nmol += the_components[i]->getNMol();
710	>	components_nmol[i] = the_components[i]->getNMol();
711	>	}
712	>	}
713	>	else{
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error.\n"
716	>	"\tSorry, the ability to specify total"
717	>	" nMols and then give molfractions in the components\n"
718	>	"\tis not currently supported."
719	>	" Please give nMol in the components.\n");
720	>	painCave.isFatal = 1;
721	>	simError();
722	>	}
723
724	<	int i, j, k, index;
725	<	double ux, uy, uz, uSqr, u;
726	<	AtomStamp* current_atom;
724	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
725	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
726	>	sprintf(painCave.errMsg,
727	>	"Sample time is not divisible by dt.\n"
728	>	"\tThis will result in samples that are not uniformly\n"
729	>	"\tdistributed in time.  If this is a problem, change\n"
730	>	"\tyour sampleTime variable.\n");
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734
735	<	DirectionalAtom* dAtom;
736	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
735	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
736	>	sprintf(painCave.errMsg,
737	>	"Status time is not divisible by dt.\n"
738	>	"\tThis will result in status reports that are not uniformly\n"
739	>	"\tdistributed in time.  If this is a problem, change \n"
740	>	"\tyour statusTime variable.\n");
741	>	painCave.isFatal = 0;
742	>	simError();
743	>	}
744
745	<	lMolIndex = 0;
746	<	molIndex = 0;
747	<	index = 0;
748	<	for( i=0; i<n_components; i++ ){
745	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
746	>	sprintf(painCave.errMsg,
747	>	"Thermal time is not divisible by dt.\n"
748	>	"\tThis will result in thermalizations that are not uniformly\n"
749	>	"\tdistributed in time.  If this is a problem, change \n"
750	>	"\tyour thermalTime variable.\n");
751	>	painCave.isFatal = 0;
752	>	simError();
753	>	}
754
755	<	for( j=0; j<components_nmol[i]; j++ ){
755	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
756	>	sprintf(painCave.errMsg,
757	>	"Reset time is not divisible by dt.\n"
758	>	"\tThis will result in integrator resets that are not uniformly\n"
759	>	"\tdistributed in time.  If this is a problem, change\n"
760	>	"\tyour resetTime variable.\n");
761	>	painCave.isFatal = 0;
762	>	simError();
763	>	}
764
765	<	#ifdef IS_MPI
923	<	if( mpiSim->getMyMolStart() <= molIndex &&
924	<	molIndex <= mpiSim->getMyMolEnd() ){
925	<	#endif // is_mpi
765	>	// set the status, sample, and thermal kick times
766
767	<	molStart = index;
768	<	nMemb = comp_stamps[i]->getNAtoms();
769	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
770	<
771	<	current_atom = comp_stamps[i]->getAtom( k );
772	<	if( current_atom->haveOrientation() ){
773	<
774	<	dAtom = new DirectionalAtom(index);
775	<	simnfo->n_oriented++;
776	<	the_atoms[index] = dAtom;
777	<
938	<	ux = current_atom->getOrntX();
939	<	uy = current_atom->getOrntY();
940	<	uz = current_atom->getOrntZ();
941	<
942	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943	<
944	<	u = sqrt( uSqr );
945	<	ux = ux / u;
946	<	uy = uy / u;
947	<	uz = uz / u;
948	<
949	<	dAtom->setSUx( ux );
950	<	dAtom->setSUy( uy );
951	<	dAtom->setSUz( uz );
952	<	}
953	<	else{
954	<	the_atoms[index] = new GeneralAtom(index);
955	<	}
956	<	the_atoms[index]->setType( current_atom->getType() );
957	<	the_atoms[index]->setIndex( index );
958	<
959	<	// increment the index and repeat;
960	<	index++;
961	<	}
962	<
963	<	molEnd = index -1;
964	<	the_molecules[lMolIndex].setNMembers( nMemb );
965	<	the_molecules[lMolIndex].setStartAtom( molStart );
966	<	the_molecules[lMolIndex].setEndAtom( molEnd );
967	<	the_molecules[lMolIndex].setStampID( i );
968	<	lMolIndex++;
767	>	for (i = 0; i < nInfo; i++){
768	>	if (globals->haveSampleTime()){
769	>	info[i].sampleTime = globals->getSampleTime();
770	>	info[i].statusTime = info[i].sampleTime;
771	>	info[i].thermalTime = info[i].sampleTime;
772	>	}
773	>	else{
774	>	info[i].sampleTime = globals->getRunTime();
775	>	info[i].statusTime = info[i].sampleTime;
776	>	info[i].thermalTime = info[i].sampleTime;
777	>	}
778
779	<	#ifdef IS_MPI
780	<	}
972	<	#endif //is_mpi
973	<
974	<	molIndex++;
779	>	if (globals->haveStatusTime()){
780	>	info[i].statusTime = globals->getStatusTime();
781		}
976	–	}
782
783	<	#ifdef IS_MPI
784	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
785	<
981	<	delete[] globalIndex;
783	>	if (globals->haveThermalTime()){
784	>	info[i].thermalTime = globals->getThermalTime();
785	>	}
786
787	<	mpiSim->mpiRefresh();
788	<	#endif //IS_MPI
789	<
790	<	the_ff->initializeAtoms();
791	<	}
787	>	info[i].resetIntegrator = 0;
788	>	if( globals->haveResetTime() ){
789	>	info[i].resetTime = globals->getResetTime();
790	>	info[i].resetIntegrator = 1;
791	>	}
792
793	<	void SimSetup::makeBonds( void ){
793	>	// check for the temperature set flag
794	>
795	>	if (globals->haveTempSet())
796	>	info[i].setTemp = globals->getTempSet();
797
798	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
992	<	bond_pair* the_bonds;
993	<	BondStamp* current_bond;
798	>	// check for the extended State init
799
800	<	the_bonds = new bond_pair[tot_bonds];
801	<	index = 0;
802	<	offset = 0;
803	<	molIndex = 0;
800	>	info[i].useInitXSstate = globals->getUseInitXSstate();
801	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
802	>
803	>	}
804	>
805	>	//setup seed for random number generator
806	>	int seedValue;
807
808	<	for( i=0; i<n_components; i++ ){
808	>	if (globals->haveSeed()){
809	>	seedValue = globals->getSeed();
810
811	<	for( j=0; j<components_nmol[i]; j++ ){
811	>	if(seedValue / 1E9 == 0){
812	>	sprintf(painCave.errMsg,
813	>	"Seed for sprng library should contain at least 9 digits\n"
814	>	"OOPSE will generate a seed for user\n");
815	>	painCave.isFatal = 0;
816	>	simError();
817
818	<	#ifdef IS_MPI
819	<	if( mpiSim->getMyMolStart() <= molIndex &&
820	<	molIndex <= mpiSim->getMyMolEnd() ){
821	<	#endif // is_mpi
822	<
823	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010	<
1011	<	current_bond = comp_stamps[i]->getBond( k );
1012	<	the_bonds[index].a = current_bond->getA() + offset;
1013	<	the_bonds[index].b = current_bond->getB() + offset;
1014	<
1015	<	exI = the_bonds[index].a;
1016	<	exJ = the_bonds[index].b;
1017	<
1018	<	// exclude_I must always be the smaller of the pair
1019	<	if( exI > exJ ){
1020	<	tempEx = exI;
1021	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
1024	<
1025	<
1026	<	#ifdef IS_MPI
1027	<
1028	<	the_excludes[index*2] =
1029	<	the_atoms[exI]->getGlobalIndex() + 1;
1030	<	the_excludes[index*2 + 1] =
1031	<	the_atoms[exJ]->getGlobalIndex() + 1;
1032	<
1033	<	#else  // isn't MPI
1034	<
1035	<	the_excludes[index*2] =     exI + 1;
1036	<	the_excludes[index*2 + 1] = exJ + 1;
1037	<	// fortran index from 1 (hence the +1 in the indexing)
1038	<	#endif  //is_mpi
1039	<
1040	<	// increment the index and repeat;
1041	<	index++;
1042	<	}
1043	<	offset += comp_stamps[i]->getNAtoms();
1044	<
1045	<	#ifdef IS_MPI
818	>	//using seed generated by system instead of invalid seed set by user
819	>	#ifndef IS_MPI
820	>	seedValue = make_sprng_seed();
821	>	#else
822	>	if (worldRank == 0){
823	>	seedValue = make_sprng_seed();
824		}
825	<	#endif //is_mpi
826	<
827	<	molIndex++;
828	<	}
825	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
826	>	#endif
827	>	}
828	>	}//end of if branch of globals->haveSeed()
829	>	else{
830	>
831	>	#ifndef IS_MPI
832	>	seedValue = make_sprng_seed();
833	>	#else
834	>	if (worldRank == 0){
835	>	seedValue = make_sprng_seed();
836	>	}
837	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
838	>	#endif
839	>	}//end of globals->haveSeed()
840	>
841	>	for (int i = 0; i < nInfo; i++){
842	>	info[i].setSeed(seedValue);
843		}
844
845	<	the_ff->initializeBonds( the_bonds );
845	>	#ifdef IS_MPI
846	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
847	>	MPIcheckPoint();
848	>	#endif // is_mpi
849		}
850
1056	–	void SimSetup::makeBends( void ){
851
852	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
853	<	bend_set* the_bends;
854	<	BendStamp* current_bend;
855	<	LinkedAssign* extras;
1062	<	LinkedAssign* current_extra;
1063	<
852	>	void SimSetup::finalInfoCheck(void){
853	>	int index;
854	>	int usesDipoles;
855	>	int i;
856
857	<	the_bends = new bend_set[tot_bends];
858	<	index = 0;
1067	<	offset = 0;
1068	<	molIndex = 0;
1069	<	for( i=0; i<n_components; i++ ){
857	>	for (i = 0; i < nInfo; i++){
858	>	// check electrostatic parameters
859
860	<	for( j=0; j<components_nmol[i]; j++ ){
860	>	index = 0;
861	>	usesDipoles = 0;
862	>	while ((index < info[i].n_atoms) && !usesDipoles){
863	>	usesDipoles = (info[i].atoms[index])->hasDipole();
864	>	index++;
865	>	}
866
867		#ifdef IS_MPI
868	<	if( mpiSim->getMyMolStart() <= molIndex &&
869	<	molIndex <= mpiSim->getMyMolEnd() ){
870	<	#endif // is_mpi
868	>	int myUse = usesDipoles;
869	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
870	>	#endif //is_mpi
871
872	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079	<
1080	<	current_bend = comp_stamps[i]->getBend( k );
1081	<	the_bends[index].a = current_bend->getA() + offset;
1082	<	the_bends[index].b = current_bend->getB() + offset;
1083	<	the_bends[index].c = current_bend->getC() + offset;
1084	<
1085	<	if( current_bend->haveExtras() ){
1086	<
1087	<	extras = current_bend->getExtras();
1088	<	current_extra = extras;
1089	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	the_bends[index].ghost =
1097	<	current_extra->getInt() + offset;
1098	<	the_bends[index].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	the_bends[index].ghost =
1103	<	(int)current_extra->getDouble() + offset;
1104	<	the_bends[index].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neiter a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	k, comp_stamps[i]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	k, comp_stamps[i]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1131	<	}
1132	<
1133	<	if( !the_bends[index].isGhost ){
1134	<
1135	<	exI = the_bends[index].a;
1136	<	exJ = the_bends[index].c;
1137	<	}
1138	<	else{
1139	<
1140	<	exI = the_bends[index].a;
1141	<	exJ = the_bends[index].b;
1142	<	}
1143	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
872	>	double theEcr, theEst;
873
874	+	if (globals->getUseRF()){
875	+	info[i].useReactionField = 1;
876
877	<	#ifdef IS_MPI
877	>	if (!globals->haveECR()){
878	>	sprintf(painCave.errMsg,
879	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
880	>	"\tOOPSE will use a default value of 15.0 angstroms"
881	>	"\tfor the electrostaticCutoffRadius.\n");
882	>	painCave.isFatal = 0;
883	>	simError();
884	>	theEcr = 15.0;
885	>	}
886	>	else{
887	>	theEcr = globals->getECR();
888	>	}
889
890	<	the_excludes[(index + tot_bonds)*2] =
891	<	the_atoms[exI]->getGlobalIndex() + 1;
892	<	the_excludes[(index + tot_bonds)*2 + 1] =
893	<	the_atoms[exJ]->getGlobalIndex() + 1;
894	<
895	<	#else  // isn't MPI
896	<
897	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
898	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163	<	// fortran index from 1 (hence the +1 in the indexing)
1164	<	#endif  //is_mpi
1165	<
1166	<
1167	<	// increment the index and repeat;
1168	<	index++;
1169	<	}
1170	<	offset += comp_stamps[i]->getNAtoms();
1171	<
1172	<	#ifdef IS_MPI
890	>	if (!globals->haveEST()){
891	>	sprintf(painCave.errMsg,
892	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
893	>	"\tOOPSE will use a default value of\n"
894	>	"\t0.05 * electrostaticCutoffRadius\n"
895	>	"\tfor the electrostaticSkinThickness\n");
896	>	painCave.isFatal = 0;
897	>	simError();
898	>	theEst = 0.05 * theEcr;
899		}
900	<	#endif //is_mpi
900	>	else{
901	>	theEst = globals->getEST();
902	>	}
903
904	<	molIndex++;
904	>	info[i].setDefaultEcr(theEcr, theEst);
905	>
906	>	if (!globals->haveDielectric()){
907	>	sprintf(painCave.errMsg,
908	>	"SimSetup Error: No Dielectric constant was set.\n"
909	>	"\tYou are trying to use Reaction Field without"
910	>	"\tsetting a dielectric constant!\n");
911	>	painCave.isFatal = 1;
912	>	simError();
913	>	}
914	>	info[i].dielectric = globals->getDielectric();
915		}
916	+	else{
917	+	if (usesDipoles){
918	+	if (!globals->haveECR()){
919	+	sprintf(painCave.errMsg,
920	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
921	+	"\tOOPSE will use a default value of 15.0 angstroms"
922	+	"\tfor the electrostaticCutoffRadius.\n");
923	+	painCave.isFatal = 0;
924	+	simError();
925	+	theEcr = 15.0;
926	+	}
927	+	else{
928	+	theEcr = globals->getECR();
929	+	}
930	+
931	+	if (!globals->haveEST()){
932	+	sprintf(painCave.errMsg,
933	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
934	+	"\tOOPSE will use a default value of\n"
935	+	"\t0.05 * electrostaticCutoffRadius\n"
936	+	"\tfor the electrostaticSkinThickness\n");
937	+	painCave.isFatal = 0;
938	+	simError();
939	+	theEst = 0.05 * theEcr;
940	+	}
941	+	else{
942	+	theEst = globals->getEST();
943	+	}
944	+
945	+	info[i].setDefaultEcr(theEcr, theEst);
946	+	}
947	+	}
948		}
1179	–
949		#ifdef IS_MPI
950	<	sprintf( checkPointMsg,
1182	<	"Successfully created the bends list.\n" );
950	>	strcpy(checkPointMsg, "post processing checks out");
951		MPIcheckPoint();
952		#endif // is_mpi
953	+	}
954
955	+	void SimSetup::initSystemCoords(void){
956	+	int i;
957
958	<	the_ff->initializeBends( the_bends );
1188	<	}
958	>	char* inName;
959
960	<	void SimSetup::makeTorsions( void ){
960	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
961
962	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
963	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
962	>	for (i = 0; i < info[0].n_atoms; i++)
963	>	info[0].atoms[i]->setCoords();
964
965	<	the_torsions = new torsion_set[tot_torsions];
966	<	index = 0;
967	<	offset = 0;
968	<	molIndex = 0;
969	<	for( i=0; i<n_components; i++ ){
965	>	if (globals->haveInitialConfig()){
966	>	InitializeFromFile* fileInit;
967	>	#ifdef IS_MPI // is_mpi
968	>	if (worldRank == 0){
969	>	#endif //is_mpi
970	>	inName = globals->getInitialConfig();
971	>	fileInit = new InitializeFromFile(inName);
972	>	#ifdef IS_MPI
973	>	}
974	>	else
975	>	fileInit = new InitializeFromFile(NULL);
976	>	#endif
977	>	fileInit->readInit(info); // default velocities on
978
979	<	for( j=0; j<components_nmol[i]; j++ ){
979	>	delete fileInit;
980	>	}
981	>	else{
982	>
983	>	// no init from bass
984	>
985	>	sprintf(painCave.errMsg,
986	>	"Cannot intialize a simulation without an initial configuration file.\n");
987	>	painCave.isFatal = 1;;
988	>	simError();
989	>
990	>	}
991
992		#ifdef IS_MPI
993	<	if( mpiSim->getMyMolStart() <= molIndex &&
994	<	molIndex <= mpiSim->getMyMolEnd() ){
995	<	#endif // is_mpi
993	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
994	>	MPIcheckPoint();
995	>	#endif // is_mpi
996	>	}
997
1209	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
998
999	<	current_torsion = comp_stamps[i]->getTorsion( k );
1000	<	the_torsions[index].a = current_torsion->getA() + offset;
1213	<	the_torsions[index].b = current_torsion->getB() + offset;
1214	<	the_torsions[index].c = current_torsion->getC() + offset;
1215	<	the_torsions[index].d = current_torsion->getD() + offset;
999	>	void SimSetup::makeOutNames(void){
1000	>	int k;
1001
1217	–	exI = the_torsions[index].a;
1218	–	exJ = the_torsions[index].d;
1002
1003	<
1221	<	// exclude_I must always be the smaller of the pair
1222	<	if( exI > exJ ){
1223	<	tempEx = exI;
1224	<	exI = exJ;
1225	<	exJ = tempEx;
1226	<	}
1227	<
1228	<
1003	>	for (k = 0; k < nInfo; k++){
1004		#ifdef IS_MPI
1005	<
1006	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1232	<	the_atoms[exI]->getGlobalIndex() + 1;
1233	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1234	<	the_atoms[exJ]->getGlobalIndex() + 1;
1235	<
1236	<	#else  // isn't MPI
1237	<
1238	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240	<	// fortran indexes from 1 (hence the +1 in the indexing)
1241	<	#endif  //is_mpi
1242	<
1005	>	if (worldRank == 0){
1006	>	#endif // is_mpi
1007
1008	<	// increment the index and repeat;
1009	<	index++;
1008	>	if (globals->haveFinalConfig()){
1009	>	strcpy(info[k].finalName, globals->getFinalConfig());
1010		}
1011	<	offset += comp_stamps[i]->getNAtoms();
1012	<
1013	<	#ifdef IS_MPI
1011	>	else{
1012	>	strcpy(info[k].finalName, inFileName);
1013	>	char* endTest;
1014	>	int nameLength = strlen(info[k].finalName);
1015	>	endTest = &(info[k].finalName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".eor");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".eor");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].finalName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".eor");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".eor");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].finalName, ".eor");
1032	>	}
1033	>	}
1034		}
1251	–	#endif //is_mpi
1035
1036	<	molIndex++;
1036	>	// make the sample and status out names
1037	>
1038	>	strcpy(info[k].sampleName, inFileName);
1039	>	char* endTest;
1040	>	int nameLength = strlen(info[k].sampleName);
1041	>	endTest = &(info[k].sampleName[nameLength - 5]);
1042	>	if (!strcmp(endTest, ".bass")){
1043	>	strcpy(endTest, ".dump");
1044	>	}
1045	>	else if (!strcmp(endTest, ".BASS")){
1046	>	strcpy(endTest, ".dump");
1047	>	}
1048	>	else{
1049	>	endTest = &(info[k].sampleName[nameLength - 4]);
1050	>	if (!strcmp(endTest, ".bss")){
1051	>	strcpy(endTest, ".dump");
1052	>	}
1053	>	else if (!strcmp(endTest, ".mdl")){
1054	>	strcpy(endTest, ".dump");
1055	>	}
1056	>	else{
1057	>	strcat(info[k].sampleName, ".dump");
1058	>	}
1059	>	}
1060	>
1061	>	strcpy(info[k].statusName, inFileName);
1062	>	nameLength = strlen(info[k].statusName);
1063	>	endTest = &(info[k].statusName[nameLength - 5]);
1064	>	if (!strcmp(endTest, ".bass")){
1065	>	strcpy(endTest, ".stat");
1066	>	}
1067	>	else if (!strcmp(endTest, ".BASS")){
1068	>	strcpy(endTest, ".stat");
1069	>	}
1070	>	else{
1071	>	endTest = &(info[k].statusName[nameLength - 4]);
1072	>	if (!strcmp(endTest, ".bss")){
1073	>	strcpy(endTest, ".stat");
1074	>	}
1075	>	else if (!strcmp(endTest, ".mdl")){
1076	>	strcpy(endTest, ".stat");
1077	>	}
1078	>	else{
1079	>	strcat(info[k].statusName, ".stat");
1080	>	}
1081	>	}
1082	>
1083	>	#ifdef IS_MPI
1084	>
1085		}
1086	+	#endif // is_mpi
1087		}
1088	+	}
1089
1090	<	the_ff->initializeTorsions( the_torsions );
1090	>
1091	>	void SimSetup::sysObjectsCreation(void){
1092	>	int i, k;
1093	>
1094	>	// create the forceField
1095	>
1096	>	createFF();
1097	>
1098	>	// extract componentList
1099	>
1100	>	compList();
1101	>
1102	>	// calc the number of atoms, bond, bends, and torsions
1103	>
1104	>	calcSysValues();
1105	>
1106	>	#ifdef IS_MPI
1107	>	// divide the molecules among the processors
1108	>
1109	>	mpiMolDivide();
1110	>	#endif //is_mpi
1111	>
1112	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1113	>
1114	>	makeSysArrays();
1115	>
1116	>	// make and initialize the molecules (all but atomic coordinates)
1117	>
1118	>	makeMolecules();
1119	>
1120	>	for (k = 0; k < nInfo; k++){
1121	>	info[k].identArray = new int[info[k].n_atoms];
1122	>	for (i = 0; i < info[k].n_atoms; i++){
1123	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1124	>	}
1125	>	}
1126		}
1127
1260	–	void SimSetup::initFromBass( void ){
1128
1129	<	int i, j, k;
1130	<	int n_cells;
1131	<	double cellx, celly, cellz;
1132	<	double temp1, temp2, temp3;
1133	<	int n_per_extra;
1267	<	int n_extra;
1268	<	int have_extra, done;
1129	>	void SimSetup::createFF(void){
1130	>	switch (ffCase){
1131	>	case FF_DUFF:
1132	>	the_ff = new DUFF();
1133	>	break;
1134
1135	<	temp1 = (double)tot_nmol / 4.0;
1136	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1137	<	temp3 = ceil( temp2 );
1135	>	case FF_LJ:
1136	>	the_ff = new LJFF();
1137	>	break;
1138
1139	<	have_extra =0;
1140	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1141	<	have_extra =1;
1139	>	case FF_EAM:
1140	>	the_ff = new EAM_FF();
1141	>	break;
1142
1143	<	n_cells = (int)temp3 - 1;
1144	<	cellx = simnfo->box_x / temp3;
1145	<	celly = simnfo->box_y / temp3;
1281	<	cellz = simnfo->box_z / temp3;
1282	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1283	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1284	<	n_per_extra = (int)ceil( temp1 );
1143	>	case FF_H2O:
1144	>	the_ff = new WATER();
1145	>	break;
1146
1147	<	if( n_per_extra > 4){
1148	<	sprintf( painCave.errMsg,
1149	<	"SimSetup error. There has been an error in constructing"
1289	<	" the non-complete lattice.\n" );
1147	>	default:
1148	>	sprintf(painCave.errMsg,
1149	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1150		painCave.isFatal = 1;
1151		simError();
1292	–	}
1152		}
1294	–	else{
1295	–	n_cells = (int)temp3;
1296	–	cellx = simnfo->box_x / temp3;
1297	–	celly = simnfo->box_y / temp3;
1298	–	cellz = simnfo->box_z / temp3;
1299	–	}
1153
1154	<	current_mol = 0;
1155	<	current_comp_mol = 0;
1156	<	current_comp = 0;
1157	<	current_atom_ndx = 0;
1154	>	#ifdef IS_MPI
1155	>	strcpy(checkPointMsg, "ForceField creation successful");
1156	>	MPIcheckPoint();
1157	>	#endif // is_mpi
1158	>	}
1159
1306	–	for( i=0; i < n_cells ; i++ ){
1307	–	for( j=0; j < n_cells; j++ ){
1308	–	for( k=0; k < n_cells; k++ ){
1160
1161	<	makeElement( i * cellx,
1162	<	j * celly,
1163	<	k * cellz );
1161	>	void SimSetup::compList(void){
1162	>	int i;
1163	>	char* id;
1164	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1165	>	LinkedMolStamp* currentStamp = NULL;
1166	>	comp_stamps = new MoleculeStamp * [n_components];
1167
1168	<	makeElement( i * cellx + 0.5 * cellx,
1169	<	j * celly + 0.5 * celly,
1316	<	k * cellz );
1168	>	// make an array of molecule stamps that match the components used.
1169	>	// also extract the used stamps out into a separate linked list
1170
1171	<	makeElement( i * cellx,
1172	<	j * celly + 0.5 * celly,
1173	<	k * cellz + 0.5 * cellz );
1171	>	for (i = 0; i < nInfo; i++){
1172	>	info[i].nComponents = n_components;
1173	>	info[i].componentsNmol = components_nmol;
1174	>	info[i].compStamps = comp_stamps;
1175	>	info[i].headStamp = headStamp;
1176	>	}
1177
1178	<	makeElement( i * cellx + 0.5 * cellx,
1179	<	j * celly,
1180	<	k * cellz + 0.5 * cellz );
1178	>
1179	>	for (i = 0; i < n_components; i++){
1180	>	id = the_components[i]->getType();
1181	>	comp_stamps[i] = NULL;
1182	>
1183	>	// check to make sure the component isn't already in the list
1184	>
1185	>	comp_stamps[i] = headStamp->match(id);
1186	>	if (comp_stamps[i] == NULL){
1187	>	// extract the component from the list;
1188	>
1189	>	currentStamp = stamps->extractMolStamp(id);
1190	>	if (currentStamp == NULL){
1191	>	sprintf(painCave.errMsg,
1192	>	"SimSetup error: Component \"%s\" was not found in the "
1193	>	"list of declared molecules\n",
1194	>	id);
1195	>	painCave.isFatal = 1;
1196	>	simError();
1197		}
1198	+
1199	+	headStamp->add(currentStamp);
1200	+	comp_stamps[i] = headStamp->match(id);
1201		}
1202		}
1203
1204	<	if( have_extra ){
1205	<	done = 0;
1204	>	#ifdef IS_MPI
1205	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1206	>	MPIcheckPoint();
1207	>	#endif // is_mpi
1208	>	}
1209
1210	<	int start_ndx;
1211	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1334	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1210	>	void SimSetup::calcSysValues(void){
1211	>	int i;
1212
1213	<	if( i < n_cells ){
1213	>	int* molMembershipArray;
1214
1215	<	if( j < n_cells ){
1216	<	start_ndx = n_cells;
1217	<	}
1218	<	else start_ndx = 0;
1219	<	}
1220	<	else start_ndx = 0;
1215	>	tot_atoms = 0;
1216	>	tot_bonds = 0;
1217	>	tot_bends = 0;
1218	>	tot_torsions = 0;
1219	>	for (i = 0; i < n_components; i++){
1220	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1221	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1222	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1223	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1224	>	}
1225
1226	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1226	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1227	>	molMembershipArray = new int[tot_atoms];
1228
1229	<	makeElement( i * cellx,
1230	<	j * celly,
1231	<	k * cellz );
1232	<	done = ( current_mol >= tot_nmol );
1229	>	for (i = 0; i < nInfo; i++){
1230	>	info[i].n_atoms = tot_atoms;
1231	>	info[i].n_bonds = tot_bonds;
1232	>	info[i].n_bends = tot_bends;
1233	>	info[i].n_torsions = tot_torsions;
1234	>	info[i].n_SRI = tot_SRI;
1235	>	info[i].n_mol = tot_nmol;
1236
1237	<	if( !done && n_per_extra > 1 ){
1238	<	makeElement( i * cellx + 0.5 * cellx,
1239	<	j * celly + 0.5 * celly,
1355	<	k * cellz );
1356	<	done = ( current_mol >= tot_nmol );
1357	<	}
1237	>	info[i].molMembershipArray = molMembershipArray;
1238	>	}
1239	>	}
1240
1241	<	if( !done && n_per_extra > 2){
1360	<	makeElement( i * cellx,
1361	<	j * celly + 0.5 * celly,
1362	<	k * cellz + 0.5 * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1364	<	}
1241	>	#ifdef IS_MPI
1242
1243	<	if( !done && n_per_extra > 3){
1244	<	makeElement( i * cellx + 0.5 * cellx,
1245	<	j * celly,
1246	<	k * cellz + 0.5 * cellz );
1247	<	done = ( current_mol >= tot_nmol );
1248	<	}
1249	<	}
1243	>	void SimSetup::mpiMolDivide(void){
1244	>	int i, j, k;
1245	>	int localMol, allMol;
1246	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1247	>
1248	>	mpiSim = new mpiSimulation(info);
1249	>
1250	>	globalIndex = mpiSim->divideLabor();
1251	>
1252	>	// set up the local variables
1253	>
1254	>	mol2proc = mpiSim->getMolToProcMap();
1255	>	molCompType = mpiSim->getMolComponentType();
1256	>
1257	>	allMol = 0;
1258	>	localMol = 0;
1259	>	local_atoms = 0;
1260	>	local_bonds = 0;
1261	>	local_bends = 0;
1262	>	local_torsions = 0;
1263	>	globalAtomIndex = 0;
1264	>
1265	>
1266	>	for (i = 0; i < n_components; i++){
1267	>	for (j = 0; j < components_nmol[i]; j++){
1268	>	if (mol2proc[allMol] == worldRank){
1269	>	local_atoms += comp_stamps[i]->getNAtoms();
1270	>	local_bonds += comp_stamps[i]->getNBonds();
1271	>	local_bends += comp_stamps[i]->getNBends();
1272	>	local_torsions += comp_stamps[i]->getNTorsions();
1273	>	localMol++;
1274	>	}
1275	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1276	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1277	>	globalAtomIndex++;
1278		}
1279	+
1280	+	allMol++;
1281		}
1282		}
1283	+	local_SRI = local_bonds + local_bends + local_torsions;
1284
1285	+	info[0].n_atoms = mpiSim->getMyNlocal();
1286
1287	<	for( i=0; i<simnfo->n_atoms; i++ ){
1288	<	simnfo->atoms[i]->set_vx( 0.0 );
1289	<	simnfo->atoms[i]->set_vy( 0.0 );
1290	<	simnfo->atoms[i]->set_vz( 0.0 );
1287	>	if (local_atoms != info[0].n_atoms){
1288	>	sprintf(painCave.errMsg,
1289	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1290	>	"\tlocalAtom (%d) are not equal.\n",
1291	>	info[0].n_atoms, local_atoms);
1292	>	painCave.isFatal = 1;
1293	>	simError();
1294		}
1295	+
1296	+	info[0].n_bonds = local_bonds;
1297	+	info[0].n_bends = local_bends;
1298	+	info[0].n_torsions = local_torsions;
1299	+	info[0].n_SRI = local_SRI;
1300	+	info[0].n_mol = localMol;
1301	+
1302	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1303	+	MPIcheckPoint();
1304		}
1305
1306	<	void SimSetup::makeElement( double x, double y, double z ){
1306	>	#endif // is_mpi
1307
1387	–	int k;
1388	–	AtomStamp* current_atom;
1389	–	DirectionalAtom* dAtom;
1390	–	double rotMat[3][3];
1308
1309	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1309	>	void SimSetup::makeSysArrays(void){
1310	>
1311	>	#ifndef IS_MPI
1312	>	int k, j;
1313	>	#endif // is_mpi
1314	>	int i, l;
1315
1316	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1317	<	if( !current_atom->havePosition() ){
1318	<	sprintf( painCave.errMsg,
1397	<	"SimSetup:initFromBass error.\n"
1398	<	"\tComponent %s, atom %s does not have a position specified.\n"
1399	<	"\tThe initialization routine is unable to give a start"
1400	<	" position.\n",
1401	<	comp_stamps[current_comp]->getID(),
1402	<	current_atom->getType() );
1403	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1316	>	Atom** the_atoms;
1317	>	Molecule* the_molecules;
1318	>	Exclude** the_excludes;
1319
1407	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1408	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1409	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1320
1321	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1321	>	for (l = 0; l < nInfo; l++){
1322	>	// create the atom and short range interaction arrays
1323
1324	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1324	>	the_atoms = new Atom * [info[l].n_atoms];
1325	>	the_molecules = new Molecule[info[l].n_mol];
1326	>	int molIndex;
1327
1328	<	rotMat[0][0] = 1.0;
1416	<	rotMat[0][1] = 0.0;
1417	<	rotMat[0][2] = 0.0;
1328	>	// initialize the molecule's stampID's
1329
1330	<	rotMat[1][0] = 0.0;
1420	<	rotMat[1][1] = 1.0;
1421	<	rotMat[1][2] = 0.0;
1330	>	#ifdef IS_MPI
1331
1423	–	rotMat[2][0] = 0.0;
1424	–	rotMat[2][1] = 0.0;
1425	–	rotMat[2][2] = 1.0;
1332
1333	<	dAtom->setA( rotMat );
1333	>	molIndex = 0;
1334	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1335	>	if (mol2proc[i] == worldRank){
1336	>	the_molecules[molIndex].setStampID(molCompType[i]);
1337	>	the_molecules[molIndex].setMyIndex(molIndex);
1338	>	the_molecules[molIndex].setGlobalIndex(i);
1339	>	molIndex++;
1340	>	}
1341		}
1342
1343	<	current_atom_ndx++;
1343	>	#else // is_mpi
1344	>
1345	>	molIndex = 0;
1346	>	globalAtomIndex = 0;
1347	>	for (i = 0; i < n_components; i++){
1348	>	for (j = 0; j < components_nmol[i]; j++){
1349	>	the_molecules[molIndex].setStampID(i);
1350	>	the_molecules[molIndex].setMyIndex(molIndex);
1351	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1352	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1353	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1354	>	globalAtomIndex++;
1355	>	}
1356	>	molIndex++;
1357	>	}
1358	>	}
1359	>
1360	>
1361	>	#endif // is_mpi
1362	>
1363	>
1364	>	if (info[l].n_SRI){
1365	>	Exclude::createArray(info[l].n_SRI);
1366	>	the_excludes = new Exclude * [info[l].n_SRI];
1367	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1368	>	the_excludes[ex] = new Exclude(ex);
1369	>	}
1370	>	info[l].globalExcludes = new int;
1371	>	info[l].n_exclude = info[l].n_SRI;
1372	>	}
1373	>	else{
1374	>	Exclude::createArray(1);
1375	>	the_excludes = new Exclude * ;
1376	>	the_excludes[0] = new Exclude(0);
1377	>	the_excludes[0]->setPair(0, 0);
1378	>	info[l].globalExcludes = new int;
1379	>	info[l].globalExcludes[0] = 0;
1380	>	info[l].n_exclude = 0;
1381	>	}
1382	>
1383	>	// set the arrays into the SimInfo object
1384	>
1385	>	info[l].atoms = the_atoms;
1386	>	info[l].molecules = the_molecules;
1387	>	info[l].nGlobalExcludes = 0;
1388	>	info[l].excludes = the_excludes;
1389	>
1390	>	the_ff->setSimInfo(info);
1391		}
1392	+	}
1393
1394	<	current_mol++;
1395	<	current_comp_mol++;
1394	>	void SimSetup::makeIntegrator(void){
1395	>	int k;
1396
1397	<	if( current_comp_mol >= components_nmol[current_comp] ){
1397	>	NVE<RealIntegrator>* myNVE = NULL;
1398	>	NVT<RealIntegrator>* myNVT = NULL;
1399	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1400	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1401	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1402	>
1403	>	for (k = 0; k < nInfo; k++){
1404	>	switch (ensembleCase){
1405	>	case NVE_ENS:
1406	>	if (globals->haveZconstraints()){
1407	>	setupZConstraint(info[k]);
1408	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1409	>	}
1410	>	else{
1411	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1412	>	}
1413	>
1414	>	info->the_integrator = myNVE;
1415	>	break;
1416
1417	<	current_comp_mol = 0;
1418	<	current_comp++;
1417	>	case NVT_ENS:
1418	>	if (globals->haveZconstraints()){
1419	>	setupZConstraint(info[k]);
1420	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1421	>	}
1422	>	else
1423	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1424	>
1425	>	myNVT->setTargetTemp(globals->getTargetTemp());
1426	>
1427	>	if (globals->haveTauThermostat())
1428	>	myNVT->setTauThermostat(globals->getTauThermostat());
1429	>	else{
1430	>	sprintf(painCave.errMsg,
1431	>	"SimSetup error: If you use the NVT\n"
1432	>	"\tensemble, you must set tauThermostat.\n");
1433	>	painCave.isFatal = 1;
1434	>	simError();
1435	>	}
1436	>
1437	>	info->the_integrator = myNVT;
1438	>	break;
1439	>
1440	>	case NPTi_ENS:
1441	>	if (globals->haveZconstraints()){
1442	>	setupZConstraint(info[k]);
1443	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1444	>	}
1445	>	else
1446	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1447	>
1448	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1449	>
1450	>	if (globals->haveTargetPressure())
1451	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1452	>	else{
1453	>	sprintf(painCave.errMsg,
1454	>	"SimSetup error: If you use a constant pressure\n"
1455	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if (globals->haveTauThermostat())
1461	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1462	>	else{
1463	>	sprintf(painCave.errMsg,
1464	>	"SimSetup error: If you use an NPT\n"
1465	>	"\tensemble, you must set tauThermostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469	>
1470	>	if (globals->haveTauBarostat())
1471	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1472	>	else{
1473	>	sprintf(painCave.errMsg,
1474	>	"SimSetup error: If you use an NPT\n"
1475	>	"\tensemble, you must set tauBarostat.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	info->the_integrator = myNPTi;
1481	>	break;
1482	>
1483	>	case NPTf_ENS:
1484	>	if (globals->haveZconstraints()){
1485	>	setupZConstraint(info[k]);
1486	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1487	>	}
1488	>	else
1489	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1490	>
1491	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1492	>
1493	>	if (globals->haveTargetPressure())
1494	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1495	>	else{
1496	>	sprintf(painCave.errMsg,
1497	>	"SimSetup error: If you use a constant pressure\n"
1498	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1499	>	painCave.isFatal = 1;
1500	>	simError();
1501	>	}
1502	>
1503	>	if (globals->haveTauThermostat())
1504	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1505	>
1506	>	else{
1507	>	sprintf(painCave.errMsg,
1508	>	"SimSetup error: If you use an NPT\n"
1509	>	"\tensemble, you must set tauThermostat.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513	>
1514	>	if (globals->haveTauBarostat())
1515	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1516	>
1517	>	else{
1518	>	sprintf(painCave.errMsg,
1519	>	"SimSetup error: If you use an NPT\n"
1520	>	"\tensemble, you must set tauBarostat.\n");
1521	>	painCave.isFatal = 1;
1522	>	simError();
1523	>	}
1524	>
1525	>	info->the_integrator = myNPTf;
1526	>	break;
1527	>
1528	>	case NPTxyz_ENS:
1529	>	if (globals->haveZconstraints()){
1530	>	setupZConstraint(info[k]);
1531	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1532	>	}
1533	>	else
1534	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1535	>
1536	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1537	>
1538	>	if (globals->haveTargetPressure())
1539	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1540	>	else{
1541	>	sprintf(painCave.errMsg,
1542	>	"SimSetup error: If you use a constant pressure\n"
1543	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if (globals->haveTauThermostat())
1549	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1550	>	else{
1551	>	sprintf(painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"\tensemble, you must set tauThermostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>
1558	>	if (globals->haveTauBarostat())
1559	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1560	>	else{
1561	>	sprintf(painCave.errMsg,
1562	>	"SimSetup error: If you use an NPT\n"
1563	>	"\tensemble, you must set tauBarostat.\n");
1564	>	painCave.isFatal = 1;
1565	>	simError();
1566	>	}
1567	>
1568	>	info->the_integrator = myNPTxyz;
1569	>	break;
1570	>
1571	>	default:
1572	>	sprintf(painCave.errMsg,
1573	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1574	>	painCave.isFatal = 1;
1575	>	simError();
1576	>	}
1577		}
1578		}
1579	+
1580	+	void SimSetup::initFortran(void){
1581	+	info[0].refreshSim();
1582	+
1583	+	if (!strcmp(info[0].mixingRule, "standard")){
1584	+	the_ff->initForceField(LB_MIXING_RULE);
1585	+	}
1586	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1587	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1588	+	}
1589	+	else{
1590	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1591	+	info[0].mixingRule);
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595	+
1596	+
1597	+	#ifdef IS_MPI
1598	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1599	+	MPIcheckPoint();
1600	+	#endif // is_mpi
1601	+	}
1602	+
1603	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1604	+	int nZConstraints;
1605	+	ZconStamp** zconStamp;
1606	+
1607	+	if (globals->haveZconstraintTime()){
1608	+	//add sample time of z-constraint  into SimInfo's property list
1609	+	DoubleData* zconsTimeProp = new DoubleData();
1610	+	zconsTimeProp->setID(ZCONSTIME_ID);
1611	+	zconsTimeProp->setData(globals->getZconsTime());
1612	+	theInfo.addProperty(zconsTimeProp);
1613	+	}
1614	+	else{
1615	+	sprintf(painCave.errMsg,
1616	+	"ZConstraint error: If you use a ZConstraint,\n"
1617	+	"\tyou must set zconsTime.\n");
1618	+	painCave.isFatal = 1;
1619	+	simError();
1620	+	}
1621	+
1622	+	//push zconsTol into siminfo, if user does not specify
1623	+	//value for zconsTol, a default value will be used
1624	+	DoubleData* zconsTol = new DoubleData();
1625	+	zconsTol->setID(ZCONSTOL_ID);
1626	+	if (globals->haveZconsTol()){
1627	+	zconsTol->setData(globals->getZconsTol());
1628	+	}
1629	+	else{
1630	+	double defaultZConsTol = 0.01;
1631	+	sprintf(painCave.errMsg,
1632	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1633	+	"\tOOPSE will use a default value of %f.\n"
1634	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1635	+	defaultZConsTol);
1636	+	painCave.isFatal = 0;
1637	+	simError();
1638	+
1639	+	zconsTol->setData(defaultZConsTol);
1640	+	}
1641	+	theInfo.addProperty(zconsTol);
1642	+
1643	+	//set Force Subtraction Policy
1644	+	StringData* zconsForcePolicy = new StringData();
1645	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1646	+
1647	+	if (globals->haveZconsForcePolicy()){
1648	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1649	+	}
1650	+	else{
1651	+	sprintf(painCave.errMsg,
1652	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1653	+	"\tOOPSE will use PolicyByMass.\n"
1654	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1655	+	painCave.isFatal = 0;
1656	+	simError();
1657	+	zconsForcePolicy->setData("BYMASS");
1658	+	}
1659	+
1660	+	theInfo.addProperty(zconsForcePolicy);
1661	+
1662	+	//Determine the name of ouput file and add it into SimInfo's property list
1663	+	//Be careful, do not use inFileName, since it is a pointer which
1664	+	//point to a string at master node, and slave nodes do not contain that string
1665	+
1666	+	string zconsOutput(theInfo.finalName);
1667	+
1668	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1669	+
1670	+	StringData* zconsFilename = new StringData();
1671	+	zconsFilename->setID(ZCONSFILENAME_ID);
1672	+	zconsFilename->setData(zconsOutput);
1673	+
1674	+	theInfo.addProperty(zconsFilename);
1675	+
1676	+	//setup index, pos and other parameters of z-constraint molecules
1677	+	nZConstraints = globals->getNzConstraints();
1678	+	theInfo.nZconstraints = nZConstraints;
1679	+
1680	+	zconStamp = globals->getZconStamp();
1681	+	ZConsParaItem tempParaItem;
1682	+
1683	+	ZConsParaData* zconsParaData = new ZConsParaData();
1684	+	zconsParaData->setID(ZCONSPARADATA_ID);
1685	+
1686	+	for (int i = 0; i < nZConstraints; i++){
1687	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1688	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1689	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1690	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1691	+
1692	+	zconsParaData->addItem(tempParaItem);
1693	+	}
1694	+
1695	+	//check the uniqueness of index
1696	+	if(!zconsParaData->isIndexUnique()){
1697	+	sprintf(painCave.errMsg,
1698	+	"ZConstraint Error: molIndex is not unique!\n");
1699	+	painCave.isFatal = 1;
1700	+	simError();
1701	+	}
1702	+
1703	+	//sort the parameters by index of molecules
1704	+	zconsParaData->sortByIndex();
1705	+
1706	+	//push data into siminfo, therefore, we can retrieve later
1707	+	theInfo.addProperty(zconsParaData);
1708	+	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines