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

Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC vs.
Revision 830 by gezelter, Tue Oct 28 16:20:28 2003 UTC

#	Line 1 | Line 1
1		#include "Integrator.hpp"
2		#include "simError.h"
3	<
3	>	#include <math.h>
4		template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5	<	: T(theInfo, the_ff), fz(NULL), indexOfZConsMols(NULL)
5	>	: T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL),
6	>	fzOut(NULL), curZconsTime(0), forcePolicy(NULL)
7		{
8
9		//get properties from SimInfo
10		GenericData* data;
11	<	IndexData* index;
11	>	ZConsParaData* zConsParaData;
12		DoubleData* sampleTime;
13	+	DoubleData* tolerance;
14	+	StringData* policy;
15		StringData* filename;
16	+	double COM[3];
17	+
18	+	//by default, the direction of constraint is z
19	+	// 0 --> x
20	+	// 1 --> y
21	+	// 2 --> z
22	+	whichDirection = 2;
23	+
24	+	//estimate the force constant of harmonical potential
25	+	double Kb = 1.986E-3 ; //in kcal/K
26
27	<
28	<	data = info->getProperty("zconsindex");
16	<	if(!data) {
27	>	double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
28	>	zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
29
30	+	//creat force Subtraction policy
31	+	data = info->getProperty(ZCONSFORCEPOLICY_ID);
32	+	if(!data){
33		sprintf( painCave.errMsg,
34	<	"ZConstraint error: If you use an ZConstraint\n"
35	<	" , you must set index of z-constraint molecules.\n");
36	<	painCave.isFatal = 1;
37	<	simError();
34	>	"ZConstraint Warning: User does not set force Subtraction policy, "
35	>	"PolicyByMass is used\n");
36	>	painCave.isFatal = 0;
37	>	simError();
38	>
39	>	forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
40		}
41		else{
42	<	index = dynamic_cast<IndexData*>(data);
42	>	policy = dynamic_cast<StringData*>(data);
43
44	<	if(!index){
28	<
44	>	if(!policy){
45		sprintf( painCave.errMsg,
46	<	"ZConstraint error: Can not get property from SimInfo\n");
47	<	painCave.isFatal = 1;
48	<	simError();
49	<
46	>	"ZConstraint Error: Convertion from GenericData to StringData failure, "
47	>	"PolicyByMass is used\n");
48	>	painCave.isFatal = 0;
49	>	simError();
50	>
51	>	forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
52		}
53		else{
54	<
55	<	indexOfAllZConsMols = index->getIndexData();
56	<
57	<	//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp)
58	<	int maxIndex;
41	<	int totalNumMol;
42	<
43	<	maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1];
44	<
45	<	#ifndef IS_MPI
46	<	totalNumMol = nMols;
47	<	#else
48	<	totalNumMol = mpiSim->getTotNmol();
49	<	#endif
50	<
51	<	if(maxIndex > totalNumMol - 1){
54	>	if(policy->getData() == "BYNUMBER")
55	>	forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this);
56	>	else if(policy->getData() == "BYMASS")
57	>	forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
58	>	else{
59		sprintf( painCave.errMsg,
60	<	"ZConstraint error: index is out of range\n");
61	<	painCave.isFatal = 1;
62	<	simError();
63	<
64	<	}
65	<
60	>	"ZConstraint Warning: unknown force Subtraction policy, "
61	>	"PolicyByMass is used\n");
62	>	painCave.isFatal = 0;
63	>	simError();
64	>	forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
65	>	}
66		}
60	–
67		}
68
63	–	//retrive sample time of z-contraint
64	–	data = info->getProperty("zconstime");
69
70	+	//retrieve sample time of z-contraint
71	+	data = info->getProperty(ZCONSTIME_ID);
72	+
73		if(!data) {
74
75		sprintf( painCave.errMsg,
#	Line 89 | Line 96 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
96
97		}
98
99	<
100	<	//retrive output filename of z force
94	<	data = info->getProperty("zconsfilename");
99	>	//retrieve output filename of z force
100	>	data = info->getProperty(ZCONSFILENAME_ID);
101		if(!data) {
102
103
#	Line 104 | Line 110 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
110		}
111		else{
112
113	<	filename = dynamic_cast<StringData*>(data);
113	>	filename = dynamic_cast<StringData*>(data);
114
115		if(!filename){
116
#	Line 118 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
124		this->zconsOutput = filename->getData();
125		}
126
121	–
127		}
128
129	<
130	<	//calculate reference z coordinate for z-constraint molecules
126	<	double totalMass_local;
127	<	double totalMass;
128	<	double totalMZ_local;
129	<	double totalMZ;
130	<	double massOfUncons_local;
131	<	double massOfCurMol;
132	<	double COM[3];
129	>	//retrieve tolerance for z-constraint molecuels
130	>	data = info->getProperty(ZCONSTOL_ID);
131
132	<	totalMass_local = 0;
133	<	totalMass = 0;
134	<	totalMZ_local = 0;
135	<	totalMZ = 0;
136	<	massOfUncons_local = 0;
137	<
140	<
141	<	for(int i = 0; i < nMols; i++){
142	<	massOfCurMol = molecules[i].getTotalMass();
143	<	molecules[i].getCOM(COM);
144	<
145	<	totalMass_local += massOfCurMol;
146	<	totalMZ_local += massOfCurMol * COM[2];
147	<
148	<	if(isZConstraintMol(&molecules[i]) == -1){
149	<
150	<	massOfUncons_local += massOfCurMol;
151	<	}
152	<
132	>	if(!data) {
133	>
134	>	sprintf( painCave.errMsg,
135	>	"ZConstraint error: can not get tolerance \n");
136	>	painCave.isFatal = 1;
137	>	simError();
138		}
139	+	else{
140
141	<
142	<	#ifdef IS_MPI
143	<	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
158	<	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
159	<	MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
160	<	#else
161	<	totalMass = totalMass_local;
162	<	totalMZ = totalMZ_local;
163	<	totalMassOfUncons = massOfUncons_local;
164	<	#endif
141	>	tolerance = dynamic_cast<DoubleData*>(data);
142	>
143	>	if(!tolerance){
144
145	<	double zsys;
146	<	zsys = totalMZ / totalMass;
147	<
148	<	#ifndef IS_MPI
149	<	for(int i = 0; i < nMols; i++){
171	<
172	<	if(isZConstraintMol(&molecules[i]) > -1 ){
173	<	molecules[i].getCOM(COM);
174	<	allRefZ.push_back(COM[2] - zsys);
145	>	sprintf( painCave.errMsg,
146	>	"ZConstraint error: Can not get property from SimInfo\n");
147	>	painCave.isFatal = 1;
148	>	simError();
149	>
150		}
151	<
151	>	else{
152	>	this->zconsTol = tolerance->getData();
153	>	}
154	>
155		}
178	–	#else
179	–
180	–	int whichNode;
181	–	enum CommType { RequestMolZPos, EndOfRequest} status;
182	–	//int status;
183	–	double zpos;
184	–	int localIndex;
185	–	MPI_Status ierr;
186	–	int tag = 0;
156
157	<	if(worldRank == 0){
158	<
159	<	int globalIndexOfCurMol;
160	<	int *MolToProcMap;
161	<	MolToProcMap = mpiSim->getMolToProcMap();
162	<
163	<	for(int i = 0; i < indexOfAllZConsMols.size(); i++){
164	<
165	<	whichNode = MolToProcMap[indexOfAllZConsMols[i]];
197	<	globalIndexOfCurMol = indexOfAllZConsMols[i];
198	<
199	<	if(whichNode == 0){
200	<
201	<	for(int j = 0; j < nMols; j++)
202	<	if(molecules[j].getGlobalIndex() == globalIndexOfCurMol){
203	<	localIndex = j;
204	<	break;
205	<	}
206	<
207	<	molecules[localIndex].getCOM(COM);
208	<	allRefZ.push_back(COM[2] - zsys);
209	<
210	<	}
211	<	else{
212	<	status = RequestMolZPos;
213	<	MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD);
214	<	MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD);
215	<	MPI_Recv(&zpos, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr);
216	<
217	<	allRefZ.push_back(zpos - zsys);
218	<
219	<	}
220	<
221	<	} //End of Request Loop
222	<
223	<	//Send ending request message to slave nodes
224	<	status = EndOfRequest;
225	<	for(int i =1; i < mpiSim->getNumberProcessors(); i++)
226	<	MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
227	<
157	>	//retrieve index of z-constraint molecules
158	>	data = info->getProperty(ZCONSPARADATA_ID);
159	>	if(!data) {
160	>
161	>	sprintf( painCave.errMsg,
162	>	"ZConstraint error: If you use an ZConstraint\n"
163	>	" , you must set index of z-constraint molecules.\n");
164	>	painCave.isFatal = 1;
165	>	simError();
166		}
167		else{
168
169	<	int whichMol;
170	<	bool done = false;
169	>	zConsParaData = dynamic_cast<ZConsParaData*>(data);
170	>
171	>	if(!zConsParaData){
172
173	<	while (!done){
174	<
175	<	MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr);
173	>	sprintf( painCave.errMsg,
174	>	"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
175	>	painCave.isFatal = 1;
176	>	simError();
177
238	–	switch (status){
239	–
240	–	case RequestMolZPos :
241	–
242	–	MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr);
243	–
244	–	for(int i = 0; i < nMols; i++)
245	–	if(molecules[i].getGlobalIndex() == whichMol){
246	–	localIndex = i;
247	–	break;
248	–	}
249	–
250	–	molecules[localIndex].getCOM(COM);
251	–	zpos = COM[2];
252	–	MPI_Send(&zpos, 1, MPI_DOUBLE_PRECISION, 0, tag, MPI_COMM_WORLD);
253	–
254	–	break;
255	–
256	–	case EndOfRequest :
257	–
258	–	done = true;
259	–	break;
260	–	}
261	–
178		}
179	<
180	<	}
179	>	else{
180	>
181	>	parameters = zConsParaData->getData();
182
183	<	//Brocast the allRefZ to slave nodes;
184	<	double* allRefZBuf;
185	<	int nZConsMols;
269	<	nZConsMols = indexOfAllZConsMols.size();
270	<
271	<	allRefZBuf = new double[nZConsMols];
272	<
273	<	if(worldRank == 0){
183	>	//check the range of zconsIndex
184	>	//and the minimum value of index is the first one (we already sorted the data)
185	>	//the maximum value of index is the last one
186
187	<	for(int i = 0; i < nZConsMols; i++)
188	<	allRefZBuf[i] = allRefZ[i];
189	<	}
190	<
191	<	MPI_Bcast(allRefZBuf, nZConsMols, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD);
192	<
193	<	if(worldRank != 0){
194	<
195	<	for(int i = 0; i < nZConsMols; i++)
196	<	allRefZ.push_back(allRefZBuf[i]);
197	<	}
198	<
199	<	delete[] allRefZBuf;
187	>	int maxIndex;
188	>	int minIndex;
189	>	int totalNumMol;
190	>
191	>	minIndex = (*parameters)[0].zconsIndex;
192	>	if(minIndex < 0){
193	>	sprintf( painCave.errMsg,
194	>	"ZConstraint error: index is out of range\n");
195	>	painCave.isFatal = 1;
196	>	simError();
197	>	}
198	>
199	>	maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
200	>
201	>	#ifndef IS_MPI
202	>	totalNumMol = nMols;
203	>	#else
204	>	totalNumMol = mpiSim->getTotNmol();
205	>	#endif
206	>
207	>	if(maxIndex > totalNumMol - 1){
208	>	sprintf( painCave.errMsg,
209	>	"ZConstraint error: index is out of range\n");
210	>	painCave.isFatal = 1;
211	>	simError();
212	>	}
213	>
214	>	//if user does not specify the zpos for the zconstraint molecule
215	>	//its initial z coordinate  will be used as default
216	>	for(int i = 0; i < (int)(parameters->size()); i++){
217	>
218	>	if(!(*parameters)[i].havingZPos){
219	>	#ifndef IS_MPI
220	>	for(int j = 0; j < nMols; j++){
221	>	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222	>	molecules[j].getCOM(COM);
223	>	break;
224	>	}
225	>	}
226	>	#else
227	>	//query which processor current zconstraint molecule belongs to
228	>	int *MolToProcMap;
229	>	int whichNode;
230	>
231	>	MolToProcMap = mpiSim->getMolToProcMap();
232	>	whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233	>
234	>	//broadcast the zpos of current z-contraint molecule
235	>	//the node which contain this
236	>
237	>	if (worldRank == whichNode ){
238	>
239	>	for(int j = 0; j < nMols; j++)
240	>	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241	>	molecules[j].getCOM(COM);
242	>	break;
243	>	}
244	>
245	>	}
246	>
247	>	MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, MPI_COMM_WORLD);
248		#endif
249	+
250	+	(*parameters)[i].zPos = COM[whichDirection];
251
252	<
252	>	sprintf( painCave.errMsg,
253	>	"ZConstraint warning: Does not specify zpos for z-constraint molecule "
254	>	"initial z coornidate will be used \n");
255	>	painCave.isFatal = 0;
256	>	simError();
257	>
258	>	}
259	>	}
260	>
261	>	}//end if (!zConsParaData)
262	>	}//end  if (!data)
263	>
264	>	//
265		#ifdef IS_MPI
266		update();
267		#else
268		int searchResult;
269	<
296	<	refZ = allRefZ;
297	<
269	>
270		for(int i = 0; i < nMols; i++){
271
272		searchResult = isZConstraintMol(&molecules[i]);
#	Line 303 | Line 275 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
275
276		zconsMols.push_back(&molecules[i]);
277		massOfZConsMols.push_back(molecules[i].getTotalMass());
278	<
278	>
279	>	zPos.push_back((*parameters)[searchResult].zPos);
280	>	//       cout << "index: "<< (*parameters)[searchResult].zconsIndex
281	>	//              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
282	>
283	>	kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284		molecules[i].getCOM(COM);
285		}
286		else
#	Line 316 | Line 293 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
293		}
294
295		fz = new double[zconsMols.size()];
296	+	curZPos = new double[zconsMols.size()];
297		indexOfZConsMols = new int [zconsMols.size()];
298
299	<	if(!fz || !indexOfZConsMols){
299	>	if(!fz || !curZPos || !indexOfZConsMols){
300		sprintf( painCave.errMsg,
301		"Memory allocation failure in class Zconstraint\n");
302		painCave.isFatal = 1;
303		simError();
304		}
305
306	<	for(int i = 0; i < zconsMols.size(); i++)
306	>	//determine the states of z-constraint molecules
307	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
308		indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309	+
310	+	zconsMols[i]->getCOM(COM);
311	+	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
312	+	states.push_back(zcsFixed);
313	+	else
314	+	states.push_back(zcsMoving);
315	+	}
316
317		#endif
318	+
319	+	//get total masss of unconstraint molecules
320	+	double totalMassOfUncons_local;
321	+	totalMassOfUncons_local = 0;
322
323	<	fzOut = new ZConsWriter(zconsOutput.c_str());
324	<
325	<	if(!fzOut){
326	<	sprintf( painCave.errMsg,
327	<	"Memory allocation failure in class Zconstraint\n");
328	<	painCave.isFatal = 1;
329	<	simError();
330	<	}
331	<
332	<	fzOut->writeRefZ(indexOfAllZConsMols, allRefZ);
323	>	for(int i = 0; i < (int)(unconsMols.size()); i++)
324	>	totalMassOfUncons_local += unconsMols[i]->getTotalMass();
325	>
326	>	#ifndef IS_MPI
327	>	totalMassOfUncons = totalMassOfUncons_local;
328	>	#else
329	>	MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
331	>	#endif
332	>
333	>	//get total number of unconstrained atoms
334	>	int nUnconsAtoms_local;
335	>	nUnconsAtoms_local = 0;
336	>	for(int i = 0; i < (int)(unconsMols.size()); i++)
337	>	nUnconsAtoms_local += unconsMols[i]->getNAtoms();
338	>
339	>	#ifndef IS_MPI
340	>	totNumOfUnconsAtoms = nUnconsAtoms_local;
341	>	#else
342	>	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343	>	MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344	>	#endif
345	>
346	>	forcePolicy->update();
347		}
348
349		template<typename T> ZConstraint<T>::~ZConstraint()
350		{
351		if(fz)
352		delete[] fz;
353	+
354	+	if(curZPos)
355	+	delete[] curZPos;
356
357		if(indexOfZConsMols)
358		delete[] indexOfZConsMols;
359
360		if(fzOut)
361		delete fzOut;
362	+
363	+	if(forcePolicy)
364	+	delete forcePolicy;
365		}
366
367	+
368	+	/**
369	+	*
370	+	*/
371	+
372		#ifdef IS_MPI
373		template<typename T> void ZConstraint<T>::update()
374		{
#	Line 362 | Line 377 | template<typename T> void ZConstraint<T>::update()
377
378		zconsMols.clear();
379		massOfZConsMols.clear();
380	<	refZ.clear();
380	>	zPos.clear();
381	>	kz.clear();
382
383		unconsMols.clear();
384		massOfUnconsMols.clear();
#	Line 376 | Line 392 | template<typename T> void ZConstraint<T>::update()
392		if(index > -1){
393
394		zconsMols.push_back(&molecules[i]);
395	+	zPos.push_back((*parameters)[index].zPos);
396	+	kz.push_back((*parameters)[index].kRatio * zForceConst);
397		massOfZConsMols.push_back(molecules[i].getTotalMass());
398
399		molecules[i].getCOM(COM);
382	–	refZ.push_back(allRefZ[index]);
400		}
401		else
402		{
#	Line 389 | Line 406 | template<typename T> void ZConstraint<T>::update()
406
407		}
408		}
409	+
410	+	//determine the states of z-constraint molecules
411	+	for(int i = 0; i < (int)(zconsMols.size()); i++){
412	+	zconsMols[i]->getCOM(COM);
413	+	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
414	+	states.push_back(zcsFixed);
415	+	else
416	+	states.push_back(zcsMoving);
417	+	}
418	+
419
420		//The reason to declare fz and indexOfZconsMols as pointer to array is
421		// that we want to make the MPI communication simple
422		if(fz)
423		delete[] fz;
424	+
425	+	if(curZPos)
426	+	delete[] curZPos;
427
428		if(indexOfZConsMols)
429		delete[] indexOfZConsMols;
430
431		if (zconsMols.size() > 0){
432		fz = new double[zconsMols.size()];
433	+	curZPos = new double[zconsMols.size()];
434		indexOfZConsMols =  new int[zconsMols.size()];
435
436	<	if(!fz || !indexOfZConsMols){
436	>	if(!fz || !curZPos || !indexOfZConsMols){
437		sprintf( painCave.errMsg,
438		"Memory allocation failure in class Zconstraint\n");
439		painCave.isFatal = 1;
440		simError();
441		}
442
443	<	for(int i = 0; i < zconsMols.size(); i++){
443	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
444		indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
445		}
446
447		}
448		else{
449		fz = NULL;
450	+	curZPos = NULL;
451		indexOfZConsMols = NULL;
452		}
453
454	+	//
455	+	forcePolicy->update();
456	+
457		}
458
459		#endif
460
461	<	/**  Function Name: isZConstraintMol
462	<	**  Parameter
463	<	**    Molecule* mol
464	<	**  Return value:
465	<	**    -1, if the molecule is not z-constraint molecule,
466	<	**    other non-negative values, its index in indexOfAllZConsMols vector
461	>	/**
462	>	*  Function Name: isZConstraintMol
463	>	*  Parameter
464	>	*    Molecule* mol
465	>	*  Return value:
466	>	*    -1, if the molecule is not z-constraint molecule,
467	>	*    other non-negative values, its index in indexOfAllZConsMols vector
468		*/
469
470		template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
#	Line 441 | Line 477 | template<typename T> int ZConstraint<T>::isZConstraint
477		index = mol->getGlobalIndex();
478
479		low = 0;
480	<	high = indexOfAllZConsMols.size() - 1;
480	>	high = parameters->size() - 1;
481
482		//Binary Search (we have sorted the array)
483		while(low <= high){
484		mid = (low + high) /2;
485	<	if (indexOfAllZConsMols[mid] == index)
485	>	if ((*parameters)[mid].zconsIndex == index)
486		return mid;
487	<	else if (indexOfAllZConsMols[mid] > index )
487	>	else if ((*parameters)[mid].zconsIndex > index )
488		high = mid -1;
489		else
490		low = mid + 1;
#	Line 457 | Line 493 | template<typename T> int ZConstraint<T>::isZConstraint
493		return -1;
494		}
495
496	<	/** Function Name: integrateStep
497	<	** Parameter:
498	<	**   int calcPot;
499	<	**   int calcStress;
464	<	** Description:
465	<	**  Advance One Step.
466	<	** Memo:
467	<	**   The best way to implement z-constraint is to override integrateStep
468	<	**   Overriding constrainB is not a good choice, since in integrateStep,
469	<	**   constrainB is invoked by below line,
470	<	**                  if(nConstrained) constrainB();
471	<	**   For instance, we would like to apply z-constraint without bond contrain,
472	<	**   In that case, if we override constrainB, Z-constrain method will never be executed;
473	<	*/
474	<	template<typename T> void ZConstraint<T>::integrateStep( int calcPot, int calcStress )
475	<	{
476	<	T::integrateStep( calcPot, calcStress );
477	<	resetZ();
496	>	template<typename T> void ZConstraint<T>::integrate(){
497	>
498	>	// creat zconsWriter
499	>	fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
500
501	<	double currZConsTime = 0;
502	<
503	<	//write out forces of z constraint
504	<	if( info->getTime() >= currZConsTime){
505	<	fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
506	<	}
507	<	}
501	>	if(!fzOut){
502	>	sprintf( painCave.errMsg,
503	>	"Memory allocation failure in class Zconstraint\n");
504	>	painCave.isFatal = 1;
505	>	simError();
506	>	}
507	>
508	>	//zero out the velocities of center of mass of unconstrained molecules
509	>	//and the velocities of center of mass of every single z-constrained molecueles
510	>	zeroOutVel();
511
512	<	/** Function Name: resetZ
513	<	** Description:
514	<	**  Reset the z coordinates
490	<	*/
512	>	curZconsTime = zconsTime + info->getTime();
513	>
514	>	T::integrate();
515
516	<	template<typename T> void ZConstraint<T>::resetZ()
517	<	{
518	<	double deltaZ;
519	<	double mzOfZCons;   //total sum of m*z of z-constrain molecules
520	<	double mzOfUncons; //total sum of m*z of unconstrain molecuels;
521	<	double totalMZOfZCons;
522	<	double totalMZOfUncons;
523	<	double COM[3];
516	>	}
517	>
518	>
519	>	/**
520	>	*
521	>	*
522	>	*
523	>	*
524	>	*/
525	>	template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
526		double zsys;
527	<	Atom** zconsAtoms;
527	>	double COM[3];
528	>	double force[3];
529	>	double zSysCOMVel;
530
531	<	mzOfZCons = 0;
532	<	mzOfUncons  = 0;
531	>	T::calcForce(calcPot, calcStress);
532	>
533	>	if (checkZConsState()){
534	>	zeroOutVel();
535	>	forcePolicy->update();
536	>	}
537
538	<	for(int i = 0; i < zconsMols.size(); i++){
539	<	mzOfZCons += massOfZConsMols[i] * refZ[i];
540	<	}
538	>	zsys = calcZSys();
539	>	zSysCOMVel = calcSysCOMVel();
540	>	#ifdef IS_MPI
541	>	if(worldRank == 0){
542	>	#endif
543	>	//cout << "---------------------------------------------------------------------" <<endl;
544	>	//cout << "current time: " << info->getTime() << endl;
545	>	//cout << "center of mass at z: " << zsys << endl;
546	>	//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
547
548		#ifdef IS_MPI
549	<	MPI_Allreduce(&mzOfZCons, &totalMZOfZCons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
512	<	#else
513	<	totalMZOfZCons = mzOfZCons;
549	>	}
550		#endif
551
552	<	for(int i = 0; i < unconsMols.size(); i++){
553	<	unconsMols[i]->getCOM(COM);
554	<	mzOfUncons += massOfUnconsMols[i] * COM[2];
552	>	//do zconstraint force;
553	>	if (haveFixedZMols())
554	>	this->doZconstraintForce();
555	>
556	>	//use harmonical poteintial to move the molecules to the specified positions
557	>	if (haveMovingZMols())
558	>	this->doHarmonic();
559	>
560	>	//write out forces and current positions of z-constraint molecules
561	>	if(info->getTime() >= curZconsTime){
562	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
563	>	zconsMols[i]->getCOM(COM);
564	>	curZPos[i] = COM[whichDirection];
565	>
566	>	//if the z-constraint molecule is still moving, just record its force
567	>	if(states[i] == zcsMoving){
568	>	fz[i] = 0;
569	>	Atom** movingZAtoms;
570	>	movingZAtoms = zconsMols[i]->getMyAtoms();
571	>	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
572	>	movingZAtoms[j]->getFrc(force);
573	>	fz[i] += force[whichDirection];
574	>	}
575	>	}
576	>	}
577	>	fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
578	>	curZconsTime += zconsTime;
579		}
580	<
580	>
581	>	zSysCOMVel = calcSysCOMVel();
582		#ifdef IS_MPI
583	<	MPI_Allreduce(&mzOfUncons, &totalMZOfUncons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
584	<	#else
585	<	totalMZOfUncons = mzOfUncons;
586	<	#endif
587	<
588	<	zsys = (totalMZOfZCons + totalMZOfUncons) /totalMassOfUncons;
583	>	if(worldRank == 0){
584	>	#endif
585	>	//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586	>	#ifdef IS_MPI
587	>	}
588	>	#endif
589	>	}
590
591	<	cout << "current time: " << info->getTime() <<endl;
592	<	for(int i = 0; i < zconsMols.size(); i++){
591	>
592	>	/**
593	>	*
594	>	*/
595	>
596	>	template<typename T> double ZConstraint<T>::calcZSys()
597	>	{
598	>	//calculate reference z coordinate for z-constraint molecules
599	>	double totalMass_local;
600	>	double totalMass;
601	>	double totalMZ_local;
602	>	double totalMZ;
603	>	double massOfCurMol;
604	>	double COM[3];
605	>
606	>	totalMass_local = 0;
607	>	totalMZ_local = 0;
608	>
609	>	for(int i = 0; i < nMols; i++){
610	>	massOfCurMol = molecules[i].getTotalMass();
611	>	molecules[i].getCOM(COM);
612	>
613	>	totalMass_local += massOfCurMol;
614	>	totalMZ_local += massOfCurMol * COM[whichDirection];
615	>
616	>	}
617	>
618	>
619	>	#ifdef IS_MPI
620	>	MPI_Allreduce(&totalMass_local, &totalMass, 1,
621	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
622	>	MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
623	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
624	>	#else
625	>	totalMass = totalMass_local;
626	>	totalMZ = totalMZ_local;
627	>	#endif
628	>
629	>	double zsys;
630	>	zsys = totalMZ / totalMass;
631	>
632	>	return zsys;
633	>	}
634	>
635	>	/**
636	>	*
637	>	*/
638	>	template<typename T> void ZConstraint<T>::thermalize( void ){
639	>
640	>	T::thermalize();
641	>	zeroOutVel();
642	>	}
643	>
644	>	/**
645	>	*
646	>	*/
647	>
648	>	template<typename T> void ZConstraint<T>::zeroOutVel(){
649	>
650	>	Atom** fixedZAtoms;
651	>	double COMvel[3];
652	>	double vel[3];
653	>	double zSysCOMVel;
654	>
655	>	//zero out the velocities of center of mass of fixed z-constrained molecules
656	>
657	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
658	>
659	>	if (states[i] == zcsFixed){
660	>
661	>	zconsMols[i]->getCOMvel(COMvel);
662	>	//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663	>
664	>	fixedZAtoms = zconsMols[i]->getMyAtoms();
665	>
666	>	for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
667	>	fixedZAtoms[j]->getVel(vel);
668	>	vel[whichDirection] -= COMvel[whichDirection];
669	>	fixedZAtoms[j]->setVel(vel);
670	>	}
671	>
672	>	zconsMols[i]->getCOMvel(COMvel);
673	>	//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674	>	}
675	>
676	>	}
677	>
678	>	//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
679	>
680	>	zSysCOMVel = calcSysCOMVel();
681	>	#ifdef IS_MPI
682	>	if(worldRank == 0){
683	>	#endif
684	>	//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;
685	>	#ifdef IS_MPI
686	>	}
687	>	#endif
688	>
689	>	// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
690	>	double MVzOfMovingMols_local;
691	>	double MVzOfMovingMols;
692	>	double totalMassOfMovingZMols_local;
693	>	double totalMassOfMovingZMols;
694	>
695	>	MVzOfMovingMols_local = 0;
696	>	totalMassOfMovingZMols_local = 0;
697	>
698	>	for(int i =0; i < (int)(unconsMols.size()); i++){
699	>	unconsMols[i]->getCOMvel(COMvel);
700	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
701	>	}
702	>
703	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
704	>	if (states[i] == zcsMoving){
705	>	zconsMols[i]->getCOMvel(COMvel);
706	>	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
707	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
708	>	}
709	>
710	>	}
711	>
712	>	#ifndef IS_MPI
713	>	MVzOfMovingMols = MVzOfMovingMols_local;
714	>	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
715	>	#else
716	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
717	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
718	>	#endif
719	>
720	>	double vzOfMovingMols;
721	>	vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
722	>
723	>	//modify the velocites of unconstrained molecules
724	>	Atom** unconsAtoms;
725	>	for(int i = 0; i < (int)(unconsMols.size()); i++){
726	>
727	>	unconsAtoms = unconsMols[i]->getMyAtoms();
728	>	for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
729	>	unconsAtoms[j]->getVel(vel);
730	>	vel[whichDirection] -= vzOfMovingMols;
731	>	unconsAtoms[j]->setVel(vel);
732	>	}
733	>
734	>	}
735	>
736	>	//modify the velocities of moving z-constrained molecuels
737	>	Atom** movingZAtoms;
738	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
739	>
740	>	if (states[i] ==zcsMoving){
741
742	<	zconsMols[i]->getCOM(COM);
742	>	movingZAtoms = zconsMols[i]->getMyAtoms();
743	>	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
744	>	movingZAtoms[j]->getVel(vel);
745	>	vel[whichDirection] -= vzOfMovingMols;
746	>	movingZAtoms[j]->setVel(vel);
747	>	}
748
749	<	cout << "global index: " << zconsMols[i]->getGlobalIndex() << "\tZ: " << COM[2] << "\t";
750	<	deltaZ = zsys + refZ[i] - COM[2];
751	<	cout << "\tdistance: " << COM[2] +deltaZ - zsys;
752	<	//update z coordinate
753	<	zconsAtoms = zconsMols[i]->getMyAtoms();
754	<	for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
755	<	zconsAtoms[j]->setZ(zconsAtoms[j]->getZ() + deltaZ);
756	<	}
749	>	}
750	>
751	>	}
752	>
753	>
754	>	zSysCOMVel = calcSysCOMVel();
755	>	#ifdef IS_MPI
756	>	if(worldRank == 0){
757	>	#endif
758	>	//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;
759	>	#ifdef IS_MPI
760	>	}
761	>	#endif
762	>
763	>	}
764	>
765	>	/**
766	>	*
767	>	*/
768	>
769	>	template<typename T> void ZConstraint<T>::doZconstraintForce(){
770	>
771	>	Atom** zconsAtoms;
772	>	double totalFZ;
773	>	double totalFZ_local;
774	>	double COM[3];
775	>	double force[3];
776	>
777	>	//constrain the molecules which do not reach the specified positions
778
779	<	//calculate z constrain force
780	<	fz[i] = massOfZConsMols[i]* deltaZ / dt2;
779	>	//Zero Out the force of z-contrained molecules
780	>	totalFZ_local = 0;
781	>
782	>	//calculate the total z-contrained force of fixed z-contrained molecules
783	>
784	>	//cout << "before zero out z-constraint force on fixed z-constraint molecuels "
785	>	//       << "total force is " << calcTotalForce() << endl;
786	>
787	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
788
789	<	cout << "\tforce: " << fz[i] << endl;
789	>	if (states[i] == zcsFixed){
790	>
791	>	zconsMols[i]->getCOM(COM);
792	>	zconsAtoms = zconsMols[i]->getMyAtoms();
793	>
794	>	fz[i] = 0;
795	>	for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
796	>	zconsAtoms[j]->getFrc(force);
797	>	fz[i] += force[whichDirection];
798	>	}
799	>	totalFZ_local += fz[i];
800	>
801	>	//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
802	>	//      <<"\tcurrent zpos: " << COM[whichDirection]
803	>	//      << "\tcurrent fz: " <<fz[i] << endl;
804	>
805	>
806	>	}
807	>
808	>	}
809	>
810	>	//calculate total z-constraint force
811	>	#ifdef IS_MPI
812	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
813	>	#else
814	>	totalFZ = totalFZ_local;
815	>	#endif
816	>
817	>
818	>	// apply negative to fixed z-constrained molecues;
819	>	force[0]= 0;
820	>	force[1]= 0;
821	>	force[2]= 0;
822	>
823	>	for(int i = 0; i < (int)(zconsMols.size()); i++){
824	>
825	>	if (states[i] == zcsFixed){
826	>
827	>	int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
828	>	zconsAtoms = zconsMols[i]->getMyAtoms();
829	>
830	>	for(int j =0; j < nAtomOfCurZConsMol; j++) {
831	>	//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
832	>	force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
833	>	zconsAtoms[j]->addFrc(force);
834	>	}
835	>
836	>	}
837	>
838	>	}
839	>
840	>	//cout << "after zero out z-constraint force on fixed z-constraint molecuels "
841	>	//      << "total force is " << calcTotalForce() << endl;
842	>
843	>
844	>	force[0]= 0;
845	>	force[1]= 0;
846	>	force[2]= 0;
847	>
848	>	//modify the forces of unconstrained molecules
849	>	for(int i = 0; i < (int)(unconsMols.size()); i++){
850	>
851	>	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
852	>
853	>	for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){
854	>	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
855	>	force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
856	>	unconsAtoms[j]->addFrc(force);
857	>	}
858	>
859	>	}
860	>
861	>	//modify the forces of moving z-constrained molecules
862	>	for(int i = 0; i < (int)(zconsMols.size()); i++) {
863	>	if (states[i] == zcsMoving){
864	>
865	>	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
866	>
867	>	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
868	>	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
869	>	force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
870	>	movingZAtoms[j]->addFrc(force);
871	>	}
872	>	}
873		}
874	+	//  cout << "after substracting z-constraint force from moving molecuels "
875	+	//        << "total force is " << calcTotalForce()  << endl;
876
877	+	}
878	+
879	+	/**
880	+	*
881	+	*
882	+	*/
883	+
884	+	template<typename T> void ZConstraint<T>::doHarmonic(){
885	+	double force[3];
886	+	double harmonicU;
887	+	double harmonicF;
888	+	double COM[3];
889	+	double diff;
890	+	double totalFZ_local;
891	+	double totalFZ;
892	+
893	+	force[0] = 0;
894	+	force[1] = 0;
895	+	force[2] = 0;
896	+
897	+	totalFZ_local = 0;
898	+
899	+	for(int i = 0; i < (int)(zconsMols.size()); i++) {
900	+
901	+	if (states[i] == zcsMoving){
902	+	zconsMols[i]->getCOM(COM);
903	+	//       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
904	+	//         << "\tcurrent zpos: " << COM[whichDirection] << endl;
905	+
906	+	diff = COM[whichDirection] -zPos[i];
907	+
908	+	harmonicU = 0.5 * kz[i] * diff * diff;
909	+	info->lrPot += harmonicU;
910	+
911	+	harmonicF =  - kz[i] * diff;
912	+	totalFZ_local += harmonicF;
913	+
914	+	//adjust force
915	+
916	+	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
917	+
918	+	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
919	+	//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
920	+	force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
921	+	movingZAtoms[j]->addFrc(force);
922	+	}
923	+	}
924	+
925	+	}
926	+
927	+	#ifndef IS_MPI
928	+	totalFZ = totalFZ_local;
929	+	#else
930	+	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
931	+	#endif
932	+
933	+	//cout << "before substracting harmonic force from moving molecuels "
934	+	//      << "total force is " << calcTotalForce()  << endl;
935	+
936	+	force[0]= 0;
937	+	force[1]= 0;
938	+	force[2]= 0;
939	+
940	+	//modify the forces of unconstrained molecules
941	+	for(int i = 0; i < (int)(unconsMols.size()); i++){
942	+
943	+	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
944	+
945	+	for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){
946	+	//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
947	+	force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
948	+	unconsAtoms[j]->addFrc(force);
949	+	}
950	+	}
951	+
952	+	//cout << "after substracting harmonic force from moving molecuels "
953	+	//      << "total force is " << calcTotalForce()  << endl;
954	+
955	+	}
956	+
957	+	/**
958	+	*
959	+	*/
960	+
961	+	template<typename T> bool ZConstraint<T>::checkZConsState(){
962	+	double COM[3];
963	+	double diff;
964	+
965	+	int changed_local;
966	+	int changed;
967	+
968	+	changed_local = 0;
969	+
970	+	for(int i =0; i < (int)(zconsMols.size()); i++){
971	+
972	+	zconsMols[i]->getCOM(COM);
973	+	diff = fabs(COM[whichDirection] - zPos[i]);
974	+	if (  diff <= zconsTol && states[i] == zcsMoving){
975	+	states[i] = zcsFixed;
976	+	changed_local = 1;
977	+	}
978	+	else if ( diff > zconsTol && states[i] == zcsFixed){
979	+	states[i] = zcsMoving;
980	+	changed_local = 1;
981	+	}
982	+
983	+	}
984	+
985	+	#ifndef IS_MPI
986	+	changed =changed_local;
987	+	#else
988	+	MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
989	+	#endif
990	+
991	+	return (changed > 0);
992	+
993	+	}
994	+
995	+	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
996	+
997	+	int havingFixed_local;
998	+	int havingFixed;
999	+
1000	+	havingFixed_local = 0;
1001	+
1002	+	for(int i = 0; i < (int)(zconsMols.size()); i++)
1003	+	if (states[i] == zcsFixed){
1004	+	havingFixed_local = 1;
1005	+	break;
1006	+	}
1007	+
1008	+	#ifndef IS_MPI
1009	+	havingFixed = havingFixed_local;
1010	+	#else
1011	+	MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1012	+	#endif
1013	+
1014	+	return (havingFixed > 0);
1015	+	}
1016	+
1017	+
1018	+	/**
1019	+	*
1020	+	*/
1021	+	template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1022	+
1023	+	int havingMoving_local;
1024	+	int havingMoving;
1025	+
1026	+	havingMoving_local = 0;
1027	+
1028	+	for(int i = 0; i < (int)(zconsMols.size()); i++)
1029	+	if (states[i] == zcsMoving){
1030	+	havingMoving_local = 1;
1031	+	break;
1032	+	}
1033	+
1034	+	#ifndef IS_MPI
1035	+	havingMoving = havingMoving_local;
1036	+	#else
1037	+	MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1038	+	#endif
1039	+
1040	+	return (havingMoving > 0);
1041	+
1042	+	}
1043	+
1044	+	/**
1045	+	*
1046	+	*/
1047	+
1048	+	template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1049	+	{
1050	+	double MVzOfMovingMols_local;
1051	+	double MVzOfMovingMols;
1052	+	double totalMassOfMovingZMols_local;
1053	+	double totalMassOfMovingZMols;
1054	+	double COMvel[3];
1055
1056	+	MVzOfMovingMols_local = 0;
1057	+	totalMassOfMovingZMols_local = 0;
1058	+
1059	+	for(int i =0; i < unconsMols.size(); i++){
1060	+	unconsMols[i]->getCOMvel(COMvel);
1061	+	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
1062	+	}
1063	+
1064	+	for(int i = 0; i < zconsMols.size(); i++){
1065	+
1066	+	if (states[i] == zcsMoving){
1067	+	zconsMols[i]->getCOMvel(COMvel);
1068	+	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
1069	+	totalMassOfMovingZMols_local += massOfZConsMols[i];
1070	+	}
1071	+
1072	+	}
1073	+
1074	+	#ifndef IS_MPI
1075	+	MVzOfMovingMols = MVzOfMovingMols_local;
1076	+	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1077	+	#else
1078	+	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079	+	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1080	+	#endif
1081	+
1082	+	double vzOfMovingMols;
1083	+	vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1084	+
1085	+	return vzOfMovingMols;
1086		}
1087	+
1088	+	/**
1089	+	*
1090	+	*/
1091	+
1092	+	template<typename T> double ZConstraint<T>::calcSysCOMVel()
1093	+	{
1094	+	double COMvel[3];
1095	+	double tempMVz_local;
1096	+	double tempMVz;
1097	+	double massOfZCons_local;
1098	+	double massOfZCons;
1099	+
1100	+
1101	+	tempMVz_local = 0;
1102	+
1103	+	for(int i =0 ; i < nMols; i++){
1104	+	molecules[i].getCOMvel(COMvel);
1105	+	tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1106	+	}
1107	+
1108	+	massOfZCons_local = 0;
1109	+
1110	+	for(int i = 0; i < (int)(massOfZConsMols.size()); i++){
1111	+	massOfZCons_local += massOfZConsMols[i];
1112	+	}
1113	+	#ifndef IS_MPI
1114	+	massOfZCons = massOfZCons_local;
1115	+	tempMVz = tempMVz_local;
1116	+	#else
1117	+	MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1118	+	MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1119	+	#endif
1120	+
1121	+	return tempMVz /(totalMassOfUncons + massOfZCons);
1122	+	}
1123	+
1124	+	/**
1125	+	*
1126	+	*/
1127	+
1128	+	template<typename T> double ZConstraint<T>::calcTotalForce(){
1129	+
1130	+	double force[3];
1131	+	double totalForce_local;
1132	+	double totalForce;
1133	+
1134	+	totalForce_local = 0;
1135	+
1136	+	for(int i = 0; i < nAtoms; i++){
1137	+	atoms[i]->getFrc(force);
1138	+	totalForce_local += force[whichDirection];
1139	+	}
1140	+
1141	+	#ifndef IS_MPI
1142	+	totalForce = totalForce_local;
1143	+	#else
1144	+	MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1145	+	#endif
1146	+
1147	+	return totalForce;
1148	+
1149	+	}
1150	+
1151	+	/**
1152	+	*
1153	+	*/
1154	+
1155	+	template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1156	+	//calculate the number of atoms of moving z-constrained molecules
1157	+	int nMovingZAtoms_local;
1158	+	int nMovingZAtoms;
1159	+
1160	+	nMovingZAtoms_local = 0;
1161	+	for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1162	+	if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1163	+	nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1164	+
1165	+	#ifdef IS_MPI
1166	+	MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1167	+	#else
1168	+	nMovingZAtoms = nMovingZAtoms_local;
1169	+	#endif
1170	+	totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1171	+	}
1172	+
1173	+	template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1174	+	return totalForce / mol->getNAtoms();
1175	+	}
1176	+
1177	+	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1178	+	return totalForce / totNumOfMovingAtoms;
1179	+	}
1180	+
1181	+	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1182	+	return totalForce / mol->getNAtoms();
1183	+	}
1184	+
1185	+	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1186	+	return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1187	+	}
1188	+
1189	+	/**
1190	+	*
1191	+	*/
1192	+
1193	+	template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1194	+	//calculate the number of atoms of moving z-constrained molecules
1195	+	double massOfMovingZAtoms_local;
1196	+	double massOfMovingZAtoms;
1197	+
1198	+	massOfMovingZAtoms_local = 0;
1199	+	for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1200	+	if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1201	+	massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1202	+
1203	+	#ifdef IS_MPI
1204	+	MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1205	+	#else
1206	+	massOfMovingZAtoms = massOfMovingZAtoms_local;
1207	+	#endif
1208	+	totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1209	+	}
1210	+
1211	+	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1212	+	return totalForce * atom->getMass() / mol->getTotalMass();
1213	+	}
1214	+
1215	+	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1216	+	return totalForce * atom->getMass() / totMassOfMovingAtoms;
1217	+	}
1218	+
1219	+	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1220	+	return totalForce * atom->getMass() / mol->getTotalMass();
1221	+	}
1222	+
1223	+	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1224	+	return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1225	+	}
1226	+

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