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

Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 2004 UTC

#	Line 1 | Line 1
1		#include "Integrator.hpp"
2		#include "simError.h"
3	<	#include <cmath>
4	<	template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5	<	: T(theInfo, the_ff), fz(NULL),
6	<	indexOfZConsMols(NULL)
7	<	{
3	>	#include <math.h>
4
5	+	const double INFINITE_TIME = 10e30;
6	+	template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo,
7	+	ForceFields* the_ff): T(theInfo, the_ff),
8	+	fzOut(NULL),
9	+	curZconsTime(0),
10	+	forcePolicy(NULL),
11	+	usingSMD(false),
12	+	hasZConsGap(false){
13		//get properties from SimInfo
14		GenericData* data;
15	<	IndexData* index;
15	>	ZConsParaData* zConsParaData;
16		DoubleData* sampleTime;
17	+	DoubleData* tolerance;
18	+	DoubleData* gap;
19	+	DoubleData* fixtime;
20	+	StringData* policy;
21		StringData* filename;
22	<
23	<	//retrieve index of z-constraint molecules
16	<	data = info->getProperty("zconsindex");
17	<	if(!data) {
22	>	IntData* smdFlag;
23	>	double COM[3];
24
25	<	sprintf( painCave.errMsg,
26	<	"ZConstraint error: If you use an ZConstraint\n"
27	<	" , you must set index of z-constraint molecules.\n");
28	<	painCave.isFatal = 1;
29	<	simError();
25	>	//by default, the direction of constraint is z
26	>	// 0 --> x
27	>	// 1 --> y
28	>	// 2 --> z
29	>	whichDirection = 2;
30	>
31	>	//estimate the force constant of harmonical potential
32	>	double Kb = 1.986E-3 ; //in kcal/K
33	>
34	>	double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /
35	>	2;
36	>	zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox);
37	>
38	>	//creat force Subtraction policy
39	>	data = info->getProperty(ZCONSFORCEPOLICY_ID);
40	>	if (!data){
41	>	sprintf(painCave.errMsg,
42	>	"ZConstraint Warning: User does not set force Subtraction policy, "
43	>	"PolicyByMass is used\n");
44	>	painCave.isFatal = 0;
45	>	simError();
46	>
47	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
48		}
49		else{
50	<	index = dynamic_cast<IndexData*>(data);
27	<
28	<	if(!index){
50	>	policy = dynamic_cast<StringData*>(data);
51
52	<	sprintf( painCave.errMsg,
53	<	"ZConstraint error: Can not get property from SimInfo\n");
54	<	painCave.isFatal = 1;
55	<	simError();
56	<
52	>	if (!policy){
53	>	sprintf(painCave.errMsg,
54	>	"ZConstraint Error: Convertion from GenericData to StringData failure, "
55	>	"PolicyByMass is used\n");
56	>	painCave.isFatal = 0;
57	>	simError();
58	>
59	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
60		}
61		else{
62	<
63	<	indexOfAllZConsMols = index->getIndexData();
64	<
65	<	//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp)
66	<	int maxIndex;
67	<	int minIndex;
68	<	int totalNumMol;
69	<
70	<	minIndex = indexOfAllZConsMols[0];
71	<	if(minIndex < 0){
72	<	sprintf( painCave.errMsg,
48	<	"ZConstraint error: index is out of range\n");
49	<	painCave.isFatal = 1;
50	<	simError();
51	<	}
52	<
53	<	maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1];
54	<
55	<	#ifndef IS_MPI
56	<	totalNumMol = nMols;
57	<	#else
58	<	totalNumMol = mpiSim->getTotNmol();
59	<	#endif
60	<
61	<	if(maxIndex > totalNumMol - 1){
62	<	sprintf( painCave.errMsg,
63	<	"ZConstraint error: index is out of range\n");
64	<	painCave.isFatal = 1;
65	<	simError();
66	<
62	>	if (policy->getData() == "BYNUMBER")
63	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this);
64	>	else if (policy->getData() == "BYMASS")
65	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
66	>	else{
67	>	sprintf(painCave.errMsg,
68	>	"ZConstraint Warning: unknown force Subtraction policy, "
69	>	"PolicyByMass is used\n");
70	>	painCave.isFatal = 0;
71	>	simError();
72	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
73		}
68	–
74		}
70	–
75		}
76	<
76	>
77	>
78		//retrieve sample time of z-contraint
79	<	data = info->getProperty("zconstime");
80	<
81	<	if(!data) {
82	<
83	<	sprintf( painCave.errMsg,
84	<	"ZConstraint error: If you use an ZConstraint\n"
80	<	" , you must set sample time.\n");
79	>	data = info->getProperty(ZCONSTIME_ID);
80	>
81	>	if (!data){
82	>	sprintf(painCave.errMsg,
83	>	"ZConstraint error: If you use an ZConstraint\n"
84	>	" , you must set sample time.\n");
85		painCave.isFatal = 1;
86	<	simError();
86	>	simError();
87		}
88		else{
85	–
89		sampleTime = dynamic_cast<DoubleData*>(data);
87	–
88	–	if(!sampleTime){
90
91	<	sprintf( painCave.errMsg,
92	<	"ZConstraint error: Can not get property from SimInfo\n");
91	>	if (!sampleTime){
92	>	sprintf(painCave.errMsg,
93	>	"ZConstraint error: Can not get property from SimInfo\n");
94		painCave.isFatal = 1;
95	<	simError();
94	<
95	>	simError();
96		}
97		else{
98		this->zconsTime = sampleTime->getData();
99		}
99	–
100		}
101	–
102	–
103	–	//retrieve output filename of z force
104	–	data = info->getProperty("zconsfilename");
105	–	if(!data) {
101
102	<
103	<	sprintf( painCave.errMsg,
104	<	"ZConstraint error: If you use an ZConstraint\n"
105	<	" , you must set output filename of z-force.\n");
102	>	//retrieve output filename of z force
103	>	data = info->getProperty(ZCONSFILENAME_ID);
104	>	if (!data){
105	>	sprintf(painCave.errMsg,
106	>	"ZConstraint error: If you use an ZConstraint\n"
107	>	" , you must set output filename of z-force.\n");
108		painCave.isFatal = 1;
109	<	simError();
109	>	simError();
110	>	}
111	>	else{
112	>	filename = dynamic_cast<StringData*>(data);
113
114	+	if (!filename){
115	+	sprintf(painCave.errMsg,
116	+	"ZConstraint error: Can not get property from SimInfo\n");
117	+	painCave.isFatal = 1;
118	+	simError();
119	+	}
120	+	else{
121	+	this->zconsOutput = filename->getData();
122	+	}
123		}
124	+
125	+	//retrieve tolerance for z-constraint molecuels
126	+	data = info->getProperty(ZCONSTOL_ID);
127	+
128	+	if (!data){
129	+	sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n");
130	+	painCave.isFatal = 1;
131	+	simError();
132	+	}
133		else{
134	+	tolerance = dynamic_cast<DoubleData*>(data);
135
136	<	filename = dynamic_cast<StringData*>(data);
137	<
138	<	if(!filename){
136	>	if (!tolerance){
137	>	sprintf(painCave.errMsg,
138	>	"ZConstraint error: Can not get property from SimInfo\n");
139	>	painCave.isFatal = 1;
140	>	simError();
141	>	}
142	>	else{
143	>	this->zconsTol = tolerance->getData();
144	>	}
145	>	}
146
147	<	sprintf( painCave.errMsg,
148	<	"ZConstraint error: Can not get property from SimInfo\n");
147	>	//quick hack here
148	>	data = info->getProperty(ZCONSGAP_ID);
149	>
150	>	if (data){
151	>	gap = dynamic_cast<DoubleData*>(data);
152	>
153	>	if (!gap){
154	>	sprintf(painCave.errMsg,
155	>	"ZConstraint error: Can not get property from SimInfo\n");
156		painCave.isFatal = 1;
157	<	simError();
125	<
157	>	simError();
158		}
159		else{
160	<	this->zconsOutput = filename->getData();
160	>	this->hasZConsGap = true;
161	>	this->zconsGap = gap->getData();
162		}
163	<
163	>	}
164
165	+
166	+
167	+	data = info->getProperty(ZCONSFIXTIME_ID);
168	+
169	+	if (data){
170	+	fixtime = dynamic_cast<DoubleData*>(data);
171	+	if (!fixtime){
172	+	sprintf(painCave.errMsg,
173	+	"ZConstraint error: Can not get zconsFixTime from SimInfo\n");
174	+	painCave.isFatal = 1;
175	+	simError();
176	+	}
177	+	else{
178	+	this->zconsFixTime = fixtime->getData();
179	+	}
180		}
181	<
181	>	else if(hasZConsGap){
182	>	sprintf(painCave.errMsg,
183	>	"ZConstraint error: must set fixtime if already set zconsGap\n");
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187	>
188	>
189	>
190	>	data = info->getProperty(ZCONSUSINGSMD_ID);
191	>
192	>	if (data){
193	>	smdFlag = dynamic_cast<IntData*>(data);
194	>
195	>	if (!smdFlag){
196	>	sprintf(painCave.errMsg,
197	>	"ZConstraint error: Can not get property from SimInfo\n");
198	>	painCave.isFatal = 1;
199	>	simError();
200	>	}
201	>	else{
202	>	this->usingSMD= smdFlag->getData() ? true : false;
203	>	}
204	>
205	>	}
206	>
207	>
208	>
209	>	//retrieve index of z-constraint molecules
210	>	data = info->getProperty(ZCONSPARADATA_ID);
211	>	if (!data){
212	>	sprintf(painCave.errMsg,
213	>	"ZConstraint error: If you use an ZConstraint\n"
214	>	" , you must set index of z-constraint molecules.\n");
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218	>	else{
219	>	zConsParaData = dynamic_cast<ZConsParaData*>(data);
220	>
221	>	if (!zConsParaData){
222	>	sprintf(painCave.errMsg,
223	>	"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	else{
228	>	parameters = zConsParaData->getData();
229	>
230	>	//check the range of zconsIndex
231	>	//and the minimum value of index is the first one (we already sorted the data)
232	>	//the maximum value of index is the last one
233	>
234	>	int maxIndex;
235	>	int minIndex;
236	>	int totalNumMol;
237	>
238	>	minIndex = (*parameters)[0].zconsIndex;
239	>	if (minIndex < 0){
240	>	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>
245	>	maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
246	>
247	>	#ifndef IS_MPI
248	>	totalNumMol = nMols;
249	>	#else
250	>	totalNumMol = mpiSim->getNMolGlobal();
251	>	#endif
252	>
253	>	if (maxIndex > totalNumMol - 1){
254	>	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
255	>	painCave.isFatal = 1;
256	>	simError();
257	>	}
258	>
259	>	//if user does not specify the zpos for the zconstraint molecule
260	>	//its initial z coordinate  will be used as default
261	>	for (int i = 0; i < (int) (parameters->size()); i++){
262	>	if (!(*parameters)[i].havingZPos){
263	>	#ifndef IS_MPI
264	>	for (int j = 0; j < nMols; j++){
265	>	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
266	>	molecules[j].getCOM(COM);
267	>	break;
268	>	}
269	>	}
270	>	#else
271	>	//query which processor current zconstraint molecule belongs to
272	>	int* MolToProcMap;
273	>	int whichNode;
274	>
275	>	MolToProcMap = mpiSim->getMolToProcMap();
276	>	whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
277	>
278	>	//broadcast the zpos of current z-contraint molecule
279	>	//the node which contain this
280	>
281	>	if (worldRank == whichNode){
282	>	for (int j = 0; j < nMols; j++)
283	>	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
284	>	molecules[j].getCOM(COM);
285	>	break;
286	>	}
287	>	}
288	>
289	>	MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode,
290	>	MPI_COMM_WORLD);
291	>	#endif
292	>
293	>	(*parameters)[i].zPos = COM[whichDirection];
294	>
295	>	sprintf(painCave.errMsg,
296	>	"ZConstraint warning: Does not specify zpos for z-constraint molecule "
297	>	"initial z coornidate will be used \n");
298	>	painCave.isFatal = 0;
299	>	simError();
300	>	}
301	>	}
302	>	}//end if (!zConsParaData)
303	>
304	>	}//end  if (!data)
305	>
306	>	//
307		#ifdef IS_MPI
308		update();
309		#else
310		int searchResult;
311	<	double COM[3];
312	<
140	<	for(int i = 0; i < nMols; i++){
141	<
311	>
312	>	for (int i = 0; i < nMols; i++){
313		searchResult = isZConstraintMol(&molecules[i]);
314	<
315	<	if(searchResult > -1){
145	<
314	>
315	>	if (searchResult > -1){
316		zconsMols.push_back(&molecules[i]);
317		massOfZConsMols.push_back(molecules[i].getTotalMass());
318	+
319	+	zPos.push_back((*parameters)[searchResult].zPos);
320	+	kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
321
322	<	molecules[i].getCOM(COM);
322	>	if(usingSMD)
323	>	cantVel.push_back((*parameters)[searchResult].cantVel);
324	>
325		}
326	<	else
152	<	{
153	<
326	>	else{
327		unconsMols.push_back(&molecules[i]);
328		massOfUnconsMols.push_back(molecules[i].getTotalMass());
156	–
329		}
330		}
331
332	<	fz = new double[zconsMols.size()];
333	<	indexOfZConsMols = new int [zconsMols.size()];
332	>	fz.resize(zconsMols.size());
333	>	curZPos.resize(zconsMols.size());
334	>	indexOfZConsMols.resize(zconsMols.size());
335
336	<	if(!fz || !indexOfZConsMols){
337	<	sprintf( painCave.errMsg,
338	<	"Memory allocation failure in class Zconstraint\n");
339	<	painCave.isFatal = 1;
340	<	simError();
336	>	//determine the states of z-constraint molecules
337	>	for (size_t i = 0; i < zconsMols.size(); i++){
338	>	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
339	>
340	>	zconsMols[i]->getCOM(COM);
341	>
342	>	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
343	>	states.push_back(zcsFixed);
344	>
345	>	if (hasZConsGap)
346	>	endFixTime.push_back(info->getTime() + zconsFixTime);
347	>	}
348	>	else{
349	>	states.push_back(zcsMoving);
350	>
351	>	if (hasZConsGap)
352	>	endFixTime.push_back(INFINITE_TIME);
353	>	}
354	>
355	>	if(usingSMD)
356	>	cantPos.push_back(COM[whichDirection]);
357		}
358
359	<	for(int i = 0; i < zconsMols.size(); i++)
360	<	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
172	<
359	>	if(usingSMD)
360	>	prevCantPos = cantPos;
361		#endif
362
363	+
364	+	//get total masss of unconstraint molecules
365	+	double totalMassOfUncons_local;
366	+	totalMassOfUncons_local = 0;
367	+
368	+	for (size_t i = 0; i < unconsMols.size(); i++)
369	+	totalMassOfUncons_local += unconsMols[i]->getTotalMass();
370	+
371	+	#ifndef IS_MPI
372	+	totalMassOfUncons = totalMassOfUncons_local;
373	+	#else
374	+	MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,
375	+	MPI_SUM, MPI_COMM_WORLD);
376	+	#endif
377	+
378		//get total number of unconstrained atoms
379		int nUnconsAtoms_local;
380		nUnconsAtoms_local = 0;
381	<	for(int i = 0; i < unconsMols.size(); i++)
381	>	for (int i = 0; i < (int) (unconsMols.size()); i++)
382		nUnconsAtoms_local += unconsMols[i]->getNAtoms();
383	<
383	>
384		#ifndef IS_MPI
385		totNumOfUnconsAtoms = nUnconsAtoms_local;
386		#else
387	<	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
388	<	#endif
387	>	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM,
388	>	MPI_COMM_WORLD);
389	>	#endif
390
391	<
188	<
189	<	fzOut = new ZConsWriter(zconsOutput.c_str());
190	<
191	<	if(!fzOut){
192	<	sprintf( painCave.errMsg,
193	<	"Memory allocation failure in class Zconstraint\n");
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
391	>	forcePolicy->update();
392		}
393
394	<	template<typename T> ZConstraint<T>::~ZConstraint()
395	<	{
396	<	if(fz)
203	<	delete[] fz;
204	<
205	<	if(indexOfZConsMols)
206	<	delete[] indexOfZConsMols;
207	<
208	<	if(fzOut)
394	>	template<typename T> ZConstraint<T>::~ZConstraint(){
395	>
396	>	if (fzOut){
397		delete fzOut;
398	+	}
399	+
400	+	if (forcePolicy){
401	+	delete forcePolicy;
402	+	}
403		}
404
405	+
406	+	/**
407	+	*
408	+	*/
409	+
410		#ifdef IS_MPI
411	<	template<typename T> void ZConstraint<T>::update()
214	<	{
411	>	template<typename T> void ZConstraint<T>::update(){
412		double COM[3];
413		int index;
414	<
414	>
415		zconsMols.clear();
416		massOfZConsMols.clear();
417	<
417	>	zPos.clear();
418	>	kz.clear();
419	>	cantPos.clear();
420	>	cantVel.clear();
421	>
422		unconsMols.clear();
423		massOfUnconsMols.clear();
223	–
424
425	+
426		//creat zconsMol and unconsMol lists
427	<	for(int i = 0; i < nMols; i++){
227	<
427	>	for (int i = 0; i < nMols; i++){
428		index = isZConstraintMol(&molecules[i]);
429	<
430	<	if(index > -1){
231	<
429	>
430	>	if (index > -1){
431		zconsMols.push_back(&molecules[i]);
432	<	massOfZConsMols.push_back(molecules[i].getTotalMass());
433	<
434	<	molecules[i].getCOM(COM);
432	>	zPos.push_back((*parameters)[index].zPos);
433	>	kz.push_back((*parameters)[index].kRatio * zForceConst);
434	>	massOfZConsMols.push_back(molecules[i].getTotalMass());
435	>
436	>	if(usingSMD)
437	>	cantVel.push_back((*parameters)[index].cantVel);
438	>
439		}
440	<	else
238	<	{
239	<
440	>	else{
441		unconsMols.push_back(&molecules[i]);
442		massOfUnconsMols.push_back(molecules[i].getTotalMass());
242	–
443		}
444		}
445	+
446	+	fz.resize(zconsMols.size());
447	+	curZPos.resize(zconsMols.size());
448	+	indexOfZConsMols.resize(zconsMols.size());
449	+
450	+	for (size_t i = 0; i < zconsMols.size(); i++){
451	+	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
452	+	}
453
454	<	//The reason to declare fz and indexOfZconsMols as pointer to array is
455	<	// that we want to make the MPI communication simple
456	<	if(fz)
457	<	delete[] fz;
454	>	//determine the states of z-constraint molecules
455	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
456	>
457	>	zconsMols[i]->getCOM(COM);
458
459	<	if(indexOfZConsMols)
460	<	delete[] indexOfZConsMols;
461	<
462	<	if (zconsMols.size() > 0){
463	<	fz = new double[zconsMols.size()];
256	<	indexOfZConsMols =  new int[zconsMols.size()];
257	<
258	<	if(!fz || !indexOfZConsMols){
259	<	sprintf( painCave.errMsg,
260	<	"Memory allocation failure in class Zconstraint\n");
261	<	painCave.isFatal = 1;
262	<	simError();
459	>	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
460	>	states.push_back(zcsFixed);
461	>
462	>	if (hasZConsGap)
463	>	endFixTime.push_back(info->getTime() + zconsFixTime);
464		}
465	<
466	<	for(int i = 0; i < zconsMols.size(); i++){
467	<	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
465	>	else{
466	>	states.push_back(zcsMoving);
467	>
468	>	if (hasZConsGap)
469	>	endFixTime.push_back(INFINITE_TIME);
470		}
471
472	<	}
473	<	else{
474	<	fz = NULL;
475	<	indexOfZConsMols = NULL;
476	<	}
477	<
472	>	if(usingSMD)
473	>	cantPos.push_back(COM[whichDirection]);
474	>	}
475	>
476	>	if(usingSMD)
477	>	prevCantPos = cantPos;
478	>
479	>	//
480	>	forcePolicy->update();
481		}
482
483		#endif
484
485	<	/**  Function Name: isZConstraintMol
486	<	**  Parameter
487	<	**    Molecule* mol
488	<	**  Return value:
489	<	**    -1, if the molecule is not z-constraint molecule,
490	<	**    other non-negative values, its index in indexOfAllZConsMols vector
485	>	/**
486	>	*  Function Name: isZConstraintMol
487	>	*  Parameter
488	>	*    Molecule* mol
489	>	*  Return value:
490	>	*    -1, if the molecule is not z-constraint molecule,
491	>	*    other non-negative values, its index in indexOfAllZConsMols vector
492		*/
493
494	<	template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
288	<	{
494	>	template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){
495		int index;
496		int low;
497		int high;
498		int mid;
499
500		index = mol->getGlobalIndex();
501	<
501	>
502		low = 0;
503	<	high = indexOfAllZConsMols.size() - 1;
504	<
503	>	high = parameters->size() - 1;
504	>
505		//Binary Search (we have sorted the array)
506	<	while(low <= high){
507	<	mid = (low + high) /2;
508	<	if (indexOfAllZConsMols[mid] == index)
506	>	while (low <= high){
507	>	mid = (low + high) / 2;
508	>	if ((*parameters)[mid].zconsIndex == index)
509		return mid;
510	<	else if (indexOfAllZConsMols[mid] > index )
511	<	high = mid -1;
512	<	else
513	<	low = mid + 1;
510	>	else if ((*parameters)[mid].zconsIndex > index)
511	>	high = mid - 1;
512	>	else
513	>	low = mid + 1;
514		}
515	<
515	>
516		return -1;
517		}
518
313	–	/**
314	–	* Description:
315	–	*  Reset the z coordinates
316	–	*/
519		template<typename T> void ZConstraint<T>::integrate(){
520	<
520	>	// creat zconsWriter
521	>	fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
522	>
523	>	if (!fzOut){
524	>	sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");
525	>	painCave.isFatal = 1;
526	>	simError();
527	>	}
528	>
529		//zero out the velocities of center of mass of unconstrained molecules
530		//and the velocities of center of mass of every single z-constrained molecueles
531		zeroOutVel();
322	–
323	–	T::integrate();
532
533	+	curZconsTime = zconsTime + info->getTime();
534	+
535	+	T::integrate();
536		}
326	–
537
538	+
539		/**
540		*
541		*
542		*
543		*
544	<	*/
334	<
335	<
544	>	*/
545		template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
546	+	double zsys;
547	+	double COM[3];
548	+	double force[3];
549	+	double zSysCOMVel;
550
551		T::calcForce(calcPot, calcStress);
552
340	–	if (checkZConsState())
341	–	zeroOutVel();
553
554	+	if (hasZConsGap){
555	+	updateZPos();
556	+	}
557	+
558	+	if (checkZConsState()){
559	+	zeroOutVel();
560	+	forcePolicy->update();
561	+	}
562	+
563	+	zsys = calcZSys();
564	+	zSysCOMVel = calcSysCOMVel();
565	+	#ifdef IS_MPI
566	+	if (worldRank == 0){
567	+	#endif
568	+	//cout << "---------------------------------------------------------------------" <<endl;
569	+	//cout << "current time: " << info->getTime() << endl;
570	+	//cout << "center of mass at z: " << zsys << endl;
571	+	//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
572	+
573	+	#ifdef IS_MPI
574	+	}
575	+	#endif
576	+
577		//do zconstraint force;
578	<	if (haveFixedZMols())
578	>	if (haveFixedZMols()){
579		this->doZconstraintForce();
580	<
581	<	//use harmonical poteintial to move the molecules to the specified positions
582	<	if (haveMovingZMols())
583	<	//this->doHarmonic();
584	<
585	<	fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
586	<
580	>	}
581	>
582	>	//use external force to move the molecules to the specified positions
583	>	if (haveMovingZMols()){
584	>	if (usingSMD)
585	>	this->doHarmonic(cantPos);
586	>	else
587	>	this->doHarmonic(zPos);
588	>	}
589	>
590	>	//write out forces and current positions of z-constraint molecules
591	>	if (info->getTime() >= curZconsTime){
592	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
593	>	zconsMols[i]->getCOM(COM);
594	>	curZPos[i] = COM[whichDirection];
595	>
596	>	//if the z-constraint molecule is still moving, just record its force
597	>	if (states[i] == zcsMoving){
598	>	fz[i] = 0;
599	>	Atom** movingZAtoms;
600	>	movingZAtoms = zconsMols[i]->getMyAtoms();
601	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
602	>	movingZAtoms[j]->getFrc(force);
603	>	fz[i] += force[whichDirection];
604	>	}
605	>	}
606	>	}
607	>	fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],
608	>	&curZPos[0], &zPos[0]);
609	>	curZconsTime += zconsTime;
610	>	}
611	>
612	>	zSysCOMVel = calcSysCOMVel();
613	>	#ifdef IS_MPI
614	>	if (worldRank == 0){
615	>	#endif
616	>	//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
617	>	#ifdef IS_MPI
618	>	}
619	>	#endif
620		}
621	<
622	<	template<typename T> double ZConstraint<T>::calcZSys()
623	<	{
621	>
622	>
623	>	/**
624	>	*
625	>	*/
626	>
627	>	template<typename T> double ZConstraint<T>::calcZSys(){
628		//calculate reference z coordinate for z-constraint molecules
629		double totalMass_local;
630		double totalMass;
631		double totalMZ_local;
632		double totalMZ;
362	–	double massOfUncons_local;
633		double massOfCurMol;
634		double COM[3];
635	<
635	>
636		totalMass_local = 0;
367	–	totalMass = 0;
637		totalMZ_local = 0;
638	<	totalMZ = 0;
639	<	massOfUncons_local = 0;
371	<
372	<
373	<	for(int i = 0; i < nMols; i++){
638	>
639	>	for (int i = 0; i < nMols; i++){
640		massOfCurMol = molecules[i].getTotalMass();
641		molecules[i].getCOM(COM);
642	<
642	>
643		totalMass_local += massOfCurMol;
644		totalMZ_local += massOfCurMol * COM[whichDirection];
379	–
380	–	if(isZConstraintMol(&molecules[i]) == -1){
381	–
382	–	massOfUncons_local += massOfCurMol;
383	–	}
384	–
645		}
646	<
647	<
646	>
647	>
648		#ifdef IS_MPI
649	<	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
650	<	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
651	<	MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
649	>	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,
650	>	MPI_COMM_WORLD);
651	>	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
652		#else
653		totalMass = totalMass_local;
654		totalMZ = totalMZ_local;
395	–	totalMassOfUncons = massOfUncons_local;
655		#endif
656
657		double zsys;
#	Line 404 | Line 663 | template<typename T> double ZConstraint<T>::calcZSys()
663		/**
664		*
665		*/
666	<	template<typename T> void ZConstraint<T>::thermalize( void ){
408	<
666	>	template<typename T> void ZConstraint<T>::thermalize(void){
667		T::thermalize();
668		zeroOutVel();
669		}
670
671		/**
672		*
415	–	*
416	–	*
673		*/
674
675		template<typename T> void ZConstraint<T>::zeroOutVel(){
420	–
676		Atom** fixedZAtoms;
677		double COMvel[3];
678		double vel[3];
679	<
679	>	double zSysCOMVel;
680	>
681		//zero out the velocities of center of mass of fixed z-constrained molecules
426	–
427	–	for(int i = 0; i < zconsMols.size(); i++){
682
683	<	if (states[i] == zcsFixed){
683	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
684	>	if (states[i] == zcsFixed){
685	>	zconsMols[i]->getCOMvel(COMvel);
686	>	//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
687
431	–	zconsMols[i]->getCOMvel(COMvel);
688		fixedZAtoms = zconsMols[i]->getMyAtoms();
689	<
690	<	for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
689	>
690	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
691		fixedZAtoms[j]->getVel(vel);
692	<	vel[whichDirection] -= COMvel[whichDirection];
693	<	fixedZAtoms[j]->setVel(vel);
692	>	vel[whichDirection] -= COMvel[whichDirection];
693	>	fixedZAtoms[j]->setVel(vel);
694		}
695	<
695	>
696	>	zconsMols[i]->getCOMvel(COMvel);
697	>	//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
698		}
441	–
699		}
700	<
700	>
701	>	//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
702	>
703	>	zSysCOMVel = calcSysCOMVel();
704	>	#ifdef IS_MPI
705	>	if (worldRank == 0){
706	>	#endif
707	>	//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;
708	>	#ifdef IS_MPI
709	>	}
710	>	#endif
711	>
712		// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
713		double MVzOfMovingMols_local;
714		double MVzOfMovingMols;
715		double totalMassOfMovingZMols_local;
716		double totalMassOfMovingZMols;
717	<
717	>
718		MVzOfMovingMols_local = 0;
719		totalMassOfMovingZMols_local = 0;
720
721	<	for(int i =0; i < unconsMols.size(); i++){
721	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
722		unconsMols[i]->getCOMvel(COMvel);
723	<	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
723	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
724		}
725
726	<	for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
459	<
726	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
727		if (states[i] == zcsMoving){
728		zconsMols[i]->getCOMvel(COMvel);
729		MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
730	<	totalMassOfMovingZMols_local += massOfZConsMols[i];
730	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
731		}
465	–
732		}
733
734		#ifndef IS_MPI
735		MVzOfMovingMols = MVzOfMovingMols_local;
736		totalMassOfMovingZMols = totalMassOfMovingZMols_local;
737		#else
738	<	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
739	<	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
738	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
739	>	MPI_SUM, MPI_COMM_WORLD);
740	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
741	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
742		#endif
743
744		double vzOfMovingMols;
745	<	vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
745	>	vzOfMovingMols = MVzOfMovingMols /
746	>	(totalMassOfUncons + totalMassOfMovingZMols);
747
748		//modify the velocites of unconstrained molecules
749		Atom** unconsAtoms;
750	<	for(int i = 0; i < unconsMols.size(); i++){
482	<
750	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
751		unconsAtoms = unconsMols[i]->getMyAtoms();
752	<	for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
752	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
753		unconsAtoms[j]->getVel(vel);
754		vel[whichDirection] -= vzOfMovingMols;
755		unconsAtoms[j]->setVel(vel);
756		}
489	–
757		}
758
759		//modify the velocities of moving z-constrained molecuels
760		Atom** movingZAtoms;
761	<	for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
762	<
496	<	if (states[i] ==zcsMoving){
497	<
761	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
762	>	if (states[i] == zcsMoving){
763		movingZAtoms = zconsMols[i]->getMyAtoms();
764	<	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
764	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
765		movingZAtoms[j]->getVel(vel);
766		vel[whichDirection] -= vzOfMovingMols;
767	<	movingZAtoms[j]->setVel(vel);
768	<	}
504	<
767	>	movingZAtoms[j]->setVel(vel);
768	>	}
769		}
506	–
770		}
771
772	+
773	+	zSysCOMVel = calcSysCOMVel();
774	+	#ifdef IS_MPI
775	+	if (worldRank == 0){
776	+	#endif
777	+	//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;
778	+	#ifdef IS_MPI
779	+	}
780	+	#endif
781		}
782
783	<	template<typename T> void ZConstraint<T>::doZconstraintForce(){
783	>	/**
784	>	*
785	>	*/
786
787	+	template<typename T> void ZConstraint<T>::doZconstraintForce(){
788		Atom** zconsAtoms;
789		double totalFZ;
790		double totalFZ_local;
516	–	double COMvel[3];
791		double COM[3];
792		double force[3];
519	–	double zsys;
793
794	<	int nMovingZMols_local;
522	<	int nMovingZMols;
794	>	//constrain the molecules which do not reach the specified positions
795
524	–	//constrain the molecules which do not reach the specified positions
525	–
526	–	zsys = calcZSys();
527	–	cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;
528	–
796		//Zero Out the force of z-contrained molecules
797		totalFZ_local = 0;
798
799		//calculate the total z-contrained force of fixed z-contrained molecules
800	<	for(int i = 0; i < zconsMols.size(); i++){
801	<
800	>
801	>	//cout << "before zero out z-constraint force on fixed z-constraint molecuels "
802	>	//       << "total force is " << calcTotalForce() << endl;
803	>
804	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
805		if (states[i] == zcsFixed){
536	–
806		zconsMols[i]->getCOM(COM);
807		zconsAtoms = zconsMols[i]->getMyAtoms();
808
809		fz[i] = 0;
810	<	for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
810	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
811		zconsAtoms[j]->getFrc(force);
812	<	fz[i] += force[whichDirection];
813	<	}
812	>	fz[i] += force[whichDirection];
813	>	}
814		totalFZ_local += fz[i];
815
816	<	cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
817	<
816	>	//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
817	>	//      <<"\tcurrent zpos: " << COM[whichDirection]
818	>	//      << "\tcurrent fz: " <<fz[i] << endl;
819		}
550	–
820		}
821
822	<	//calculate the number of atoms of moving z-constrained molecules
554	<	nMovingZMols_local = 0;
555	<	for(int i = 0; zconsMols.size(); i++){
556	<	if(states[i] == zcsMoving)
557	<	nMovingZMols_local += massOfZConsMols[i];
558	<	}
822	>	//calculate total z-constraint force
823		#ifdef IS_MPI
824	<	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
561	<	MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
824	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
825		#else
826		totalFZ = totalFZ_local;
564	–	nMovingZMols = nMovingZMols_local;
827		#endif
828
567	–	force[0]= 0;
568	–	force[1]= 0;
569	–	force[2]= 0;
570	–	force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
829
830	<	//modify the velocites of unconstrained molecules
831	<	for(int i = 0; i < unconsMols.size(); i++){
832	<
833	<	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
576	<
577	<	for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)
578	<	unconsAtoms[j]->addFrc(force);
579	<
580	<	}
830	>	// apply negative to fixed z-constrained molecues;
831	>	force[0] = 0;
832	>	force[1] = 0;
833	>	force[2] = 0;
834
835	<	//modify the velocities of moving z-constrained molecules
836	<	for(int i = 0; i < zconsMols.size(); i++) {
584	<	if (states[i] == zcsMoving){
585	<
586	<	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
587	<
588	<	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
589	<	movingZAtoms[j]->addFrc(force);
590	<	}
591	<	}
592	<
593	<	// apply negative to fixed z-constrained molecues;
594	<	force[0]= 0;
595	<	force[1]= 0;
596	<	force[2]= 0;
597	<
598	<	for(int i = 0; i < zconsMols.size(); i++){
599	<
600	<	if (states[i] == zcsFixed){
601	<
835	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
836	>	if (states[i] == zcsFixed){
837		int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
838		zconsAtoms = zconsMols[i]->getMyAtoms();
839	<
840	<	for(int j =0; j < nAtomOfCurZConsMol; j++) {
841	<	force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
839	>
840	>	for (int j = 0; j < nAtomOfCurZConsMol; j++){
841	>	//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
842	>	force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],
843	>	zconsAtoms[j],
844	>	fz[i]);
845		zconsAtoms[j]->addFrc(force);
846		}
609	–
847		}
611	–
848		}
849
850	+	//cout << "after zero out z-constraint force on fixed z-constraint molecuels "
851	+	//      << "total force is " << calcTotalForce() << endl;
852	+
853	+
854	+	force[0] = 0;
855	+	force[1] = 0;
856	+	force[2] = 0;
857	+
858	+	//modify the forces of unconstrained molecules
859	+	for (int i = 0; i < (int) (unconsMols.size()); i++){
860	+	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
861	+
862	+	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
863	+	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
864	+	force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],
865	+	totalFZ);
866	+	unconsAtoms[j]->addFrc(force);
867	+	}
868	+	}
869	+
870	+	//modify the forces of moving z-constrained molecules
871	+	for (int i = 0; i < (int) (zconsMols.size()); i++){
872	+	if (states[i] == zcsMoving){
873	+	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
874	+
875	+	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
876	+	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
877	+	force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],
878	+	totalFZ);
879	+	movingZAtoms[j]->addFrc(force);
880	+	}
881	+	}
882	+	}
883	+	//  cout << "after substracting z-constraint force from moving molecuels "
884	+	//        << "total force is " << calcTotalForce()  << endl;
885		}
886
887	<	template<typename T> bool ZConstraint<T>::checkZConsState(){
887	>	/**
888	>	*
889	>	*
890	>	*/
891	>
892	>	template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
893	>	double force[3];
894	>	double harmonicU;
895	>	double harmonicF;
896		double COM[3];
897		double diff;
898	<
899	<	bool changed;
621	<
622	<	changed = false;
623	<
624	<	for(int i =0; i < zconsMols.size(); i++){
898	>	double totalFZ_local;
899	>	double totalFZ;
900
901	<	zconsMols[i]->getCOM(COM);
902	<	diff = fabs(COM[whichDirection] - ZPos[i]);
903	<	if (  diff <= ztol && states[i] == zcsMoving){
904	<	states[i] = zcsFixed;
905	<	changed = true;
901	>	force[0] = 0;
902	>	force[1] = 0;
903	>	force[2] = 0;
904	>
905	>	totalFZ_local = 0;
906	>
907	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
908	>	if (states[i] == zcsMoving){
909	>	zconsMols[i]->getCOM(COM);
910	>	//       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
911	>	//     << "\tcurrent zpos: " << COM[whichDirection] << endl;
912	>
913	>	diff = COM[whichDirection] - resPos[i];
914	>
915	>	harmonicU = 0.5 * kz[i] * diff * diff;
916	>	info->lrPot += harmonicU;
917	>
918	>	harmonicF = -kz[i] * diff;
919	>	totalFZ_local += harmonicF;
920	>
921	>	//adjust force
922	>
923	>	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
924	>
925	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
926	>	//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
927	>	force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
928	>	movingZAtoms[j],
929	>	harmonicF);
930	>	movingZAtoms[j]->addFrc(force);
931	>	}
932		}
632	–	else if ( diff > ztol && states[i] == zcsFixed){
633	–	states[i] = zcsMoving;
634	–	changed = true;
635	–	}
636	–
933		}
934
935	<	return changed;
936	<	}
935	>	#ifndef IS_MPI
936	>	totalFZ = totalFZ_local;
937	>	#else
938	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
939	>	#endif
940
941	<	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
942	<	for(int i = 0; i < zconsMols.size(); i++)
644	<	if (states[i] == zcsFixed)
645	<	return true;
941	>	//cout << "before substracting harmonic force from moving molecuels "
942	>	//      << "total force is " << calcTotalForce()  << endl;
943
944	<	return false;
944	>	force[0] = 0;
945	>	force[1] = 0;
946	>	force[2] = 0;
947	>
948	>	//modify the forces of unconstrained molecules
949	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
950	>	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
951	>
952	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
953	>	//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
954	>	force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],
955	>	totalFZ);
956	>	unconsAtoms[j]->addFrc(force);
957	>	}
958	>	}
959	>
960	>	//cout << "after substracting harmonic force from moving molecuels "
961	>	//      << "total force is " << calcTotalForce()  << endl;
962		}
963
964	+	/**
965	+	*
966	+	*/
967
968	+	template<typename T> bool ZConstraint<T>::checkZConsState(){
969	+	double COM[3];
970	+	double diff;
971	+
972	+	int changed_local;
973	+	int changed;
974	+
975	+	changed_local = 0;
976	+
977	+	for (int i = 0; i < (int) (zconsMols.size()); i++){
978	+	zconsMols[i]->getCOM(COM);
979	+	diff = fabs(COM[whichDirection] - zPos[i]);
980	+	if (diff <= zconsTol && states[i] == zcsMoving){
981	+	states[i] = zcsFixed;
982	+	changed_local = 1;
983	+
984	+	if(usingSMD)
985	+	prevCantPos = cantPos;
986	+
987	+	if (hasZConsGap)
988	+	endFixTime[i] = info->getTime() + zconsFixTime;
989	+	}
990	+	else if (diff > zconsTol && states[i] == zcsFixed){
991	+	states[i] = zcsMoving;
992	+	changed_local = 1;
993	+
994	+	if(usingSMD)
995	+	cantPos = prevCantPos;
996	+
997	+	if (hasZConsGap)
998	+	endFixTime[i] = INFINITE_TIME;
999	+	}
1000	+	}
1001	+
1002	+	#ifndef IS_MPI
1003	+	changed = changed_local;
1004	+	#else
1005	+	MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1006	+	#endif
1007	+
1008	+	return (changed > 0);
1009	+	}
1010	+
1011	+	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1012	+	int havingFixed_local;
1013	+	int havingFixed;
1014	+
1015	+	havingFixed_local = 0;
1016	+
1017	+	for (int i = 0; i < (int) (zconsMols.size()); i++)
1018	+	if (states[i] == zcsFixed){
1019	+	havingFixed_local = 1;
1020	+	break;
1021	+	}
1022	+
1023	+	#ifndef IS_MPI
1024	+	havingFixed = havingFixed_local;
1025	+	#else
1026	+	MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
1027	+	MPI_COMM_WORLD);
1028	+	#endif
1029	+
1030	+	return (havingFixed > 0);
1031	+	}
1032	+
1033	+
1034		/**
1035		*
1036		*/
1037		template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1038	<	for(int i = 0; i < zconsMols.size(); i++)
1039	<	if (states[i] == zcsMoving)
657	<	return true;
1038	>	int havingMoving_local;
1039	>	int havingMoving;
1040
1041	<	return false;
1041	>	havingMoving_local = 0;
1042	>
1043	>	for (int i = 0; i < (int) (zconsMols.size()); i++)
1044	>	if (states[i] == zcsMoving){
1045	>	havingMoving_local = 1;
1046	>	break;
1047	>	}
1048	>
1049	>	#ifndef IS_MPI
1050	>	havingMoving = havingMoving_local;
1051	>	#else
1052	>	MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
1053	>	MPI_COMM_WORLD);
1054	>	#endif
1055	>
1056	>	return (havingMoving > 0);
1057	>	}
1058	>
1059	>	/**
1060	>	*
1061	>	*/
1062	>
1063	>	template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
1064	>	double MVzOfMovingMols_local;
1065	>	double MVzOfMovingMols;
1066	>	double totalMassOfMovingZMols_local;
1067	>	double totalMassOfMovingZMols;
1068	>	double COMvel[3];
1069	>
1070	>	MVzOfMovingMols_local = 0;
1071	>	totalMassOfMovingZMols_local = 0;
1072	>
1073	>	for (int i = 0; i < unconsMols.size(); i++){
1074	>	unconsMols[i]->getCOMvel(COMvel);
1075	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
1076	>	}
1077	>
1078	>	for (int i = 0; i < zconsMols.size(); i++){
1079	>	if (states[i] == zcsMoving){
1080	>	zconsMols[i]->getCOMvel(COMvel);
1081	>	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
1082	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
1083	>	}
1084	>	}
1085	>
1086	>	#ifndef IS_MPI
1087	>	MVzOfMovingMols = MVzOfMovingMols_local;
1088	>	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1089	>	#else
1090	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
1091	>	MPI_SUM, MPI_COMM_WORLD);
1092	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
1093	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1094	>	#endif
1095	>
1096	>	double vzOfMovingMols;
1097	>	vzOfMovingMols = MVzOfMovingMols /
1098	>	(totalMassOfUncons + totalMassOfMovingZMols);
1099	>
1100	>	return vzOfMovingMols;
1101	>	}
1102	>
1103	>	/**
1104	>	*
1105	>	*/
1106	>
1107	>	template<typename T> double ZConstraint<T>::calcSysCOMVel(){
1108	>	double COMvel[3];
1109	>	double tempMVz_local;
1110	>	double tempMVz;
1111	>	double massOfZCons_local;
1112	>	double massOfZCons;
1113	>
1114	>
1115	>	tempMVz_local = 0;
1116	>
1117	>	for (int i = 0 ; i < nMols; i++){
1118	>	molecules[i].getCOMvel(COMvel);
1119	>	tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];
1120	>	}
1121	>
1122	>	massOfZCons_local = 0;
1123	>
1124	>	for (int i = 0; i < (int) (massOfZConsMols.size()); i++){
1125	>	massOfZCons_local += massOfZConsMols[i];
1126	>	}
1127	>	#ifndef IS_MPI
1128	>	massOfZCons = massOfZCons_local;
1129	>	tempMVz = tempMVz_local;
1130	>	#else
1131	>	MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,
1132	>	MPI_COMM_WORLD);
1133	>	MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1134	>	#endif
1135	>
1136	>	return tempMVz / (totalMassOfUncons + massOfZCons);
1137	>	}
1138	>
1139	>	/**
1140	>	*
1141	>	*/
1142	>
1143	>	template<typename T> double ZConstraint<T>::calcTotalForce(){
1144	>	double force[3];
1145	>	double totalForce_local;
1146	>	double totalForce;
1147	>
1148	>	totalForce_local = 0;
1149	>
1150	>	for (int i = 0; i < nAtoms; i++){
1151	>	atoms[i]->getFrc(force);
1152	>	totalForce_local += force[whichDirection];
1153	>	}
1154	>
1155	>	#ifndef IS_MPI
1156	>	totalForce = totalForce_local;
1157	>	#else
1158	>	MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,
1159	>	MPI_COMM_WORLD);
1160	>	#endif
1161	>
1162	>	return totalForce;
1163	>	}
1164	>
1165	>	/**
1166	>	*
1167	>	*/
1168	>
1169	>	template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1170	>	//calculate the number of atoms of moving z-constrained molecules
1171	>	int nMovingZAtoms_local;
1172	>	int nMovingZAtoms;
1173	>
1174	>	nMovingZAtoms_local = 0;
1175	>	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1176	>	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1177	>	nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1178	>	}
1179	>
1180	>	#ifdef IS_MPI
1181	>	MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,
1182	>	MPI_COMM_WORLD);
1183	>	#else
1184	>	nMovingZAtoms = nMovingZAtoms_local;
1185	>	#endif
1186	>	totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1187	>	}
1188	>
1189	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,
1190	>	Atom* atom,
1191	>	double totalForce){
1192	>	return totalForce / mol->getNAtoms();
1193	>	}
1194	>
1195	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,
1196	>	double totalForce){
1197	>	return totalForce / totNumOfMovingAtoms;
1198	>	}
1199	>
1200	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,
1201	>	Atom* atom,
1202	>	double totalForce){
1203	>	return totalForce / mol->getNAtoms();
1204	>	}
1205	>
1206	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,
1207	>	double totalForce){
1208	>	return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1209	>	}
1210	>
1211	>	/**
1212	>	*
1213	>	*/
1214	>
1215	>	template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1216	>	//calculate the number of atoms of moving z-constrained molecules
1217	>	double massOfMovingZAtoms_local;
1218	>	double massOfMovingZAtoms;
1219	>
1220	>	massOfMovingZAtoms_local = 0;
1221	>	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1222	>	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1223	>	massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1224	>	}
1225	>
1226	>	#ifdef IS_MPI
1227	>	MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,
1228	>	MPI_SUM, MPI_COMM_WORLD);
1229	>	#else
1230	>	massOfMovingZAtoms = massOfMovingZAtoms_local;
1231	>	#endif
1232	>	totMassOfMovingAtoms = massOfMovingZAtoms +
1233	>	zconsIntegrator->totalMassOfUncons;
1234	>	}
1235	>
1236	>	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,
1237	>	Atom* atom,
1238	>	double totalForce){
1239	>	return totalForce * atom->getMass() / mol->getTotalMass();
1240	>	}
1241	>
1242	>	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,
1243	>	double totalForce){
1244	>	return totalForce * atom->getMass() / totMassOfMovingAtoms;
1245	>	}
1246	>
1247	>	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,
1248	>	Atom* atom,
1249	>	double totalForce){
1250	>	return totalForce * atom->getMass() / mol->getTotalMass();
1251	>	}
1252	>
1253	>	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,
1254	>	double totalForce){
1255	>	return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1256	>	}
1257	>
1258	>	template<typename T> void ZConstraint<T>::updateZPos(){
1259	>	double curTime;
1260	>	double COM[3];
1261
1262	<	}
1262	>	curTime = info->getTime();
1263	>
1264	>	for (size_t i = 0; i < zconsMols.size(); i++){
1265	>
1266	>	if (states[i] == zcsFixed && curTime >= endFixTime[i]){
1267	>	zPos[i] += zconsGap;
1268	>
1269	>	if (usingSMD){
1270	>	zconsMols[i]->getCOM(COM);
1271	>	cantPos[i] = COM[whichDirection];
1272	>	}
1273	>
1274	>	}
1275	>
1276	>	}
1277	>
1278	>	}
1279	>
1280	>	template<typename T> void ZConstraint<T>::updateCantPos(){
1281	>	double curTime;
1282	>	double dt;
1283	>
1284	>	curTime = info->getTime();
1285	>	dt = info->dt;
1286	>
1287	>	for (size_t i = 0; i < zconsMols.size(); i++){
1288	>	if (states[i] == zcsMoving){
1289	>	cantPos[i] += cantVel[i] * dt;
1290	>	}
1291	>	}
1292	>
1293	>	}

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