# | Line 1 | Line 1 | |
---|---|---|
1 | < | /* |
1 | > | /* |
2 | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. | |
3 | * | |
4 | * The University of Notre Dame grants you ("Licensee") a | |
# | Line 6 | Line 6 | |
6 | * redistribute this software in source and binary code form, provided | |
7 | * that the following conditions are met: | |
8 | * | |
9 | < | * 1. Acknowledgement of the program authors must be made in any |
10 | < | * publication of scientific results based in part on use of the |
11 | < | * program. An acceptable form of acknowledgement is citation of |
12 | < | * the article in which the program was described (Matthew |
13 | < | * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 | < | * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 | < | * Parallel Simulation Engine for Molecular Dynamics," |
16 | < | * J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 | < | * |
18 | < | * 2. Redistributions of source code must retain the above copyright |
9 | > | * 1. Redistributions of source code must retain the above copyright |
10 | * notice, this list of conditions and the following disclaimer. | |
11 | * | |
12 | < | * 3. Redistributions in binary form must reproduce the above copyright |
12 | > | * 2. Redistributions in binary form must reproduce the above copyright |
13 | * notice, this list of conditions and the following disclaimer in the | |
14 | * documentation and/or other materials provided with the | |
15 | * distribution. | |
# | Line 37 | Line 28 | |
28 | * arising out of the use of or inability to use software, even if the | |
29 | * University of Notre Dame has been advised of the possibility of | |
30 | * such damages. | |
31 | + | * |
32 | + | * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
33 | + | * research, please cite the appropriate papers when you publish your |
34 | + | * work. Good starting points are: |
35 | + | * |
36 | + | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
37 | + | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
38 | + | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
39 | + | * [4] Vardeman & Gezelter, in progress (2009). |
40 | */ | |
41 | ||
42 | #include <algorithm> | |
# | Line 46 | Line 46 | |
46 | ||
47 | #include "io/ZConsWriter.hpp" | |
48 | #include "utils/simError.h" | |
49 | + | #ifdef IS_MPI |
50 | + | #include <mpi.h> |
51 | + | #endif |
52 | ||
53 | < | |
54 | < | namespace oopse { |
55 | < | ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { |
53 | < | //use master - slave mode, only master node writes to disk |
53 | > | namespace OpenMD { |
54 | > | ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { |
55 | > | //use master - slave mode, only master node writes to disk |
56 | #ifdef IS_MPI | |
57 | if(worldRank == 0){ | |
58 | #endif | |
59 | ||
60 | < | output_.open(filename.c_str()); |
60 | > | output_.open(filename.c_str()); |
61 | ||
62 | < | if(!output_){ |
63 | < | sprintf( painCave.errMsg, |
64 | < | "Could not open %s for z constrain output_ \n", filename.c_str()); |
65 | < | painCave.isFatal = 1; |
66 | < | simError(); |
67 | < | } |
62 | > | if(!output_){ |
63 | > | sprintf( painCave.errMsg, |
64 | > | "Could not open %s for z constrain output_ \n", filename.c_str()); |
65 | > | painCave.isFatal = 1; |
66 | > | simError(); |
67 | > | } |
68 | ||
69 | < | output_ << "//time(fs)" << std::endl; |
70 | < | output_ << "//number of fixed z-constrain molecules" << std::endl; |
71 | < | output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl; |
69 | > | output_ << "//time(fs)" << std::endl; |
70 | > | output_ << "//number of fixed z-constrain molecules" << std::endl; |
71 | > | output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl; |
72 | ||
73 | #ifdef IS_MPI | |
74 | } | |
75 | #endif | |
76 | ||
77 | < | } |
77 | > | } |
78 | ||
79 | < | ZConsWriter::~ZConsWriter() |
80 | < | { |
79 | > | ZConsWriter::~ZConsWriter() |
80 | > | { |
81 | ||
82 | #ifdef IS_MPI | |
83 | < | if(worldRank == 0 ){ |
83 | > | if(worldRank == 0 ){ |
84 | #endif | |
85 | < | output_.close(); |
85 | > | output_.close(); |
86 | #ifdef IS_MPI | |
87 | < | } |
87 | > | } |
88 | #endif | |
89 | < | } |
89 | > | } |
90 | ||
91 | < | void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){ |
91 | > | void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){ |
92 | #ifndef IS_MPI | |
93 | output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; | |
94 | output_ << fixedZmols.size() << std::endl; | |
95 | ||
96 | std::list<ZconstraintMol>::const_iterator i; | |
97 | for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) { | |
98 | < | output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl; |
98 | > | output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl; |
99 | } | |
100 | #else | |
101 | int nproc; | |
# | Line 110 | Line 112 | void ZConsWriter::writeFZ(const std::list<ZconstraintM | |
112 | ||
113 | MPI_Status ierr; | |
114 | int zmolIndex; | |
115 | < | double data[3]; |
115 | > | RealType data[3]; |
116 | ||
117 | if (masterNode == 0) { | |
118 | ||
119 | < | std::vector<ZconsData> zconsData; |
120 | < | ZconsData tmpData; |
121 | < | for(int i =0 ; i < nproc; ++i) { |
122 | < | if (i == masterNode) { |
123 | < | std::list<ZconstraintMol>::const_iterator j; |
124 | < | for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
125 | < | tmpData.zmolIndex = j->mol->getGlobalIndex() ; |
126 | < | tmpData.zforce= j->fz; |
127 | < | tmpData.zpos = j->zpos; |
128 | < | tmpData.zconsPos = j->param.zTargetPos; |
129 | < | zconsData.push_back(tmpData); |
130 | < | } |
119 | > | std::vector<ZconsData> zconsData; |
120 | > | ZconsData tmpData; |
121 | > | for(int i =0 ; i < nproc; ++i) { |
122 | > | if (i == masterNode) { |
123 | > | std::list<ZconstraintMol>::const_iterator j; |
124 | > | for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
125 | > | tmpData.zmolIndex = j->mol->getGlobalIndex() ; |
126 | > | tmpData.zforce= j->fz; |
127 | > | tmpData.zpos = j->zpos; |
128 | > | tmpData.zconsPos = j->param.zTargetPos; |
129 | > | zconsData.push_back(tmpData); |
130 | > | } |
131 | ||
132 | < | } else { |
133 | < | for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { |
134 | < | MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); |
135 | < | MPI_Recv(data, 3, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr); |
136 | < | tmpData.zmolIndex = zmolIndex; |
137 | < | tmpData.zforce= data[0]; |
138 | < | tmpData.zpos = data[1]; |
139 | < | tmpData.zconsPos = data[2]; |
140 | < | zconsData.push_back(tmpData); |
141 | < | } |
142 | < | } |
132 | > | } else { |
133 | > | for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { |
134 | > | MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); |
135 | > | MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr); |
136 | > | tmpData.zmolIndex = zmolIndex; |
137 | > | tmpData.zforce= data[0]; |
138 | > | tmpData.zpos = data[1]; |
139 | > | tmpData.zconsPos = data[2]; |
140 | > | zconsData.push_back(tmpData); |
141 | > | } |
142 | > | } |
143 | ||
144 | < | } |
144 | > | } |
145 | ||
146 | ||
147 | < | output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; |
148 | < | output_ << zconsData.size() << std::endl; |
147 | > | output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; |
148 | > | output_ << zconsData.size() << std::endl; |
149 | ||
150 | < | std::vector<ZconsData>::iterator l; |
151 | < | for (l = zconsData.begin(); l != zconsData.end(); ++l) { |
152 | < | output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl; |
153 | < | } |
150 | > | std::vector<ZconsData>::iterator l; |
151 | > | for (l = zconsData.begin(); l != zconsData.end(); ++l) { |
152 | > | output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl; |
153 | > | } |
154 | ||
155 | } else { | |
156 | ||
157 | < | std::list<ZconstraintMol>::const_iterator j; |
158 | < | for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
159 | < | zmolIndex = j->mol->getGlobalIndex(); |
160 | < | data[0] = j->fz; |
161 | < | data[1] = j->zpos; |
162 | < | data[2] = j->param.zTargetPos; |
163 | < | MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
164 | < | MPI_Send(data, 3, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD); |
157 | > | std::list<ZconstraintMol>::const_iterator j; |
158 | > | for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
159 | > | zmolIndex = j->mol->getGlobalIndex(); |
160 | > | data[0] = j->fz; |
161 | > | data[1] = j->zpos; |
162 | > | data[2] = j->param.zTargetPos; |
163 | > | MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
164 | > | MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD); |
165 | ||
166 | < | } |
166 | > | } |
167 | } | |
168 | #endif | |
169 | < | } |
169 | > | } |
170 | ||
171 | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |