# | Line 1 | Line 1 | |
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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 "io/ZConsReader.hpp" | |
43 | #include "utils/simError.h" | |
44 | #include "utils/StringUtils.hpp" | |
45 | < | namespace oopse { |
45 | > | namespace OpenMD { |
46 | ||
47 | < | ZConsReader::ZConsReader(SimInfo* info) : info_(info){ |
47 | > | ZConsReader::ZConsReader(SimInfo* info) : info_(info){ |
48 | ||
49 | std::string zconsFileName_ = getPrefix(info_->getFinalConfigFileName()) + ".fz"; | |
50 | istream_.open(zconsFileName_.c_str()); | |
51 | ||
52 | if (!istream_){ | |
53 | < | std::cerr << "open " << zconsFileName_ << "error" << std::endl; |
54 | < | exit(1); |
53 | > | std::cerr << "open " << zconsFileName_ << "error" << std::endl; |
54 | > | exit(1); |
55 | } | |
56 | ||
57 | Globals* simParam = info_->getSimParams(); | |
58 | < | int nZconstraints = simParam->getNzConstraints(); |
59 | < | ZconStamp** stamp = simParam->getZconStamp(); |
58 | > | int nZconstraints = simParam->getNZconsStamps(); |
59 | > | std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
60 | for (int i = 0; i < nZconstraints; i++){ | |
61 | < | allZmols_.push_back(stamp[i]->getMolIndex()); |
61 | > | allZmols_.push_back(stamp[i]->getMolIndex()); |
62 | } | |
63 | < | } |
63 | > | } |
64 | ||
65 | < | ZConsReader::~ZConsReader(){ |
66 | < | istream_.close(); |
67 | < | } |
65 | > | ZConsReader::~ZConsReader(){ |
66 | > | istream_.close(); |
67 | > | } |
68 | ||
69 | < | void ZConsReader::readNextFrame(){ |
69 | > | void ZConsReader::readNextFrame(){ |
70 | char line[MAXBUFFERSIZE]; | |
71 | int nFixedZmol; | |
72 | int sscanfCount; | |
# | Line 76 | Line 76 | void ZConsReader::readNextFrame(){ | |
76 | while(istream_.getline(line, MAXBUFFERSIZE) && line[0] == '/' && line[1] == '/'); | |
77 | sscanfCount = sscanf(line, "%lf", &curTime_); | |
78 | if (sscanfCount != 1){ | |
79 | < | std::cerr << "ZConsReader Error : reading file error" << std::endl; |
80 | < | exit(1); |
79 | > | std::cerr << "ZConsReader Error : reading file error" << std::endl; |
80 | > | exit(1); |
81 | } | |
82 | ||
83 | istream_.getline(line, MAXBUFFERSIZE); | |
84 | sscanfCount = sscanf(line, "%d", &nFixedZmol); | |
85 | if (sscanfCount != 1){ | |
86 | < | std::cerr << "ZConsReader Error : reading file error" << std::endl; |
87 | < | exit(1); |
86 | > | std::cerr << "ZConsReader Error : reading file error" << std::endl; |
87 | > | exit(1); |
88 | } | |
89 | ||
90 | ZconsData data; | |
91 | for(int i = 0; i < nFixedZmol; i++){ | |
92 | < | istream_.getline(line, MAXBUFFERSIZE); |
93 | < | sscanfCount = sscanf(line, "%d\t%lf\t%lf\t%lf", &data.zmolIndex, &data.zforce, &data.zpos,&data.zconsPos); |
94 | < | if (sscanfCount != 4){ |
95 | < | std::cerr << "ZConsReader Error : reading file error" << std::endl; |
96 | < | exit(1); |
97 | < | } |
92 | > | istream_.getline(line, MAXBUFFERSIZE); |
93 | > | sscanfCount = sscanf(line, "%d\t%lf\t%lf\t%lf", &data.zmolIndex, &data.zforce, &data.zpos,&data.zconsPos); |
94 | > | if (sscanfCount != 4){ |
95 | > | std::cerr << "ZConsReader Error : reading file error" << std::endl; |
96 | > | exit(1); |
97 | > | } |
98 | ||
99 | < | fixedZmolData_.push_back(data); |
99 | > | fixedZmolData_.push_back(data); |
100 | } | |
101 | ||
102 | < | } |
102 | > | } |
103 | ||
104 | < | bool ZConsReader::hasNextFrame(){ |
105 | < | return istream_.peek() != EOF ? true : false; |
106 | < | } |
104 | > | bool ZConsReader::hasNextFrame(){ |
105 | > | return istream_.peek() != EOF ? true : false; |
106 | > | } |
107 | ||
108 | } |
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