OpenMD 3.0
Molecular Dynamics in the Open
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NanoVolume.cpp
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
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9 * this list of conditions and the following disclaimer.
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12 * this list of conditions and the following disclaimer in the documentation
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17 * this software without specific prior written permission.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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28 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29 * POSSIBILITY OF SUCH DAMAGE.
30 *
31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#include "applications/staticProps/NanoVolume.hpp"
46#if defined(HAVE_QHULL)
47#include "math/AlphaHull.hpp"
48#include "math/ConvexHull.hpp"
49#endif
50#include "io/DumpReader.hpp"
52#include "utils/simError.h"
53
54using namespace OpenMD;
55
56NanoVolume::NanoVolume(SimInfo* info, const std::string& filename,
57 const std::string& sele) :
58 StaticAnalyser(info, filename, 1),
59 selectionScript_(sele), seleMan_(info), evaluator_(info) {
60 setOutputName(getPrefix(filename) + ".avol");
61
62 osq.open(getOutputFileName().c_str());
63
64 evaluator_.loadScriptString(sele);
65 if (!evaluator_.isDynamic()) {
66 seleMan_.setSelectionSet(evaluator_.evaluate());
67 }
68 frameCounter_ = 0;
69}
70
71void NanoVolume::process() {
72#if defined(HAVE_QHULL)
73 StuntDouble* sd;
74 Vector3d vec;
75 int i;
76
77 // Do convex hull for now - alpha has issues with perfect structures
78 // AlphaHull* thishull = new AlphaHull(2.0);
79 ConvexHull* thishull = new ConvexHull();
80
81 DumpReader reader(info_, dumpFilename_);
82 int nFrames = reader.getNFrames();
83 frameCounter_ = 0;
84
85 theAtoms_.reserve(info_->getNGlobalAtoms());
86
87 for (int istep = 0; istep < nFrames; istep += step_) {
88 reader.readFrame(istep);
89 frameCounter_++;
90 currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
91 RealType time = currentSnapshot_->getTime();
92
93 // Clear pos vector between each frame.
94 theAtoms_.clear();
95
96 if (evaluator_.isDynamic()) {
97 seleMan_.setSelectionSet(evaluator_.evaluate());
98 }
99
100 // outer loop is over the selected StuntDoubles:
101
102 for (sd = seleMan_.beginSelected(i); sd != NULL;
103 sd = seleMan_.nextSelected(i)) {
104 theAtoms_.push_back(sd);
105 }
106
107 /* variant below for single atoms, not StuntDoubles:
108 for (mol = info_->beginMolecule(mi); mol != NULL;
109 mol = info_->nextMolecule(mi)) {
110 for (atom = mol->beginAtom(ai); atom != NULL;
111 atom = mol->nextAtom(ai)) {
112 theAtoms_.push_back(atom);
113 }
114 }
115 */
116
117 // Generate convex hull for this frame.
118 thishull->computeHull(theAtoms_);
119 RealType volume = thishull->getVolume();
120 RealType surfaceArea = thishull->getArea();
121
122 osq.precision(7);
123 if (osq.is_open()) {
124 osq << time << "\t" << volume << "\t" << surfaceArea << std::endl;
125 }
126 }
127 osq.close();
128
129#else
130 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
131 "NanoVolume: qhull support was not compiled in!\n");
132 painCave.isFatal = 1;
133 simError();
134#endif
135}
bool isDynamic()
Tests if the result from evaluation of script is dynamic.
StuntDouble * nextSelected(int &i)
Finds the next selected StuntDouble in the selection.
StuntDouble * beginSelected(int &i)
Finds the first selected StuntDouble in the selection.
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
int getNGlobalAtoms()
Returns the total number of atoms in the system.
Definition SimInfo.hpp:129
SnapshotManager * getSnapshotManager()
Returns the snapshot manager.
Definition SimInfo.hpp:248
Snapshot * getCurrentSnapshot()
Returns the pointer of current snapshot.
"Don't move, or you're dead! Stand up! Captain, we've got them!"
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
std::string getPrefix(const std::string &str)