1 |
< |
#include "OtherVisitor.hpp" |
2 |
< |
#include "DirectionalAtom.hpp" |
3 |
< |
#include "RigidBody.hpp" |
4 |
< |
#include "Molecule.hpp" |
5 |
< |
#include "SimInfo.hpp" |
6 |
< |
//----------------------------------------------------------------------------// |
7 |
< |
void IgnoreVisitor::visit(Atom* atom){ |
8 |
< |
if(isIgnoreType(atom->getType())) |
1 |
> |
/* |
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> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
12 |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
23 |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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> |
#include "selection/SelectionManager.hpp" |
42 |
> |
#include "visitors/OtherVisitor.hpp" |
43 |
> |
#include "primitives/DirectionalAtom.hpp" |
44 |
> |
#include "primitives/RigidBody.hpp" |
45 |
> |
#include "primitives/Molecule.hpp" |
46 |
> |
#include "brains/SimInfo.hpp" |
47 |
> |
namespace oopse { |
48 |
> |
|
49 |
> |
void WrappingVisitor::visit(Atom *atom) { |
50 |
|
internalVisit(atom); |
51 |
< |
} |
51 |
> |
} |
52 |
|
|
53 |
< |
void IgnoreVisitor::visit(DirectionalAtom* datom){ |
13 |
< |
if(isIgnoreType(datom->getType())) |
53 |
> |
void WrappingVisitor::visit(DirectionalAtom *datom) { |
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|
internalVisit(datom); |
55 |
< |
} |
55 |
> |
} |
56 |
|
|
57 |
< |
void IgnoreVisitor::visit(RigidBody* rb){ |
18 |
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vector<Atom*> myAtoms; |
19 |
< |
vector<Atom*>::iterator atomIter; |
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< |
AtomInfo* atomInfo; |
21 |
< |
|
22 |
< |
if(isIgnoreType(rb->getType())){ |
23 |
< |
|
57 |
> |
void WrappingVisitor::visit(RigidBody *rb) { |
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|
internalVisit(rb); |
59 |
+ |
} |
60 |
|
|
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myAtoms = rb->getAtoms(); |
62 |
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|
63 |
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for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
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< |
internalVisit(*atomIter); |
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> |
void WrappingVisitor::internalVisit(StuntDouble *sd) { |
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> |
GenericData * data; |
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> |
AtomData * atomData; |
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> |
AtomInfo * atomInfo; |
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> |
std::vector<AtomInfo *>::iterator i; |
66 |
|
|
67 |
< |
} |
32 |
< |
|
33 |
< |
} |
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> |
data = sd->getPropertyByName("ATOMDATA"); |
68 |
|
|
69 |
< |
bool IgnoreVisitor::isIgnoreType(const string& name){ |
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return itList.find(name) != itList.end() ? true : false; |
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< |
} |
69 |
> |
if (data != NULL) { |
70 |
> |
atomData = dynamic_cast<AtomData *>(data); |
71 |
|
|
72 |
< |
void IgnoreVisitor::internalVisit(StuntDouble* sd){ |
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< |
GenericData* data; |
74 |
< |
data = sd->getProperty("IGNORE"); |
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> |
if (atomData == NULL) |
73 |
> |
return; |
74 |
> |
} else |
75 |
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return; |
76 |
|
|
77 |
< |
//if this stuntdoulbe is already marked as ignore just skip it |
44 |
< |
if (data == NULL){ |
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< |
data = new GenericData; |
46 |
< |
data->setID("IGNORE"); |
47 |
< |
sd->addProperty(data); |
48 |
< |
} |
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> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
78 |
|
|
79 |
< |
} |
79 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) { |
80 |
> |
currSnapshot->wrapVector(atomInfo->pos); |
81 |
> |
} |
82 |
> |
} |
83 |
|
|
84 |
< |
const string IgnoreVisitor::toString(){ |
85 |
< |
char buffer[65535]; |
86 |
< |
string result; |
55 |
< |
set<string>::iterator i; |
56 |
< |
|
57 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
58 |
< |
result += buffer; |
84 |
> |
const std::string WrappingVisitor::toString() { |
85 |
> |
char buffer[65535]; |
86 |
> |
std::string result; |
87 |
|
|
88 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
89 |
< |
result += buffer; |
88 |
> |
sprintf(buffer, |
89 |
> |
"------------------------------------------------------------------\n"); |
90 |
> |
result += buffer; |
91 |
|
|
92 |
< |
sprintf(buffer ,"Visitor Description: ignore stuntdoubles\n"); |
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result += buffer; |
92 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
93 |
> |
result += buffer; |
94 |
|
|
95 |
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//print the ignore type list |
96 |
< |
sprintf(buffer , "Ignore type list contains below types:\n"); |
97 |
< |
result += buffer; |
95 |
> |
sprintf(buffer, |
96 |
> |
"Visitor Description: wrapping atoms back to periodic box\n"); |
97 |
> |
result += buffer; |
98 |
|
|
99 |
< |
for(i = itList.begin(); i != itList.end(); ++i){ |
100 |
< |
sprintf(buffer ,"%s\t", i->c_str()); |
99 |
> |
sprintf(buffer, |
100 |
> |
"------------------------------------------------------------------\n"); |
101 |
|
result += buffer; |
102 |
|
|
103 |
+ |
return result; |
104 |
|
} |
75 |
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sprintf(buffer ,"\n"); |
76 |
– |
result += buffer; |
105 |
|
|
106 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
79 |
< |
result += buffer; |
106 |
> |
//----------------------------------------------------------------------------// |
107 |
|
|
108 |
< |
return result; |
109 |
< |
} |
108 |
> |
ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
109 |
> |
BaseVisitor() { |
110 |
> |
this->info = info; |
111 |
> |
visitorName = "ReplicateVisitor"; |
112 |
> |
this->replicateOpt = opt; |
113 |
|
|
114 |
< |
//----------------------------------------------------------------------------// |
114 |
> |
//generate the replicate directions |
115 |
> |
for( int i = 0; i <= replicateOpt[0]; i++ ) { |
116 |
> |
for( int j = 0; j <= replicateOpt[1]; j++ ) { |
117 |
> |
for( int k = 0; k <= replicateOpt[2]; k++ ) { |
118 |
> |
//skip original frame |
119 |
> |
if (i == 0 && j == 0 && k == 0) { |
120 |
> |
continue; |
121 |
> |
} else { |
122 |
> |
dir.push_back(Vector3i(i, j, k)); |
123 |
> |
} |
124 |
> |
} |
125 |
> |
} |
126 |
> |
} |
127 |
> |
|
128 |
> |
} |
129 |
|
|
130 |
< |
void WrappingVisitor::visit(Atom* atom){ |
131 |
< |
internalVisit(atom); |
132 |
< |
} |
89 |
< |
void WrappingVisitor::visit(DirectionalAtom* datom){ |
90 |
< |
internalVisit(datom); |
91 |
< |
} |
130 |
> |
void ReplicateVisitor::visit(Atom *atom) { |
131 |
> |
internalVisit(atom); |
132 |
> |
} |
133 |
|
|
134 |
< |
void WrappingVisitor::visit(RigidBody* rb){ |
135 |
< |
internalVisit(rb); |
136 |
< |
} |
134 |
> |
void ReplicateVisitor::visit(DirectionalAtom *datom) { |
135 |
> |
internalVisit(datom); |
136 |
> |
} |
137 |
|
|
138 |
< |
void WrappingVisitor::internalVisit(StuntDouble* sd){ |
139 |
< |
GenericData* data; |
99 |
< |
AtomData* atomData; |
100 |
< |
AtomInfo* atomInfo; |
101 |
< |
vector<AtomInfo*>::iterator i; |
102 |
< |
|
103 |
< |
data = sd->getProperty("ATOMDATA"); |
104 |
< |
if(data != NULL){ |
105 |
< |
atomData = dynamic_cast<AtomData*>(data); |
106 |
< |
if(atomData == NULL) |
107 |
< |
return; |
138 |
> |
void ReplicateVisitor::visit(RigidBody *rb) { |
139 |
> |
internalVisit(rb); |
140 |
|
} |
109 |
– |
else |
110 |
– |
return; |
141 |
|
|
142 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)) |
143 |
< |
info->wrapVector(atomInfo->pos); |
142 |
> |
void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
143 |
> |
GenericData * data; |
144 |
> |
AtomData * atomData; |
145 |
|
|
146 |
< |
|
147 |
< |
} |
146 |
> |
//if there is not atom data, just skip it |
147 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
148 |
|
|
149 |
< |
const string WrappingVisitor::toString(){ |
150 |
< |
char buffer[65535]; |
120 |
< |
string result; |
121 |
< |
|
122 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
123 |
< |
result += buffer; |
149 |
> |
if (data != NULL) { |
150 |
> |
atomData = dynamic_cast<AtomData *>(data); |
151 |
|
|
152 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
153 |
< |
result += buffer; |
152 |
> |
if (atomData == NULL) { |
153 |
> |
return; |
154 |
> |
} |
155 |
> |
} else { |
156 |
> |
return; |
157 |
> |
} |
158 |
|
|
159 |
< |
sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n"); |
160 |
< |
result += buffer; |
130 |
< |
|
131 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
132 |
< |
result += buffer; |
159 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
160 |
> |
Mat3x3d box = currSnapshot->getHmat(); |
161 |
|
|
162 |
< |
return result; |
135 |
< |
} |
162 |
> |
std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
163 |
|
|
164 |
< |
//----------------------------------------------------------------------------// |
164 |
> |
replicate(atomInfoList, atomData, box); |
165 |
> |
} |
166 |
|
|
167 |
< |
ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){ |
168 |
< |
this->info = info; |
169 |
< |
visitorName = "ReplicateVisitor"; |
170 |
< |
this->replicateOpt = opt; |
143 |
< |
//generate the replicate directions |
144 |
< |
for(int i = 0; i <= replicateOpt[0]; i ++) |
145 |
< |
for(int j = 0; j <= replicateOpt[1]; j ++) |
146 |
< |
for(int k = 0; k <= replicateOpt[2]; k ++) |
147 |
< |
//skip original frame |
148 |
< |
if(i == 0 && j ==0 && k ==0) |
149 |
< |
continue; |
150 |
< |
else |
151 |
< |
dir.push_back(IntVec3(i, j, k)); |
152 |
< |
|
153 |
< |
} |
154 |
< |
void ReplicateVisitor::visit(Atom* atom){ |
155 |
< |
internalVisit(atom); |
156 |
< |
} |
157 |
< |
void ReplicateVisitor::visit(DirectionalAtom* datom){ |
158 |
< |
internalVisit(datom); |
159 |
< |
} |
167 |
> |
void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
168 |
> |
AtomInfo* newAtomInfo; |
169 |
> |
std::vector<Vector3i>::iterator dirIter; |
170 |
> |
std::vector<AtomInfo *>::iterator i; |
171 |
|
|
172 |
< |
void ReplicateVisitor::visit(RigidBody* rb){ |
173 |
< |
internalVisit(rb); |
174 |
< |
} |
172 |
> |
for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
173 |
> |
for( i = infoList.begin(); i != infoList.end(); i++ ) { |
174 |
> |
newAtomInfo = new AtomInfo(); |
175 |
> |
*newAtomInfo = *(*i); |
176 |
|
|
177 |
< |
void ReplicateVisitor::internalVisit(StuntDouble* sd){ |
178 |
< |
GenericData* data; |
179 |
< |
AtomData* atomData; |
180 |
< |
AtomInfo* atomInfo; |
181 |
< |
double box[3][3]; |
182 |
< |
vector<AtomInfo*> atomInfoList; |
171 |
< |
IntVec3 dir; |
172 |
< |
|
173 |
< |
//if there is not atom data, just skip it |
174 |
< |
data = sd->getProperty("ATOMDATA"); |
175 |
< |
if(data != NULL){ |
176 |
< |
atomData = dynamic_cast<AtomData*>(data); |
177 |
< |
if(atomData == NULL) |
178 |
< |
return; |
177 |
> |
for( int j = 0; j < 3; j++ ) |
178 |
> |
newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
179 |
> |
|
180 |
> |
data->addAtomInfo(newAtomInfo); |
181 |
> |
} |
182 |
> |
} // end for(dirIter) |
183 |
|
} |
180 |
– |
else |
181 |
– |
return; |
184 |
|
|
185 |
< |
|
186 |
< |
info->getBoxM(box); |
185 |
> |
const std::string ReplicateVisitor::toString() { |
186 |
> |
char buffer[65535]; |
187 |
> |
std::string result; |
188 |
> |
std::set<std::string>::iterator i; |
189 |
|
|
190 |
< |
atomInfoList = atomData->getData(); |
191 |
< |
|
192 |
< |
replicate(atomInfoList, atomData, box); |
190 |
> |
sprintf(buffer, |
191 |
> |
"------------------------------------------------------------------\n"); |
192 |
> |
result += buffer; |
193 |
|
|
194 |
< |
} |
194 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
195 |
> |
result += buffer; |
196 |
|
|
197 |
< |
void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){ |
198 |
< |
AtomInfo * newAtomInfo; |
199 |
< |
vector<IntVec3>::iterator dirIter; |
195 |
< |
vector<AtomInfo*>::iterator i; |
196 |
< |
|
197 |
< |
for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){ |
198 |
< |
for(i = infoList.begin(); i != infoList.end(); i++){ |
199 |
< |
newAtomInfo = new AtomInfo; |
200 |
< |
*newAtomInfo = *(*i); |
197 |
> |
sprintf(buffer, |
198 |
> |
"Visitor Description: replicate the atoms in different direction\n"); |
199 |
> |
result += buffer; |
200 |
|
|
201 |
< |
for(int j = 0; j < 3; j++) |
202 |
< |
newAtomInfo->pos[j] += (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2]; |
201 |
> |
//print the replicate direction |
202 |
> |
sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]); |
203 |
> |
result += buffer; |
204 |
|
|
205 |
< |
data->addAtomInfo(newAtomInfo); |
206 |
< |
} |
207 |
< |
}// end for(dirIter) |
208 |
< |
} |
205 |
> |
sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]); |
206 |
> |
result += buffer; |
207 |
|
|
208 |
< |
const string ReplicateVisitor::toString(){ |
209 |
< |
char buffer[65535]; |
212 |
< |
string result; |
213 |
< |
set<string>::iterator i; |
214 |
< |
|
215 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
216 |
< |
result += buffer; |
208 |
> |
sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]); |
209 |
> |
result += buffer; |
210 |
|
|
211 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
212 |
< |
result += buffer; |
211 |
> |
sprintf(buffer, |
212 |
> |
"------------------------------------------------------------------\n"); |
213 |
> |
result += buffer; |
214 |
|
|
215 |
< |
sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n"); |
216 |
< |
result += buffer; |
223 |
< |
|
224 |
< |
//print the replicate direction |
225 |
< |
sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]); |
226 |
< |
result += buffer; |
215 |
> |
return result; |
216 |
> |
} |
217 |
|
|
218 |
< |
sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]); |
229 |
< |
result += buffer; |
218 |
> |
//----------------------------------------------------------------------------// |
219 |
|
|
220 |
< |
sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]); |
221 |
< |
result += buffer; |
220 |
> |
XYZVisitor::XYZVisitor(SimInfo *info) : |
221 |
> |
BaseVisitor(), seleMan(info), evaluator(info){ |
222 |
> |
this->info = info; |
223 |
> |
visitorName = "XYZVisitor"; |
224 |
|
|
225 |
+ |
evaluator.loadScriptString("select all"); |
226 |
|
|
227 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
228 |
< |
result += buffer; |
227 |
> |
if (!evaluator.isDynamic()) { |
228 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
229 |
> |
} |
230 |
|
|
231 |
< |
return result; |
239 |
< |
} |
231 |
> |
} |
232 |
|
|
233 |
< |
//----------------------------------------------------------------------------// |
233 |
> |
XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
234 |
> |
BaseVisitor(), seleMan(info), evaluator(info) { |
235 |
> |
this->info = info; |
236 |
> |
visitorName = "XYZVisitor"; |
237 |
|
|
238 |
< |
XYZVisitor::XYZVisitor(SimInfo* info, bool printDipole) : BaseVisitor(){ |
244 |
< |
this->info = info; |
245 |
< |
visitorName = "XYZVisitor"; |
246 |
< |
this->printDipole = printDipole; |
247 |
< |
} |
238 |
> |
evaluator.loadScriptString(script); |
239 |
|
|
240 |
< |
void XYZVisitor::visit(Atom* atom){ |
241 |
< |
if(!isIgnore(atom)) |
242 |
< |
internalVisit(atom); |
243 |
< |
} |
244 |
< |
|
245 |
< |
void XYZVisitor::visit(DirectionalAtom* datom){ |
246 |
< |
if(!isIgnore(datom)) |
247 |
< |
internalVisit(datom); |
248 |
< |
} |
258 |
< |
|
259 |
< |
void XYZVisitor::visit(RigidBody* rb){ |
260 |
< |
if(!isIgnore(rb)) |
261 |
< |
internalVisit(rb); |
262 |
< |
|
263 |
< |
} |
264 |
< |
|
265 |
< |
void XYZVisitor::internalVisit(StuntDouble* sd){ |
266 |
< |
GenericData* data; |
267 |
< |
AtomData* atomData; |
268 |
< |
AtomInfo* atomInfo; |
269 |
< |
vector<AtomInfo*>::iterator i; |
270 |
< |
char buffer[1024]; |
271 |
< |
|
272 |
< |
//if there is not atom data, just skip it |
273 |
< |
data = sd->getProperty("ATOMDATA"); |
274 |
< |
if(data != NULL){ |
275 |
< |
atomData = dynamic_cast<AtomData*>(data); |
276 |
< |
if(atomData == NULL) |
277 |
< |
return; |
240 |
> |
if (!evaluator.isDynamic()) { |
241 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
242 |
> |
} |
243 |
> |
|
244 |
> |
} |
245 |
> |
|
246 |
> |
void XYZVisitor::visit(Atom *atom) { |
247 |
> |
if (isSelected(atom)) |
248 |
> |
internalVisit(atom); |
249 |
|
} |
279 |
– |
else |
280 |
– |
return; |
250 |
|
|
251 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
252 |
< |
|
253 |
< |
if(printDipole) |
254 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
286 |
< |
atomInfo->AtomType.c_str(), |
287 |
< |
atomInfo->pos[0], |
288 |
< |
atomInfo->pos[1], |
289 |
< |
atomInfo->pos[2], |
290 |
< |
atomInfo->dipole[0], |
291 |
< |
atomInfo->dipole[1], |
292 |
< |
atomInfo->dipole[2]); |
293 |
< |
else |
294 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
295 |
< |
atomInfo->AtomType.c_str(), |
296 |
< |
atomInfo->pos[0], |
297 |
< |
atomInfo->pos[1], |
298 |
< |
atomInfo->pos[2]); |
251 |
> |
void XYZVisitor::visit(DirectionalAtom *datom) { |
252 |
> |
if (isSelected(datom)) |
253 |
> |
internalVisit(datom); |
254 |
> |
} |
255 |
|
|
256 |
< |
frame.push_back(buffer); |
257 |
< |
|
256 |
> |
void XYZVisitor::visit(RigidBody *rb) { |
257 |
> |
if (isSelected(rb)) |
258 |
> |
internalVisit(rb); |
259 |
|
} |
260 |
|
|
261 |
< |
} |
261 |
> |
void XYZVisitor::update() { |
262 |
> |
//if dynamic, we need to re-evaluate the selection |
263 |
> |
if (evaluator.isDynamic()) { |
264 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
265 |
> |
} |
266 |
> |
} |
267 |
|
|
268 |
< |
bool XYZVisitor::isIgnore(StuntDouble* sd){ |
269 |
< |
GenericData* data; |
270 |
< |
|
271 |
< |
data = sd->getProperty("IGNORE"); |
272 |
< |
return data ==NULL ? false : true; |
273 |
< |
} |
268 |
> |
void XYZVisitor::internalVisit(StuntDouble *sd) { |
269 |
> |
GenericData * data; |
270 |
> |
AtomData * atomData; |
271 |
> |
AtomInfo * atomInfo; |
272 |
> |
std::vector<AtomInfo *>::iterator i; |
273 |
> |
char buffer[1024]; |
274 |
|
|
275 |
< |
void XYZVisitor::writeFrame(ostream& outStream){ |
276 |
< |
vector<string>::iterator i; |
315 |
< |
double box[3][3]; |
316 |
< |
char buffer[1024]; |
275 |
> |
//if there is not atom data, just skip it |
276 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
277 |
|
|
278 |
< |
if(frame.size() == 0) |
279 |
< |
cerr << "Current Frame does not contain any atoms" << endl; |
278 |
> |
if (data != NULL) { |
279 |
> |
atomData = dynamic_cast<AtomData *>(data); |
280 |
|
|
281 |
< |
//total number of atoms |
282 |
< |
outStream << frame.size() << endl; |
281 |
> |
if (atomData == NULL) |
282 |
> |
return; |
283 |
> |
} else |
284 |
> |
return; |
285 |
|
|
286 |
< |
//write comment line |
287 |
< |
info->getBoxM(box); |
288 |
< |
sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
289 |
< |
info->getTime(), |
290 |
< |
box[0][0], box[0][1], box[0][2], |
291 |
< |
box[1][0], box[1][1], box[1][2], |
292 |
< |
box[2][0], box[2][1], box[2][2]); |
286 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
287 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
288 |
> |
sprintf(buffer, |
289 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
290 |
> |
atomInfo->atomTypeName.c_str(), |
291 |
> |
atomInfo->pos[0], |
292 |
> |
atomInfo->pos[1], |
293 |
> |
atomInfo->pos[2], |
294 |
> |
atomInfo->dipole[0], |
295 |
> |
atomInfo->dipole[1], |
296 |
> |
atomInfo->dipole[2]); |
297 |
> |
frame.push_back(buffer); |
298 |
> |
} |
299 |
> |
} |
300 |
|
|
301 |
< |
outStream << buffer << endl; |
301 |
> |
bool XYZVisitor::isSelected(StuntDouble *sd) { |
302 |
> |
return seleMan.isSelected(sd); |
303 |
> |
} |
304 |
|
|
305 |
< |
for(i = frame.begin(); i != frame.end(); ++i) |
306 |
< |
outStream << *i << endl; |
307 |
< |
} |
305 |
> |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
306 |
> |
std::vector<std::string>::iterator i; |
307 |
> |
char buffer[1024]; |
308 |
|
|
309 |
< |
const string XYZVisitor::toString(){ |
310 |
< |
char buffer[65535]; |
340 |
< |
string result; |
341 |
< |
|
342 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
343 |
< |
result += buffer; |
309 |
> |
if (frame.size() == 0) |
310 |
> |
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
311 |
|
|
312 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
313 |
< |
result += buffer; |
312 |
> |
//total number of atoms |
313 |
> |
outStream << frame.size() << std::endl; |
314 |
|
|
315 |
< |
sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n"); |
316 |
< |
result += buffer; |
317 |
< |
|
318 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
319 |
< |
result += buffer; |
315 |
> |
//write comment line |
316 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
317 |
> |
Mat3x3d box = currSnapshot->getHmat(); |
318 |
> |
|
319 |
> |
sprintf(buffer, |
320 |
> |
"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
321 |
> |
currSnapshot->getTime(), |
322 |
> |
box(0, 0), box(0, 1), box(0, 2), |
323 |
> |
box(1, 0), box(1, 1), box(1, 2), |
324 |
> |
box(2, 0), box(2, 1), box(2, 2)); |
325 |
|
|
326 |
< |
return result; |
355 |
< |
} |
326 |
> |
outStream << buffer << std::endl; |
327 |
|
|
328 |
< |
//----------------------------------------------------------------------------// |
328 |
> |
for( i = frame.begin(); i != frame.end(); ++i ) |
329 |
> |
outStream << *i << std::endl; |
330 |
> |
} |
331 |
|
|
332 |
< |
void PrepareVisitor::internalVisit(Atom * atom){ |
333 |
< |
GenericData* data; |
334 |
< |
AtomData* atomData; |
332 |
> |
const std::string XYZVisitor::toString() { |
333 |
> |
char buffer[65535]; |
334 |
> |
std::string result; |
335 |
|
|
336 |
< |
//if visited property is existed, remove it |
337 |
< |
data = atom->getProperty("VISITED"); |
338 |
< |
if(data != NULL){ |
366 |
< |
atom->removeProperty("VISITED"); |
367 |
< |
} |
336 |
> |
sprintf(buffer, |
337 |
> |
"------------------------------------------------------------------\n"); |
338 |
> |
result += buffer; |
339 |
|
|
340 |
< |
//remove atomdata |
341 |
< |
data = atom->getProperty("ATOMDATA"); |
371 |
< |
if(data != NULL){ |
372 |
< |
atomData = dynamic_cast<AtomData*>(data); |
373 |
< |
if(atomData != NULL) |
374 |
< |
atom->removeProperty("ATOMDATA"); |
375 |
< |
} |
376 |
< |
|
377 |
< |
} |
340 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
341 |
> |
result += buffer; |
342 |
|
|
343 |
< |
void PrepareVisitor::internalVisit(RigidBody * rb){ |
344 |
< |
GenericData* data; |
345 |
< |
AtomData* atomData; |
346 |
< |
vector<Atom*> myAtoms; |
347 |
< |
vector<Atom*>::iterator atomIter; |
348 |
< |
|
349 |
< |
//if visited property is existed, remove it |
350 |
< |
data = rb->getProperty("VISITED"); |
351 |
< |
if(data != NULL){ |
388 |
< |
rb->removeProperty("VISITED"); |
343 |
> |
sprintf(buffer, |
344 |
> |
"Visitor Description: assemble the atom data and output xyz file\n"); |
345 |
> |
result += buffer; |
346 |
> |
|
347 |
> |
sprintf(buffer, |
348 |
> |
"------------------------------------------------------------------\n"); |
349 |
> |
result += buffer; |
350 |
> |
|
351 |
> |
return result; |
352 |
|
} |
353 |
|
|
354 |
< |
//remove atomdata |
355 |
< |
data = rb->getProperty("ATOMDATA"); |
356 |
< |
if(data != NULL){ |
357 |
< |
atomData = dynamic_cast<AtomData*>(data); |
358 |
< |
if(atomData != NULL) |
359 |
< |
rb->removeProperty("ATOMDATA"); |
354 |
> |
//----------------------------------------------------------------------------// |
355 |
> |
|
356 |
> |
void PrepareVisitor::internalVisit(Atom *atom) { |
357 |
> |
GenericData *data; |
358 |
> |
AtomData * atomData; |
359 |
> |
|
360 |
> |
//if visited property is existed, remove it |
361 |
> |
data = atom->getPropertyByName("VISITED"); |
362 |
> |
|
363 |
> |
if (data != NULL) { |
364 |
> |
atom->removeProperty("VISITED"); |
365 |
> |
} |
366 |
> |
|
367 |
> |
//remove atomdata |
368 |
> |
data = atom->getPropertyByName("ATOMDATA"); |
369 |
> |
|
370 |
> |
if (data != NULL) { |
371 |
> |
atomData = dynamic_cast<AtomData *>(data); |
372 |
> |
|
373 |
> |
if (atomData != NULL) |
374 |
> |
atom->removeProperty("ATOMDATA"); |
375 |
> |
} |
376 |
|
} |
377 |
|
|
378 |
< |
myAtoms = rb->getAtoms(); |
379 |
< |
|
380 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
381 |
< |
internalVisit (*atomIter); |
382 |
< |
} |
378 |
> |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
379 |
> |
GenericData* data; |
380 |
> |
AtomData* atomData; |
381 |
> |
std::vector<Atom *> myAtoms; |
382 |
> |
std::vector<Atom *>::iterator atomIter; |
383 |
|
|
384 |
< |
const string PrepareVisitor::toString(){ |
385 |
< |
char buffer[65535]; |
407 |
< |
string result; |
408 |
< |
|
409 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
410 |
< |
result += buffer; |
384 |
> |
//if visited property is existed, remove it |
385 |
> |
data = rb->getPropertyByName("VISITED"); |
386 |
|
|
387 |
< |
sprintf(buffer ,"Visitor name: %s", visitorName.c_str()); |
388 |
< |
result += buffer; |
387 |
> |
if (data != NULL) { |
388 |
> |
rb->removeProperty("VISITED"); |
389 |
> |
} |
390 |
|
|
391 |
< |
sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n"); |
392 |
< |
result += buffer; |
391 |
> |
//remove atomdata |
392 |
> |
data = rb->getPropertyByName("ATOMDATA"); |
393 |
|
|
394 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
395 |
< |
result += buffer; |
394 |
> |
if (data != NULL) { |
395 |
> |
atomData = dynamic_cast<AtomData *>(data); |
396 |
|
|
397 |
< |
return result; |
398 |
< |
} |
397 |
> |
if (atomData != NULL) |
398 |
> |
rb->removeProperty("ATOMDATA"); |
399 |
> |
} |
400 |
|
|
401 |
< |
//----------------------------------------------------------------------------// |
401 |
> |
myAtoms = rb->getAtoms(); |
402 |
|
|
403 |
< |
WaterTypeVisitor:: WaterTypeVisitor(){ |
404 |
< |
visitorName = "WaterTypeVisitor"; |
405 |
< |
waterTypeList.insert("TIP3P_RB_0"); |
429 |
< |
waterTypeList.insert("TIP4P_RB_0"); |
430 |
< |
waterTypeList.insert("TIP5P_RB_0"); |
431 |
< |
waterTypeList.insert("SPCE_RB_0"); |
432 |
< |
} |
403 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
404 |
> |
internalVisit(*atomIter); |
405 |
> |
} |
406 |
|
|
407 |
+ |
const std::string PrepareVisitor::toString() { |
408 |
+ |
char buffer[65535]; |
409 |
+ |
std::string result; |
410 |
+ |
|
411 |
+ |
sprintf(buffer, |
412 |
+ |
"------------------------------------------------------------------\n"); |
413 |
+ |
result += buffer; |
414 |
+ |
|
415 |
+ |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
416 |
+ |
result += buffer; |
417 |
+ |
|
418 |
+ |
sprintf(buffer, |
419 |
+ |
"Visitor Description: prepare for operation of other vistors\n"); |
420 |
+ |
result += buffer; |
421 |
+ |
|
422 |
+ |
sprintf(buffer, |
423 |
+ |
"------------------------------------------------------------------\n"); |
424 |
+ |
result += buffer; |
425 |
+ |
|
426 |
+ |
return result; |
427 |
+ |
} |
428 |
|
|
429 |
< |
void WaterTypeVisitor:: visit(RigidBody* rb){ |
436 |
< |
string rbName; |
437 |
< |
vector<Atom*> myAtoms; |
438 |
< |
vector<Atom*>::iterator atomIter; |
439 |
< |
GenericData* data; |
440 |
< |
AtomData* atomData; |
441 |
< |
AtomInfo* atomInfo; |
442 |
< |
vector<AtomInfo*>::iterator i; |
443 |
< |
|
444 |
< |
rbName = rb->getType(); |
429 |
> |
//----------------------------------------------------------------------------// |
430 |
|
|
431 |
< |
if(waterTypeList.find(rbName) != waterTypeList.end()){ |
431 |
> |
WaterTypeVisitor::WaterTypeVisitor() { |
432 |
> |
visitorName = "WaterTypeVisitor"; |
433 |
> |
waterTypeList.insert("TIP3P_RB_0"); |
434 |
> |
waterTypeList.insert("TIP4P_RB_0"); |
435 |
> |
waterTypeList.insert("TIP5P_RB_0"); |
436 |
> |
waterTypeList.insert("SPCE_RB_0"); |
437 |
> |
} |
438 |
|
|
439 |
< |
myAtoms = rb->getAtoms(); |
440 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){ |
439 |
> |
void WaterTypeVisitor::visit(RigidBody *rb) { |
440 |
> |
std::string rbName; |
441 |
> |
std::vector<Atom *> myAtoms; |
442 |
> |
std::vector<Atom *>::iterator atomIter; |
443 |
> |
GenericData* data; |
444 |
> |
AtomData* atomData; |
445 |
> |
AtomInfo* atomInfo; |
446 |
> |
std::vector<AtomInfo *>::iterator i; |
447 |
|
|
448 |
< |
data = (*atomIter)->getProperty("ATOMDATA"); |
452 |
< |
if(data != NULL){ |
453 |
< |
atomData = dynamic_cast<AtomData*>(data); |
454 |
< |
if(atomData == NULL) |
455 |
< |
continue; |
456 |
< |
} |
457 |
< |
else |
458 |
< |
continue; |
459 |
< |
|
460 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
461 |
< |
replaceType(atomInfo->AtomType); |
462 |
< |
}//end for(atomInfo) |
448 |
> |
rbName = rb->getType(); |
449 |
|
|
450 |
< |
}//end for(atomIter) |
451 |
< |
|
466 |
< |
}//end if (waterTypeList.find(rbName) != waterTypeList.end()) |
467 |
< |
|
468 |
< |
} |
450 |
> |
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
451 |
> |
myAtoms = rb->getAtoms(); |
452 |
|
|
453 |
< |
void WaterTypeVisitor:: replaceType(string& atomType){ |
454 |
< |
atomType = atomType.substr(0, atomType.find('_')); |
455 |
< |
} |
453 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
454 |
> |
++atomIter ) { |
455 |
> |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
456 |
|
|
457 |
< |
const string WaterTypeVisitor:: toString(){ |
458 |
< |
char buffer[65535]; |
476 |
< |
string result; |
477 |
< |
|
478 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
479 |
< |
result += buffer; |
457 |
> |
if (data != NULL) { |
458 |
> |
atomData = dynamic_cast<AtomData *>(data); |
459 |
|
|
460 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
461 |
< |
result += buffer; |
460 |
> |
if (atomData == NULL) |
461 |
> |
continue; |
462 |
> |
} else |
463 |
> |
continue; |
464 |
|
|
465 |
< |
sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n"); |
466 |
< |
result += buffer; |
465 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
466 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
467 |
> |
atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName); |
468 |
> |
} //end for(atomInfo) |
469 |
> |
} //end for(atomIter) |
470 |
> |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
471 |
> |
} |
472 |
|
|
473 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
474 |
< |
result += buffer; |
473 |
> |
std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) { |
474 |
> |
return atomTypeName.substr(0, atomTypeName.find('_')); |
475 |
> |
} |
476 |
|
|
477 |
< |
return result; |
478 |
< |
} |
477 |
> |
const std::string WaterTypeVisitor::toString() { |
478 |
> |
char buffer[65535]; |
479 |
> |
std::string result; |
480 |
|
|
481 |
+ |
sprintf(buffer, |
482 |
+ |
"------------------------------------------------------------------\n"); |
483 |
+ |
result += buffer; |
484 |
+ |
|
485 |
+ |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
486 |
+ |
result += buffer; |
487 |
+ |
|
488 |
+ |
sprintf(buffer, |
489 |
+ |
"Visitor Description: Replace the atom type in water model\n"); |
490 |
+ |
result += buffer; |
491 |
+ |
|
492 |
+ |
sprintf(buffer, |
493 |
+ |
"------------------------------------------------------------------\n"); |
494 |
+ |
result += buffer; |
495 |
+ |
|
496 |
+ |
return result; |
497 |
+ |
} |
498 |
+ |
|
499 |
+ |
} //namespace oopse |