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. |
3 |
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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 |
6 |
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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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> |
* 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 |
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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)) |
16 |
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* |
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* 2. Redistributions of source code must retain the above copyright |
18 |
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* notice, this list of conditions and the following disclaimer. |
19 |
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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 |
22 |
> |
* 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" |
41 |
> |
#include "visitors/OtherVisitor.hpp" |
42 |
> |
#include "primitives/DirectionalAtom.hpp" |
43 |
> |
#include "primitives/RigidBody.hpp" |
44 |
> |
#include "primitives/Molecule.hpp" |
45 |
> |
#include "brains/SimInfo.hpp" |
46 |
> |
namespace oopse { |
47 |
> |
|
48 |
> |
void WrappingVisitor::visit(Atom *atom) { |
49 |
|
internalVisit(atom); |
50 |
< |
} |
50 |
> |
} |
51 |
|
|
52 |
< |
void IgnoreVisitor::visit(DirectionalAtom* datom){ |
13 |
< |
if(isIgnoreType(datom->getType())) |
52 |
> |
void WrappingVisitor::visit(DirectionalAtom *datom) { |
53 |
|
internalVisit(datom); |
54 |
< |
} |
54 |
> |
} |
55 |
|
|
56 |
< |
void IgnoreVisitor::visit(RigidBody* rb){ |
18 |
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vector<Atom*> myAtoms; |
19 |
< |
vector<Atom*>::iterator atomIter; |
20 |
< |
AtomInfo* atomInfo; |
21 |
< |
|
22 |
< |
if(isIgnoreType(rb->getType())){ |
23 |
< |
|
56 |
> |
void WrappingVisitor::visit(RigidBody *rb) { |
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|
internalVisit(rb); |
58 |
+ |
} |
59 |
|
|
60 |
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myAtoms = rb->getAtoms(); |
61 |
< |
|
62 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
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< |
internalVisit(*atomIter); |
60 |
> |
void WrappingVisitor::internalVisit(StuntDouble *sd) { |
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> |
GenericData * data; |
62 |
> |
AtomData * atomData; |
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> |
AtomInfo * atomInfo; |
64 |
> |
std::vector<AtomInfo *>::iterator i; |
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|
|
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< |
} |
32 |
< |
|
33 |
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} |
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> |
data = sd->getPropertyByName("ATOMDATA"); |
67 |
|
|
68 |
< |
bool IgnoreVisitor::isIgnoreType(const string& name){ |
69 |
< |
return itList.find(name) != itList.end() ? true : false; |
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< |
} |
68 |
> |
if (data != NULL) { |
69 |
> |
atomData = dynamic_cast<AtomData *>(data); |
70 |
|
|
71 |
< |
void IgnoreVisitor::internalVisit(StuntDouble* sd){ |
72 |
< |
GenericData* data; |
73 |
< |
data = sd->getProperty("IGNORE"); |
71 |
> |
if (atomData == NULL) |
72 |
> |
return; |
73 |
> |
} else |
74 |
> |
return; |
75 |
|
|
76 |
< |
//if this stuntdoulbe is already marked as ignore just skip it |
44 |
< |
if (data == NULL){ |
45 |
< |
data = new GenericData; |
46 |
< |
data->setID("IGNORE"); |
47 |
< |
sd->addProperty(data); |
48 |
< |
} |
76 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
77 |
|
|
78 |
< |
} |
78 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) { |
79 |
> |
Vector3d newPos = atomInfo->pos - origin_; |
80 |
> |
currSnapshot->wrapVector(newPos); |
81 |
> |
atomInfo->pos = newPos; |
82 |
> |
} |
83 |
> |
} |
84 |
|
|
85 |
< |
const string IgnoreVisitor::toString(){ |
86 |
< |
char buffer[65535]; |
87 |
< |
string result; |
88 |
< |
set<string>::iterator i; |
85 |
> |
void WrappingVisitor::update() { |
86 |
> |
if (useCom_){ |
87 |
> |
origin_ = info->getCom(); |
88 |
> |
} |
89 |
> |
} |
90 |
|
|
91 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
92 |
< |
result += buffer; |
91 |
> |
const std::string WrappingVisitor::toString() { |
92 |
> |
char buffer[65535]; |
93 |
> |
std::string result; |
94 |
|
|
95 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
96 |
< |
result += buffer; |
95 |
> |
sprintf(buffer, |
96 |
> |
"------------------------------------------------------------------\n"); |
97 |
> |
result += buffer; |
98 |
|
|
99 |
< |
sprintf(buffer ,"Visitor Description: ignore stuntdoubles\n"); |
100 |
< |
result += buffer; |
99 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
100 |
> |
result += buffer; |
101 |
|
|
102 |
< |
//print the ignore type list |
103 |
< |
sprintf(buffer , "Ignore type list contains below types:\n"); |
104 |
< |
result += buffer; |
102 |
> |
sprintf(buffer, |
103 |
> |
"Visitor Description: wrapping atoms back to periodic box\n"); |
104 |
> |
result += buffer; |
105 |
|
|
106 |
< |
for(i = itList.begin(); i != itList.end(); ++i){ |
107 |
< |
sprintf(buffer ,"%s\t", i->c_str()); |
106 |
> |
sprintf(buffer, |
107 |
> |
"------------------------------------------------------------------\n"); |
108 |
|
result += buffer; |
109 |
|
|
110 |
+ |
return result; |
111 |
|
} |
75 |
– |
sprintf(buffer ,"\n"); |
76 |
– |
result += buffer; |
112 |
|
|
113 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
79 |
< |
result += buffer; |
113 |
> |
//----------------------------------------------------------------------------// |
114 |
|
|
115 |
< |
return result; |
116 |
< |
} |
115 |
> |
ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
116 |
> |
BaseVisitor() { |
117 |
> |
this->info = info; |
118 |
> |
visitorName = "ReplicateVisitor"; |
119 |
> |
this->replicateOpt = opt; |
120 |
|
|
121 |
< |
//----------------------------------------------------------------------------// |
121 |
> |
//generate the replicate directions |
122 |
> |
for( int i = 0; i <= replicateOpt[0]; i++ ) { |
123 |
> |
for( int j = 0; j <= replicateOpt[1]; j++ ) { |
124 |
> |
for( int k = 0; k <= replicateOpt[2]; k++ ) { |
125 |
> |
//skip original frame |
126 |
> |
if (i == 0 && j == 0 && k == 0) { |
127 |
> |
continue; |
128 |
> |
} else { |
129 |
> |
dir.push_back(Vector3i(i, j, k)); |
130 |
> |
} |
131 |
> |
} |
132 |
> |
} |
133 |
> |
} |
134 |
> |
|
135 |
> |
} |
136 |
|
|
137 |
< |
void WrappingVisitor::visit(Atom* atom){ |
138 |
< |
internalVisit(atom); |
139 |
< |
} |
89 |
< |
void WrappingVisitor::visit(DirectionalAtom* datom){ |
90 |
< |
internalVisit(datom); |
91 |
< |
} |
137 |
> |
void ReplicateVisitor::visit(Atom *atom) { |
138 |
> |
internalVisit(atom); |
139 |
> |
} |
140 |
|
|
141 |
< |
void WrappingVisitor::visit(RigidBody* rb){ |
142 |
< |
internalVisit(rb); |
143 |
< |
} |
141 |
> |
void ReplicateVisitor::visit(DirectionalAtom *datom) { |
142 |
> |
internalVisit(datom); |
143 |
> |
} |
144 |
|
|
145 |
< |
void WrappingVisitor::internalVisit(StuntDouble* sd){ |
146 |
< |
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; |
145 |
> |
void ReplicateVisitor::visit(RigidBody *rb) { |
146 |
> |
internalVisit(rb); |
147 |
|
} |
109 |
– |
else |
110 |
– |
return; |
148 |
|
|
149 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)) |
150 |
< |
info->wrapVector(atomInfo->pos); |
149 |
> |
void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
150 |
> |
GenericData * data; |
151 |
> |
AtomData * atomData; |
152 |
|
|
153 |
< |
|
154 |
< |
} |
153 |
> |
//if there is not atom data, just skip it |
154 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
155 |
|
|
156 |
< |
const string WrappingVisitor::toString(){ |
157 |
< |
char buffer[65535]; |
120 |
< |
string result; |
121 |
< |
|
122 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
123 |
< |
result += buffer; |
156 |
> |
if (data != NULL) { |
157 |
> |
atomData = dynamic_cast<AtomData *>(data); |
158 |
|
|
159 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
160 |
< |
result += buffer; |
159 |
> |
if (atomData == NULL) { |
160 |
> |
return; |
161 |
> |
} |
162 |
> |
} else { |
163 |
> |
return; |
164 |
> |
} |
165 |
|
|
166 |
< |
sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n"); |
167 |
< |
result += buffer; |
130 |
< |
|
131 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
132 |
< |
result += buffer; |
166 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
167 |
> |
Mat3x3d box = currSnapshot->getHmat(); |
168 |
|
|
169 |
< |
return result; |
135 |
< |
} |
169 |
> |
std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
170 |
|
|
171 |
< |
//----------------------------------------------------------------------------// |
171 |
> |
replicate(atomInfoList, atomData, box); |
172 |
> |
} |
173 |
|
|
174 |
< |
ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){ |
175 |
< |
this->info = info; |
176 |
< |
visitorName = "ReplicateVisitor"; |
177 |
< |
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 |
< |
} |
174 |
> |
void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
175 |
> |
AtomInfo* newAtomInfo; |
176 |
> |
std::vector<Vector3i>::iterator dirIter; |
177 |
> |
std::vector<AtomInfo *>::iterator i; |
178 |
|
|
179 |
< |
void ReplicateVisitor::visit(RigidBody* rb){ |
180 |
< |
internalVisit(rb); |
181 |
< |
} |
179 |
> |
for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
180 |
> |
for( i = infoList.begin(); i != infoList.end(); i++ ) { |
181 |
> |
newAtomInfo = new AtomInfo(); |
182 |
> |
*newAtomInfo = *(*i); |
183 |
|
|
184 |
< |
void ReplicateVisitor::internalVisit(StuntDouble* sd){ |
185 |
< |
GenericData* data; |
186 |
< |
AtomData* atomData; |
187 |
< |
AtomInfo* atomInfo; |
188 |
< |
double box[3][3]; |
189 |
< |
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; |
184 |
> |
for( int j = 0; j < 3; j++ ) |
185 |
> |
newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
186 |
> |
|
187 |
> |
data->addAtomInfo(newAtomInfo); |
188 |
> |
} |
189 |
> |
} // end for(dirIter) |
190 |
|
} |
180 |
– |
else |
181 |
– |
return; |
191 |
|
|
192 |
< |
|
193 |
< |
info->getBoxM(box); |
192 |
> |
const std::string ReplicateVisitor::toString() { |
193 |
> |
char buffer[65535]; |
194 |
> |
std::string result; |
195 |
> |
std::set<std::string>::iterator i; |
196 |
|
|
197 |
< |
atomInfoList = atomData->getData(); |
198 |
< |
|
199 |
< |
replicate(atomInfoList, atomData, box); |
197 |
> |
sprintf(buffer, |
198 |
> |
"------------------------------------------------------------------\n"); |
199 |
> |
result += buffer; |
200 |
|
|
201 |
< |
} |
201 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
202 |
> |
result += buffer; |
203 |
|
|
204 |
< |
void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){ |
205 |
< |
AtomInfo * newAtomInfo; |
206 |
< |
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); |
204 |
> |
sprintf(buffer, |
205 |
> |
"Visitor Description: replicate the atoms in different direction\n"); |
206 |
> |
result += buffer; |
207 |
|
|
208 |
< |
for(int j = 0; j < 3; j++) |
209 |
< |
newAtomInfo->pos[j] += (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2]; |
208 |
> |
//print the replicate direction |
209 |
> |
sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]); |
210 |
> |
result += buffer; |
211 |
|
|
212 |
< |
data->addAtomInfo(newAtomInfo); |
213 |
< |
} |
207 |
< |
}// end for(dirIter) |
208 |
< |
} |
212 |
> |
sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]); |
213 |
> |
result += buffer; |
214 |
|
|
215 |
< |
const string ReplicateVisitor::toString(){ |
216 |
< |
char buffer[65535]; |
212 |
< |
string result; |
213 |
< |
set<string>::iterator i; |
214 |
< |
|
215 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
216 |
< |
result += buffer; |
215 |
> |
sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]); |
216 |
> |
result += buffer; |
217 |
|
|
218 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
219 |
< |
result += buffer; |
218 |
> |
sprintf(buffer, |
219 |
> |
"------------------------------------------------------------------\n"); |
220 |
> |
result += buffer; |
221 |
|
|
222 |
< |
sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n"); |
223 |
< |
result += buffer; |
223 |
< |
|
224 |
< |
//print the replicate direction |
225 |
< |
sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]); |
226 |
< |
result += buffer; |
222 |
> |
return result; |
223 |
> |
} |
224 |
|
|
225 |
< |
sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]); |
229 |
< |
result += buffer; |
225 |
> |
//----------------------------------------------------------------------------// |
226 |
|
|
227 |
< |
sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]); |
228 |
< |
result += buffer; |
227 |
> |
XYZVisitor::XYZVisitor(SimInfo *info) : |
228 |
> |
BaseVisitor(), seleMan(info), evaluator(info){ |
229 |
> |
this->info = info; |
230 |
> |
visitorName = "XYZVisitor"; |
231 |
|
|
232 |
+ |
evaluator.loadScriptString("select all"); |
233 |
|
|
234 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
235 |
< |
result += buffer; |
234 |
> |
if (!evaluator.isDynamic()) { |
235 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
236 |
> |
} |
237 |
> |
posOnly_ = false; |
238 |
> |
} |
239 |
|
|
240 |
< |
return result; |
241 |
< |
} |
240 |
> |
XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
241 |
> |
BaseVisitor(), seleMan(info), evaluator(info) { |
242 |
> |
this->info = info; |
243 |
> |
visitorName = "XYZVisitor"; |
244 |
|
|
245 |
< |
//----------------------------------------------------------------------------// |
245 |
> |
evaluator.loadScriptString(script); |
246 |
|
|
247 |
< |
XYZVisitor::XYZVisitor(SimInfo* info, bool printDipole) : BaseVisitor(){ |
248 |
< |
this->info = info; |
249 |
< |
visitorName = "XYZVisitor"; |
250 |
< |
this->printDipole = printDipole; |
251 |
< |
} |
247 |
> |
if (!evaluator.isDynamic()) { |
248 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
249 |
> |
} |
250 |
> |
posOnly_ = false; |
251 |
> |
} |
252 |
> |
|
253 |
> |
void XYZVisitor::visit(Atom *atom) { |
254 |
> |
if (isSelected(atom)) |
255 |
> |
internalVisit(atom); |
256 |
> |
} |
257 |
|
|
258 |
< |
void XYZVisitor::visit(Atom* atom){ |
259 |
< |
if(!isIgnore(atom)) |
260 |
< |
internalVisit(atom); |
261 |
< |
} |
258 |
> |
void XYZVisitor::visit(DirectionalAtom *datom) { |
259 |
> |
if (isSelected(datom)) |
260 |
> |
internalVisit(datom); |
261 |
> |
} |
262 |
|
|
263 |
< |
void XYZVisitor::visit(DirectionalAtom* datom){ |
264 |
< |
if(!isIgnore(datom)) |
265 |
< |
internalVisit(datom); |
257 |
< |
} |
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; |
263 |
> |
void XYZVisitor::visit(RigidBody *rb) { |
264 |
> |
if (isSelected(rb)) |
265 |
> |
internalVisit(rb); |
266 |
|
} |
279 |
– |
else |
280 |
– |
return; |
267 |
|
|
268 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
269 |
< |
|
270 |
< |
if(printDipole) |
271 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
272 |
< |
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]); |
299 |
< |
|
300 |
< |
frame.push_back(buffer); |
301 |
< |
|
268 |
> |
void XYZVisitor::update() { |
269 |
> |
//if dynamic, we need to re-evaluate the selection |
270 |
> |
if (evaluator.isDynamic()) { |
271 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
272 |
> |
} |
273 |
|
} |
274 |
|
|
275 |
< |
} |
275 |
> |
void XYZVisitor::internalVisit(StuntDouble *sd) { |
276 |
> |
GenericData * data; |
277 |
> |
AtomData * atomData; |
278 |
> |
AtomInfo * atomInfo; |
279 |
> |
std::vector<AtomInfo *>::iterator i; |
280 |
> |
char buffer[1024]; |
281 |
|
|
282 |
< |
bool XYZVisitor::isIgnore(StuntDouble* sd){ |
283 |
< |
GenericData* data; |
308 |
< |
|
309 |
< |
data = sd->getProperty("IGNORE"); |
310 |
< |
return data ==NULL ? false : true; |
311 |
< |
} |
282 |
> |
//if there is not atom data, just skip it |
283 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
284 |
|
|
285 |
< |
void XYZVisitor::writeFrame(ostream& outStream){ |
286 |
< |
vector<string>::iterator i; |
315 |
< |
double box[3][3]; |
316 |
< |
char buffer[1024]; |
285 |
> |
if (data != NULL) { |
286 |
> |
atomData = dynamic_cast<AtomData *>(data); |
287 |
|
|
288 |
< |
if(frame.size() == 0) |
289 |
< |
cerr << "Current Frame does not contain any atoms" << endl; |
288 |
> |
if (atomData == NULL) |
289 |
> |
return; |
290 |
> |
} else |
291 |
> |
return; |
292 |
|
|
293 |
< |
//total number of atoms |
294 |
< |
outStream << frame.size() << endl; |
293 |
> |
AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType(); |
294 |
> |
std::string bn = baseTypeName(at); |
295 |
|
|
296 |
< |
//write comment line |
297 |
< |
info->getBoxM(box); |
298 |
< |
sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
299 |
< |
info->getTime(), |
300 |
< |
box[0][0], box[0][1], box[0][2], |
301 |
< |
box[1][0], box[1][1], box[1][2], |
302 |
< |
box[2][0], box[2][1], box[2][2]); |
296 |
> |
if (posOnly_){ |
297 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
298 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
299 |
> |
if (atomInfo->hasCharge) { |
300 |
> |
sprintf(buffer, |
301 |
> |
"%s%15.8f%15.8f%15.8f%15.8f", |
302 |
> |
bn.c_str(), |
303 |
> |
atomInfo->pos[0], |
304 |
> |
atomInfo->pos[1], |
305 |
> |
atomInfo->pos[2], |
306 |
> |
atomInfo->charge); |
307 |
> |
} else { |
308 |
> |
sprintf(buffer, |
309 |
> |
"%s%15.8f%15.8f%15.8f", |
310 |
> |
bn.c_str(), |
311 |
> |
atomInfo->pos[0], |
312 |
> |
atomInfo->pos[1], |
313 |
> |
atomInfo->pos[2]); |
314 |
> |
} |
315 |
> |
frame.push_back(buffer); |
316 |
> |
} |
317 |
> |
}else{ |
318 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
319 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
320 |
> |
if (atomInfo->hasCharge) { |
321 |
> |
sprintf(buffer, |
322 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
323 |
> |
bn.c_str(), |
324 |
> |
atomInfo->pos[0], |
325 |
> |
atomInfo->pos[1], |
326 |
> |
atomInfo->pos[2], |
327 |
> |
atomInfo->charge, |
328 |
> |
atomInfo->dipole[0], |
329 |
> |
atomInfo->dipole[1], |
330 |
> |
atomInfo->dipole[2]); |
331 |
> |
} else { |
332 |
> |
sprintf(buffer, |
333 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
334 |
> |
bn.c_str(), |
335 |
> |
atomInfo->pos[0], |
336 |
> |
atomInfo->pos[1], |
337 |
> |
atomInfo->pos[2], |
338 |
> |
atomInfo->dipole[0], |
339 |
> |
atomInfo->dipole[1], |
340 |
> |
atomInfo->dipole[2]); |
341 |
> |
} |
342 |
> |
frame.push_back(buffer); |
343 |
> |
} |
344 |
> |
} |
345 |
> |
} |
346 |
|
|
347 |
< |
outStream << buffer << endl; |
347 |
> |
bool XYZVisitor::isSelected(StuntDouble *sd) { |
348 |
> |
return seleMan.isSelected(sd); |
349 |
> |
} |
350 |
|
|
351 |
< |
for(i = frame.begin(); i != frame.end(); ++i) |
352 |
< |
outStream << *i << endl; |
353 |
< |
} |
351 |
> |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
352 |
> |
std::vector<std::string>::iterator i; |
353 |
> |
char buffer[1024]; |
354 |
|
|
355 |
< |
const string XYZVisitor::toString(){ |
356 |
< |
char buffer[65535]; |
340 |
< |
string result; |
341 |
< |
|
342 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
343 |
< |
result += buffer; |
355 |
> |
if (frame.size() == 0) |
356 |
> |
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
357 |
|
|
358 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
359 |
< |
result += buffer; |
358 |
> |
//total number of atoms |
359 |
> |
outStream << frame.size() << std::endl; |
360 |
|
|
361 |
< |
sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n"); |
362 |
< |
result += buffer; |
363 |
< |
|
364 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
365 |
< |
result += buffer; |
361 |
> |
//write comment line |
362 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
363 |
> |
Mat3x3d box = currSnapshot->getHmat(); |
364 |
> |
|
365 |
> |
sprintf(buffer, |
366 |
> |
"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
367 |
> |
currSnapshot->getTime(), |
368 |
> |
box(0, 0), box(0, 1), box(0, 2), |
369 |
> |
box(1, 0), box(1, 1), box(1, 2), |
370 |
> |
box(2, 0), box(2, 1), box(2, 2)); |
371 |
|
|
372 |
< |
return result; |
355 |
< |
} |
372 |
> |
outStream << buffer << std::endl; |
373 |
|
|
374 |
< |
//----------------------------------------------------------------------------// |
374 |
> |
for( i = frame.begin(); i != frame.end(); ++i ) |
375 |
> |
outStream << *i << std::endl; |
376 |
> |
} |
377 |
|
|
378 |
< |
void PrepareVisitor::internalVisit(Atom * atom){ |
379 |
< |
GenericData* data; |
361 |
< |
AtomData* atomData; |
362 |
< |
|
363 |
< |
//if visited property is existed, remove it |
364 |
< |
data = atom->getProperty("VISITED"); |
365 |
< |
if(data != NULL){ |
366 |
< |
atom->removeProperty("VISITED"); |
378 |
> |
std::string XYZVisitor::trimmedName(const std::string&atomTypeName) { |
379 |
> |
return atomTypeName.substr(0, atomTypeName.find('-')); |
380 |
|
} |
381 |
|
|
382 |
< |
//remove atomdata |
383 |
< |
data = atom->getProperty("ATOMDATA"); |
384 |
< |
if(data != NULL){ |
372 |
< |
atomData = dynamic_cast<AtomData*>(data); |
373 |
< |
if(atomData != NULL) |
374 |
< |
atom->removeProperty("ATOMDATA"); |
382 |
> |
std::string XYZVisitor::baseTypeName(AtomType* at) { |
383 |
> |
std::vector<AtomType*> ayb = at->allYourBase(); |
384 |
> |
return ayb[ayb.size()-1]->getName(); |
385 |
|
} |
376 |
– |
|
377 |
– |
} |
386 |
|
|
387 |
< |
void PrepareVisitor::internalVisit(RigidBody * rb){ |
388 |
< |
GenericData* data; |
389 |
< |
AtomData* atomData; |
390 |
< |
vector<Atom*> myAtoms; |
391 |
< |
vector<Atom*>::iterator atomIter; |
392 |
< |
|
393 |
< |
//if visited property is existed, remove it |
394 |
< |
data = rb->getProperty("VISITED"); |
395 |
< |
if(data != NULL){ |
396 |
< |
rb->removeProperty("VISITED"); |
387 |
> |
const std::string XYZVisitor::toString() { |
388 |
> |
char buffer[65535]; |
389 |
> |
std::string result; |
390 |
> |
|
391 |
> |
sprintf(buffer, |
392 |
> |
"------------------------------------------------------------------\n"); |
393 |
> |
result += buffer; |
394 |
> |
|
395 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
396 |
> |
result += buffer; |
397 |
> |
|
398 |
> |
sprintf(buffer, |
399 |
> |
"Visitor Description: assemble the atom data and output xyz file\n"); |
400 |
> |
result += buffer; |
401 |
> |
|
402 |
> |
sprintf(buffer, |
403 |
> |
"------------------------------------------------------------------\n"); |
404 |
> |
result += buffer; |
405 |
> |
|
406 |
> |
return result; |
407 |
|
} |
408 |
|
|
409 |
< |
//remove atomdata |
410 |
< |
data = rb->getProperty("ATOMDATA"); |
411 |
< |
if(data != NULL){ |
412 |
< |
atomData = dynamic_cast<AtomData*>(data); |
413 |
< |
if(atomData != NULL) |
414 |
< |
rb->removeProperty("ATOMDATA"); |
409 |
> |
//----------------------------------------------------------------------------// |
410 |
> |
|
411 |
> |
void PrepareVisitor::internalVisit(Atom *atom) { |
412 |
> |
GenericData *data; |
413 |
> |
AtomData * atomData; |
414 |
> |
|
415 |
> |
//if visited property is existed, remove it |
416 |
> |
data = atom->getPropertyByName("VISITED"); |
417 |
> |
|
418 |
> |
if (data != NULL) { |
419 |
> |
atom->removeProperty("VISITED"); |
420 |
> |
} |
421 |
> |
|
422 |
> |
//remove atomdata |
423 |
> |
data = atom->getPropertyByName("ATOMDATA"); |
424 |
> |
|
425 |
> |
if (data != NULL) { |
426 |
> |
atomData = dynamic_cast<AtomData *>(data); |
427 |
> |
|
428 |
> |
if (atomData != NULL) |
429 |
> |
atom->removeProperty("ATOMDATA"); |
430 |
> |
} |
431 |
|
} |
432 |
|
|
433 |
< |
myAtoms = rb->getAtoms(); |
434 |
< |
|
435 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
436 |
< |
internalVisit (*atomIter); |
437 |
< |
} |
433 |
> |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
434 |
> |
GenericData* data; |
435 |
> |
AtomData* atomData; |
436 |
> |
std::vector<Atom *> myAtoms; |
437 |
> |
std::vector<Atom *>::iterator atomIter; |
438 |
|
|
439 |
< |
const string PrepareVisitor::toString(){ |
440 |
< |
char buffer[65535]; |
407 |
< |
string result; |
408 |
< |
|
409 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
410 |
< |
result += buffer; |
439 |
> |
//if visited property is existed, remove it |
440 |
> |
data = rb->getPropertyByName("VISITED"); |
441 |
|
|
442 |
< |
sprintf(buffer ,"Visitor name: %s", visitorName.c_str()); |
443 |
< |
result += buffer; |
442 |
> |
if (data != NULL) { |
443 |
> |
rb->removeProperty("VISITED"); |
444 |
> |
} |
445 |
|
|
446 |
< |
sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n"); |
447 |
< |
result += buffer; |
446 |
> |
//remove atomdata |
447 |
> |
data = rb->getPropertyByName("ATOMDATA"); |
448 |
|
|
449 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
450 |
< |
result += buffer; |
449 |
> |
if (data != NULL) { |
450 |
> |
atomData = dynamic_cast<AtomData *>(data); |
451 |
|
|
452 |
< |
return result; |
453 |
< |
} |
452 |
> |
if (atomData != NULL) |
453 |
> |
rb->removeProperty("ATOMDATA"); |
454 |
> |
} |
455 |
|
|
456 |
< |
//----------------------------------------------------------------------------// |
456 |
> |
myAtoms = rb->getAtoms(); |
457 |
|
|
458 |
< |
WaterTypeVisitor:: WaterTypeVisitor(){ |
459 |
< |
visitorName = "WaterTypeVisitor"; |
460 |
< |
waterTypeList.insert("TIP3P_RB_0"); |
429 |
< |
waterTypeList.insert("TIP4P_RB_0"); |
430 |
< |
waterTypeList.insert("TIP5P_RB_0"); |
431 |
< |
waterTypeList.insert("SPCE_RB_0"); |
432 |
< |
} |
458 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
459 |
> |
internalVisit(*atomIter); |
460 |
> |
} |
461 |
|
|
462 |
+ |
const std::string PrepareVisitor::toString() { |
463 |
+ |
char buffer[65535]; |
464 |
+ |
std::string result; |
465 |
+ |
|
466 |
+ |
sprintf(buffer, |
467 |
+ |
"------------------------------------------------------------------\n"); |
468 |
+ |
result += buffer; |
469 |
+ |
|
470 |
+ |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
471 |
+ |
result += buffer; |
472 |
+ |
|
473 |
+ |
sprintf(buffer, |
474 |
+ |
"Visitor Description: prepare for operation of other vistors\n"); |
475 |
+ |
result += buffer; |
476 |
+ |
|
477 |
+ |
sprintf(buffer, |
478 |
+ |
"------------------------------------------------------------------\n"); |
479 |
+ |
result += buffer; |
480 |
+ |
|
481 |
+ |
return result; |
482 |
+ |
} |
483 |
|
|
484 |
< |
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(); |
484 |
> |
//----------------------------------------------------------------------------// |
485 |
|
|
486 |
< |
if(waterTypeList.find(rbName) != waterTypeList.end()){ |
486 |
> |
WaterTypeVisitor::WaterTypeVisitor() { |
487 |
> |
visitorName = "WaterTypeVisitor"; |
488 |
> |
waterTypeList.insert("TIP3P_RB_0"); |
489 |
> |
waterTypeList.insert("TIP4P_RB_0"); |
490 |
> |
waterTypeList.insert("TIP5P_RB_0"); |
491 |
> |
waterTypeList.insert("SPCE_RB_0"); |
492 |
> |
} |
493 |
|
|
494 |
< |
myAtoms = rb->getAtoms(); |
495 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){ |
494 |
> |
void WaterTypeVisitor::visit(RigidBody *rb) { |
495 |
> |
std::string rbName; |
496 |
> |
std::vector<Atom *> myAtoms; |
497 |
> |
std::vector<Atom *>::iterator atomIter; |
498 |
> |
GenericData* data; |
499 |
> |
AtomData* atomData; |
500 |
> |
AtomInfo* atomInfo; |
501 |
> |
std::vector<AtomInfo *>::iterator i; |
502 |
|
|
503 |
< |
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) |
503 |
> |
rbName = rb->getType(); |
504 |
|
|
505 |
< |
}//end for(atomIter) |
506 |
< |
|
466 |
< |
}//end if (waterTypeList.find(rbName) != waterTypeList.end()) |
467 |
< |
|
468 |
< |
} |
505 |
> |
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
506 |
> |
myAtoms = rb->getAtoms(); |
507 |
|
|
508 |
< |
void WaterTypeVisitor:: replaceType(string& atomType){ |
509 |
< |
atomType = atomType.substr(0, atomType.find('_')); |
510 |
< |
} |
508 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
509 |
> |
++atomIter ) { |
510 |
> |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
511 |
|
|
512 |
< |
const string WaterTypeVisitor:: toString(){ |
513 |
< |
char buffer[65535]; |
476 |
< |
string result; |
477 |
< |
|
478 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
479 |
< |
result += buffer; |
512 |
> |
if (data != NULL) { |
513 |
> |
atomData = dynamic_cast<AtomData *>(data); |
514 |
|
|
515 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
516 |
< |
result += buffer; |
515 |
> |
if (atomData == NULL) |
516 |
> |
continue; |
517 |
> |
} else |
518 |
> |
continue; |
519 |
|
|
520 |
< |
sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n"); |
521 |
< |
result += buffer; |
520 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
521 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
522 |
> |
atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName); |
523 |
> |
} //end for(atomInfo) |
524 |
> |
} //end for(atomIter) |
525 |
> |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
526 |
> |
} |
527 |
|
|
528 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
529 |
< |
result += buffer; |
528 |
> |
std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) { |
529 |
> |
return atomTypeName.substr(0, atomTypeName.find('_')); |
530 |
> |
} |
531 |
|
|
532 |
< |
return result; |
533 |
< |
} |
532 |
> |
const std::string WaterTypeVisitor::toString() { |
533 |
> |
char buffer[65535]; |
534 |
> |
std::string result; |
535 |
|
|
536 |
+ |
sprintf(buffer, |
537 |
+ |
"------------------------------------------------------------------\n"); |
538 |
+ |
result += buffer; |
539 |
+ |
|
540 |
+ |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
541 |
+ |
result += buffer; |
542 |
+ |
|
543 |
+ |
sprintf(buffer, |
544 |
+ |
"Visitor Description: Replace the atom type in water model\n"); |
545 |
+ |
result += buffer; |
546 |
+ |
|
547 |
+ |
sprintf(buffer, |
548 |
+ |
"------------------------------------------------------------------\n"); |
549 |
+ |
result += buffer; |
550 |
+ |
|
551 |
+ |
return result; |
552 |
+ |
} |
553 |
+ |
|
554 |
+ |
} //namespace oopse |