| 58 |
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#include "utils/simError.h" |
| 59 |
|
#include "utils/MemoryUtils.hpp" |
| 60 |
|
#include "utils/StringTokenizer.hpp" |
| 61 |
+ |
#include "brains/Thermo.hpp" |
| 62 |
|
|
| 63 |
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#ifdef IS_MPI |
| 63 |
– |
|
| 64 |
|
#include <mpi.h> |
| 65 |
< |
#define TAKE_THIS_TAG_CHAR 0 |
| 66 |
< |
#define TAKE_THIS_TAG_INT 1 |
| 65 |
> |
#endif |
| 66 |
|
|
| 68 |
– |
#endif // is_mpi |
| 67 |
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|
| 70 |
– |
|
| 68 |
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namespace OpenMD { |
| 69 |
|
|
| 70 |
|
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
| 242 |
|
|
| 243 |
|
if (needCOMprops_) { |
| 244 |
|
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 245 |
+ |
Thermo thermo(info_); |
| 246 |
|
Vector3d com; |
| 249 |
– |
Vector3d comvel; |
| 250 |
– |
Vector3d comw; |
| 251 |
– |
if (needPos_ && needVel_){ |
| 252 |
– |
info_->getComAll(com, comvel); |
| 253 |
– |
comw = info_->getAngularMomentum(); |
| 254 |
– |
}else{ |
| 255 |
– |
com = info_->getCom(); |
| 256 |
– |
comvel = 0.0; |
| 257 |
– |
comw = 0.0; |
| 258 |
– |
} |
| 259 |
– |
s->setCOMprops(com, comvel, comw); |
| 260 |
– |
} |
| 247 |
|
|
| 248 |
+ |
if (needPos_ && needVel_) { |
| 249 |
+ |
Vector3d comvel; |
| 250 |
+ |
Vector3d comw; |
| 251 |
+ |
thermo.getComAll(com, comvel); |
| 252 |
+ |
comw = thermo.getAngularMomentum(); |
| 253 |
+ |
} else { |
| 254 |
+ |
com = thermo.getCom(); |
| 255 |
+ |
} |
| 256 |
+ |
} |
| 257 |
|
} |
| 258 |
|
|
| 259 |
|
void DumpReader::readSet(int whichFrame) { |
| 709 |
|
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
| 710 |
|
s->setHmat(hmat); |
| 711 |
|
} else if (propertyName == "Thermostat") { |
| 712 |
< |
RealType chi = tokenizer.nextTokenAsDouble(); |
| 713 |
< |
RealType integralOfChiDt = tokenizer.nextTokenAsDouble(); |
| 714 |
< |
s->setChi(chi); |
| 715 |
< |
s->setIntegralOfChiDt(integralOfChiDt); |
| 712 |
> |
pair<RealType, RealType> thermostat; |
| 713 |
> |
thermostat.first = tokenizer.nextTokenAsDouble(); |
| 714 |
> |
thermostat.second = tokenizer.nextTokenAsDouble(); |
| 715 |
> |
s->setThermostat(thermostat); |
| 716 |
|
} else if (propertyName == "Barostat") { |
| 717 |
|
Mat3x3d eta; |
| 718 |
|
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
| 724 |
|
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
| 725 |
|
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
| 726 |
|
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
| 727 |
< |
s->setEta(eta); |
| 727 |
> |
s->setBarostat(eta); |
| 728 |
|
} else { |
| 729 |
|
sprintf(painCave.errMsg, |
| 730 |
|
"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); |
