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Addin an openACC interface to ParallelTaskManager
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| #! FIELDS time d2 | ||
| 0.000000 1.000000 | ||
| 0.050000 9.000000 |
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| type=driver | ||
| plumed_needs="dlopen" | ||
| arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz" | ||
| export NVCOMPILER_ACC_NOTIFY=31 |
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| /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ||
| Copyright (c) 2013 The plumed team | ||
| (see the PEOPLE file at the root of the distribution for a list of names) | ||
| See http://www.plumed-code.org for more information. | ||
| This file is part of plumed, version 2.0. | ||
| plumed is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU Lesser General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| plumed is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU Lesser General Public License for more details. | ||
| You should have received a copy of the GNU Lesser General Public License | ||
| along with plumed. If not, see <http://www.gnu.org/licenses/>. | ||
| +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ | ||
| #include "colvar/Colvar.h" | ||
| #include "core/ActionRegister.h" | ||
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| #include <string> | ||
| #include <cmath> | ||
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| using namespace std; | ||
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| namespace PLMD{ | ||
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| class Distance : public colvar::Colvar { | ||
| bool components; | ||
| bool pbc; | ||
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| public: | ||
| static void registerKeywords( Keywords& keys ); | ||
| Distance(const ActionOptions&); | ||
| // active methods: | ||
| virtual void calculate(); | ||
| }; | ||
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| PLUMED_REGISTER_ACTION(Distance,"TESTPBCS") | ||
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| void Distance::registerKeywords( Keywords& keys ){ | ||
| Colvar::registerKeywords( keys ); | ||
| keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between"); | ||
| keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z"); | ||
| } | ||
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| Distance::Distance(const ActionOptions&ao): | ||
| PLUMED_COLVAR_INIT(ao), | ||
| components(false), | ||
| pbc(true) | ||
| { | ||
| vector<AtomNumber> atoms; | ||
| parseAtomList("ATOMS",atoms); | ||
| if(atoms.size()!=2) | ||
| error("Number of specified atoms should be 2"); | ||
| parseFlag("COMPONENTS",components); | ||
| pbc=true; | ||
| checkRead(); | ||
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| log.printf(" between atoms %d %d\n",atoms[0].serial(),atoms[1].serial()); | ||
| if(pbc) log.printf(" using periodic boundary conditions\n"); | ||
| else log.printf(" without periodic boundary conditions\n"); | ||
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| if(!components){ | ||
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| addValueWithDerivatives(); setNotPeriodic(); | ||
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| } else{ | ||
| addComponentWithDerivatives("x"); componentIsNotPeriodic("x"); | ||
| addComponentWithDerivatives("y"); componentIsNotPeriodic("y"); | ||
| addComponentWithDerivatives("z"); componentIsNotPeriodic("z"); | ||
| } | ||
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| requestAtoms(atoms); | ||
| } | ||
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| void Distance::calculate(){ | ||
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| Vector a=getPosition(0); | ||
| Vector b=getPosition(1); | ||
| std::vector<Vector> d(1); | ||
| auto & pbc=getPbc(); | ||
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| //doing this on the GPU losing A lot of time, to check if pbc is correcly there | ||
| #pragma acc data copyin(a[0:3],b[0:3]) copyout(d[0:1]) | ||
| { | ||
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| #pragma acc kernels present(pbc) | ||
| { | ||
| d[0]=delta(a,b); | ||
| pbc.apply(d); | ||
| } | ||
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| } | ||
| auto distance=d[0]; | ||
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| const double value=distance.modulo(); | ||
| const double invvalue=1.0/value; | ||
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| if(!components){ | ||
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| setAtomsDerivatives(0,-invvalue*distance); | ||
| setAtomsDerivatives(1,invvalue*distance); | ||
| setBoxDerivatives (-invvalue*Tensor(distance,distance)); | ||
| setValue (value); | ||
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| }else{ | ||
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| Value* valuex=getPntrToComponent("x"); | ||
| Value* valuey=getPntrToComponent("y"); | ||
| Value* valuez=getPntrToComponent("z"); | ||
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| setAtomsDerivatives (valuex,0,Vector(-1,0,0)); | ||
| setAtomsDerivatives (valuex,1,Vector(+1,0,0)); | ||
| setBoxDerivatives (valuex,Tensor(distance,Vector(-1,0,0))); | ||
| valuex->set(distance[0]); | ||
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| setAtomsDerivatives (valuey,0,Vector(0,-1,0)); | ||
| setAtomsDerivatives (valuey,1,Vector(0,+1,0)); | ||
| setBoxDerivatives (valuey,Tensor(distance,Vector(0,-1,0))); | ||
| valuey->set(distance[1]); | ||
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| setAtomsDerivatives (valuez,0,Vector(0,0,-1)); | ||
| setAtomsDerivatives (valuez,1,Vector(0,0,+1)); | ||
| setBoxDerivatives (valuez,Tensor(distance,Vector(0,0,-1))); | ||
| valuez->set(distance[2]); | ||
| }; | ||
| } | ||
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| } |
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| # This is loading a collective variable on the fly: | ||
| LOAD FILE=./pbctest.cpp | ||
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| d2: TESTPBCS ATOMS=1,2 | ||
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| PRINT FILE=COLVAR ARG=d2 | ||
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| ENDPLUMED |
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