From 8d872824b04afc23e2d4c9f73791f398e881a35d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 30 Aug 2017 09:48:32 +0200
Subject: [PATCH] Make sure position, velocity etc. information is preserved
when reinitializeing openmm context
---
modules/mol/mm/doc/simulation.rst | 22 +++++++++++++++++++++-
modules/mol/mm/src/simulation.cc | 24 +++++++++++++++++++-----
modules/mol/mm/src/simulation.hh | 2 ++
3 files changed, 42 insertions(+), 6 deletions(-)
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index bbcf1c802..3fd443aea 100644
--- a/modules/mol/mm/doc/simulation.rst
+++ b/modules/mol/mm/doc/simulation.rst
@@ -201,6 +201,10 @@ mapped back to the attached structure at any time.
.. method:: AddPositionConstraint(index)
Fixes the position of the particle with index given in the argument.
+ This requires to reinitialize the internal openmm Context
+ (this is expensive!). Positions, velocities, forces, energies etc.
+ are properly preserved but e.g. states of random number generators etc.
+ might be lost.
:param index: Particle to be fixed
:type index: :class:`int`
@@ -211,6 +215,10 @@ mapped back to the attached structure at any time.
.. method:: AddPositionConstraints(indices)
Fixes the position of the atoms with the indices given in in the argument.
+ This requires to reinitialize the internal openmm Context
+ (this is expensive!). Positions, velocities, forces, energies etc.
+ are properly preserved but e.g. states of random number generators etc.
+ might be lost.
:param indices: Particles to be fixed
:type indices: :class:`list`
@@ -221,6 +229,10 @@ mapped back to the attached structure at any time.
.. method:: ResetPositionConstraints()
Removes all position constraints.
+ This requires to reinitialize the internal openmm Context
+ (this is expensive!). Positions, velocities, forces, energies etc.
+ are properly preserved but e.g. states of random number generators etc.
+ might be lost.
.. method:: ResetHarmonicBond(index, bond_length, force_constant)
@@ -347,7 +359,11 @@ mapped back to the attached structure at any time.
.. method:: ResetDistanceConstraint(index, constraint_length)
Update of the distance constraint parameters in the simulation **and**
- in the attached :class:`Topology`
+ in the attached :class:`Topology`.
+ This requires to reinitialize the internal openmm Context
+ (this is expensive!). Positions, velocities, forces, energies etc.
+ are properly preserved but e.g. states of random number generators etc.
+ might be lost.
:param index: Distance constraint to be reset
:param constraint_length: New constraint length in nm
@@ -445,6 +461,10 @@ mapped back to the attached structure at any time.
Update of the mass in the simulation **and**
in the attached :class:`Topology`
+ This requires to reinitialize the internal openmm Context
+ (this is expensive!). Positions, velocities, forces, energies etc.
+ are properly preserved but e.g. states of random number generators etc.
+ might be lost.
:param index: Mass to be reset
:param mass: New mass
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
index 8288f1a5e..09f6465a2 100644
--- a/modules/mol/mm/src/simulation.cc
+++ b/modules/mol/mm/src/simulation.cc
@@ -694,7 +694,7 @@ void Simulation::ResetDistanceConstraint(uint index, Real constraint_length){
int particle1, particle2;
system_->getConstraintParameters(index,particle1,particle2,dummy);
system_->setConstraintParameters(index,particle1,particle2,constraint_length);
- context_->reinitialize();
+ this->ReinitializeContext();
top_->SetDistanceConstraintParameters(index, constraint_length);
}
@@ -703,7 +703,7 @@ void Simulation::AddPositionConstraint(uint index){
throw ost::Error("Provided index exceeds number of atoms!");
}
system_->setParticleMass(index,0.0);
- context_->reinitialize();
+ this->ReinitializeContext();
top_->AddPositionConstraint(index);
}
@@ -717,7 +717,7 @@ void Simulation::AddPositionConstraints(const std::vector<uint>& index){
system_->setParticleMass(*i,0.0);
top_->AddPositionConstraint(*i);
}
- context_->reinitialize();
+ this->ReinitializeContext();
}
void Simulation::ResetPositionConstraints(){
@@ -726,7 +726,7 @@ void Simulation::ResetPositionConstraints(){
system_->setParticleMass(i,original_masses[i]);
}
top_->ResetPositionConstraints();
- context_->reinitialize();
+ this->ReinitializeContext();
}
void Simulation::ResetHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
@@ -872,7 +872,7 @@ void Simulation::ResetMass(uint index, Real mass){
throw ost::Error("Provided index exceeds number of atoms!");
}
system_->setParticleMass(index,mass);
- context_->reinitialize();
+ this->ReinitializeContext();
top_->SetMass(index,mass);
}
@@ -896,5 +896,19 @@ void Simulation::SetPeriodicBoxExtents(geom::Vec3& vec){
context_->setPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
}
+void Simulation::ReinitializeContext() {
+ // reinitializing requires to reset all those things!
+ // Be aware, state of random number generators etc might not be
+ // preserved!
+ OpenMM::State state = context_->getState(OpenMM::State::Positions |
+ OpenMM::State::Velocities |
+ OpenMM::State::Forces |
+ OpenMM::State::Energy |
+ OpenMM::State::Parameters |
+ OpenMM::State::ParameterDerivatives);
+ context_->reinitialize();
+ context_->setState(state);
+}
+
}}}
diff --git a/modules/mol/mm/src/simulation.hh b/modules/mol/mm/src/simulation.hh
index 52aaaa001..89c58b10e 100644
--- a/modules/mol/mm/src/simulation.hh
+++ b/modules/mol/mm/src/simulation.hh
@@ -147,6 +147,8 @@ private:
int TimeToNextNotification();
+ void ReinitializeContext();
+
// loads plugins from directory for OpenMM BUT only once per unique path!
static void EnsurePluginsLoaded(const String& plugin_path);
--
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