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Commit 4ffd8e67 authored by peastman's avatar peastman
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Merge pull request #481 from peastman/exclusions 

Force field XML files can specify CustomNonbondedForces
parents 11082d76 9b6f5dc2
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docs/usersguide/application.rst
View file @ 4ffd8e67
......@@ -2186,6 +2186,49 @@ second atom has class OS and the third has class P:
<Proper class1="" class2="OS" class3="P" class4="" per="3" phase="0.0" k="0.66944"/>
<CustomNonbondedForce>
===============
To add a CustomNonbondedForce to the System, include a tag that looks like this:
.. code-block:: xml
<CustomNonbondedForce energy="scale*epsilon1*epsilon2*((sigma1+sigma2)/r)^12" bondCutoff="3">
<GlobalParameter name="scale" defaultValue="1"/>
<PerParticleParameter name="sigma"/>
<PerParticleParameter name="epsilon"/>
<Atom type="0" sigma="0.3249" epsilon="0.7112"/>
<Atom type="1" sigma="0.1069" epsilon="0.0656"/>
<Atom type="2" sigma="0.3399" epsilon="0.4577"/>
...
</CustomNonbondedForce>
The energy expression for the CustomNonbondedForce is specified by the
:code:`energy` attribute. This is a mathematical expression that gives the
energy of each pairwise interaction as a function of the distance *r*\ . It
also may depend on an arbitrary list of global or per-particle parameters. Use
a :code:`<GlobalParameter>` tag to define a global parameter, and a
:code:`<PerParticleParameter>` tag to define a per-particle parameter.
Exclusions are created automatically based on the :code:`bondCutoff` attribute.
After setting the nonbonded parameters for all atoms, the force field calls
:code:`createExclusionsFromBonds()` on the CustomNonbondedForce, passing in this
value as its argument. To avoid creating exclusions, set :code:`bondCutoff` to 0.
Each :code:`<Atom>` tag specifies the parameters for one atom type
(specified with the :code:`type` attribute) or atom class (specified with
the :code:`class` attribute). It is fine to mix these two methods, having
some tags specify a type and others specify a class. However you do it, you
must make sure that a unique set of parameters is defined for every atom type.
The remaining attributes are the values to use for the per-atom parameters. All
per-atom parameters must be specified for every :code:`<Atom>` tag, and the
attribute name must match the name of the parameter. For instance, if there is
a per-atom parameter with the name “radius”, then every :code:`<Atom>` tag
must include an attribute called :code:`radius`\ .
CustomNonbondedForce also allows you to define tabulated functions. See section
:ref:`tabulated-functions` for details.
<CustomGBForce>
===============
......@@ -2243,30 +2286,8 @@ attribute name must match the name of the parameter. For instance, if there is
a per-atom parameter with the name “radius”, then every :code:`<Atom>` tag
must include an attribute called :code:`radius`\ .
CustomGBForce also allows you to define tabulated functions. To define a
function, include a :code:`<Function>` tag inside the
:code:`<CustomGBForce>` tag:
.. code-block:: xml
<Function name="myfn" min="-5" max="5">
0.983674857694 -0.980096396266 -0.975743130031 -0.970451936613 -0.964027580076
-0.956237458128 -0.946806012846 -0.935409070603 -0.921668554406 -0.905148253645
-0.885351648202 -0.861723159313 -0.833654607012 -0.800499021761 -0.761594155956
-0.716297870199 -0.664036770268 -0.604367777117 -0.537049566998 -0.46211715726
-0.379948962255 -0.291312612452 -0.197375320225 -0.099667994625 0.0
0.099667994625 0.197375320225 0.291312612452 0.379948962255 0.46211715726
0.537049566998 0.604367777117 0.664036770268 0.716297870199 0.761594155956
0.800499021761 0.833654607012 0.861723159313 0.885351648202 0.905148253645
0.921668554406 0.935409070603 0.946806012846 0.956237458128 0.964027580076
0.970451936613 0.975743130031 0.980096396266 0.983674857694 0.986614298151
0.989027402201
</Function>
The tag’s attributes define the name of the function and the range of values for
which it is defined. The tabulated values are listed inside the body of the
tag, with successive values separated by white space. Again, see the API
documentation for more details.
CustomGBForce also allows you to define tabulated functions. See section
:ref:`tabulated-functions` for details.
Writing Custom Expressions
==========================
......@@ -2303,6 +2324,55 @@ is exactly equivalent to
The definition of an intermediate value may itself involve other intermediate
values. All uses of a value must appear *before* that value’s definition.
.. _tabulated-functions:
TabulatedFunctions
==================
Some forces, such as CustomNonbondedForce and CustomGBForce, allow you to define
tabulated functions. To define a function, include a :code:`<Function>` tag inside the
:code:`<CustomNonbondedForce>` or :code:`<CustomGBForce>` tag:
.. code-block:: xml
<Function name="myfn" type="Continuous1D" min="-5" max="5">
0.983674857694 -0.980096396266 -0.975743130031 -0.970451936613 -0.964027580076
-0.956237458128 -0.946806012846 -0.935409070603 -0.921668554406 -0.905148253645
-0.885351648202 -0.861723159313 -0.833654607012 -0.800499021761 -0.761594155956
-0.716297870199 -0.664036770268 -0.604367777117 -0.537049566998 -0.46211715726
-0.379948962255 -0.291312612452 -0.197375320225 -0.099667994625 0.0
0.099667994625 0.197375320225 0.291312612452 0.379948962255 0.46211715726
0.537049566998 0.604367777117 0.664036770268 0.716297870199 0.761594155956
0.800499021761 0.833654607012 0.861723159313 0.885351648202 0.905148253645
0.921668554406 0.935409070603 0.946806012846 0.956237458128 0.964027580076
0.970451936613 0.975743130031 0.980096396266 0.983674857694 0.986614298151
0.989027402201
</Function>
The tag’s attributes define the name of the function, the type of function, and
the range of values for which it is defined. The required set of attributed
depends on the function type:
.. tabularcolumns:: |l|L|
============ =======================================================
Type Required Attributes
============ =======================================================
Continuous1D min, max
Continuous2D xmin, ymin, xmax, ymax, xsize, ysize
Continuous3D xmin, ymin, zmin, xmax, ymax, zmax, xsize, ysize, zsize
Discrete1D
Discrete2D xsize, ysize
Discrete3D xsize, ysize, zsize
============ =======================================================
The "min" and "max" attributes define the range of the independent variables for
a continuous function. The "size" attributes define the size of the table along
each axis. The tabulated values are listed inside the body of the tag, with
successive values separated by white space. See the API documentation for more
details.
Using Multiple Files
********************
......
openmmapi/include/openmm/CustomNonbondedForce.h
View file @ 4ffd8e67
......@@ -343,6 +343,8 @@ public:
void setParticleParameters(int index, const std::vector<double>& parameters);
/**
* Add a particle pair to the list of interactions that should be excluded.
*
* In many cases, you can use createExclusionsFromBonds() rather than adding each exclusion explicitly.
*
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
......@@ -365,6 +367,15 @@ public:
* @param particle2 the index of the second particle in the pair
*/
void setExclusionParticles(int index, int particle1, int particle2);
/**
* Identify exclusions based on the molecular topology. Particles which are separated by up to a specified number of
* bonds are added as exclusions.
*
* @param bonds the set of bonds based on which to construct exclusions. Each element specifies the indices of
* two particles that are bonded to each other.
* @param bondCutoff pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions
*/
void createExclusionsFromBonds(const std::vector<std::pair<int, int> >& bonds, int bondCutoff);
/**
* Add a tabulated function that may appear in the energy expression.
*
......
openmmapi/src/CustomNonbondedForce.cpp
View file @ 4ffd8e67
......@@ -174,6 +174,33 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
exclusions[index].particle1 = particle1;
exclusions[index].particle2 = particle2;
}
void CustomNonbondedForce::createExclusionsFromBonds(const vector<pair<int, int> >& bonds, int bondCutoff) {
if (bondCutoff < 1)
return;
vector<set<int> > exclusions(particles.size());
vector<set<int> > bonded12(exclusions.size());
for (int i = 0; i < (int) bonds.size(); ++i) {
int p1 = bonds[i].first;
int p2 = bonds[i].second;
exclusions[p1].insert(p2);
exclusions[p2].insert(p1);
bonded12[p1].insert(p2);
bonded12[p2].insert(p1);
}
for (int level = 0; level < bondCutoff-1; level++) {
vector<set<int> > currentExclusions = exclusions;
for (int i = 0; i < (int) particles.size(); i++) {
for (set<int>::const_iterator iter = currentExclusions[i].begin(); iter != currentExclusions[i].end(); ++iter)
exclusions[*iter].insert(bonded12[i].begin(), bonded12[i].end());
}
}
for (int i = 0; i < (int) exclusions.size(); ++i)
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
if (*iter < i)
addExclusion(*iter, i);
}
int CustomNonbondedForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
......
tests/TestFindExclusions.cpp
View file @ 4ffd8e67
......@@ -30,6 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/OpenMMException.h"
#include <iostream>
......@@ -166,10 +167,62 @@ void testReplaceExceptions() {
ASSERT(charge == 5.0);
}
/**
* This is the same as testFindExceptions(), except it tests adding exclusions to a CustomNonbondedForce.
*/
void testFindCustomExclusions() {
CustomNonbondedForce nonbonded("r");
vector<pair<int, int> > bonds;
vector<double> params;
for (int i = 0; i < NUM_ATOMS; i++)
nonbonded.addParticle(params);
// loop over all main-chain atoms (even numbered atoms)
for (int i = 0; i < NUM_ATOMS-1; i += 2)
{
// side-chain bonds
bonds.push_back(pair<int, int>(i, i+1));
// main-chain bonds
if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
bonds.push_back(pair<int, int>(i, i+2));
}
nonbonded.createExclusionsFromBonds(bonds, 3);
// Build lists of the expected exclusions.
vector<set<int> > expectedExclusions(NUM_ATOMS);
int totalExclusions = 0;
for (int i = 0; i < NUM_ATOMS; i += 2) {
addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+5, expectedExclusions, totalExclusions);
addAtomsToExclusions(i, i+6, expectedExclusions, totalExclusions);
addAtomsToExclusions(i+1, i+3, expectedExclusions, totalExclusions);
addAtomsToExclusions(i+1, i+4, expectedExclusions, totalExclusions);
}
for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
int particle1, particle2;
nonbonded.getExclusionParticles(i, particle1, particle2);
}
// Compare them to the exceptions that were generated.
ASSERT_EQUAL(totalExclusions, nonbonded.getNumExclusions());
for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
int particle1, particle2;
nonbonded.getExclusionParticles(i, particle1, particle2);
ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
}
}
int main() {
try {
testFindExceptions();
testReplaceExceptions();
testFindCustomExclusions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 4ffd8e67
......@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2013 Stanford University and the Authors.
Portions copyright (c) 2012-2014 Stanford University and the Authors.
Authors: Peter Eastman, Mark Friedrichs
Contributors:
......@@ -1485,6 +1485,104 @@ class CustomTorsionGenerator:
parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
## @private
class CustomNonbondedGenerator:
"""A CustomNonbondedGenerator constructs a CustomNonbondedForce."""
def __init__(self, energy, bondCutoff):
self.energy = energy
self.bondCutoff = bondCutoff
self.typeMap = {}
self.globalParams = {}
self.perParticleParams = []
self.functions = []
@staticmethod
def parseElement(element, ff):
generator = CustomNonbondedGenerator(element.attrib['energy'], int(element.attrib['bondCutoff']))
ff._forces.append(generator)
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerParticleParameter'):
generator.perParticleParams.append(param.attrib['name'])
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if None not in types:
values = [float(atom.attrib[param]) for param in generator.perParticleParams]
for t in types[0]:
generator.typeMap[t] = values
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic}
if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
force = mm.CustomNonbondedForce(self.energy)
for param in self.globalParams:
force.addGlobalParameter(param, self.globalParams[param])
for param in self.perParticleParams:
force.addPerParticleParameter(param)
for (name, type, values, params) in self.functions:
if type == 'Continuous1D':
force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
elif type == 'Continuous2D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
elif type == 'Continuous3D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
elif type == 'Discrete1D':
force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
elif type == 'Discrete2D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
elif type == 'Discrete3D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
for atom in data.atoms:
t = data.atomType[atom]
if t in self.typeMap:
values = self.typeMap[t]
force.addParticle(self.typeMap[t])
else:
raise ValueError('No CustomNonbonded parameters defined for atom type '+t)
force.setNonbondedMethod(methodMap[nonbondedMethod])
force.setCutoffDistance(nonbondedCutoff)
sys.addForce(force)
def postprocessSystem(self, sys, data, args):
# Create exceptions based on bonds, virtual sites, and Drude particles.
if self.bondCutoff == 0:
return
bondIndices = []
for bond in data.bonds:
bondIndices.append((bond.atom1, bond.atom2))
for i in range(sys.getNumParticles()):
if sys.isVirtualSite(i):
site = sys.getVirtualSite(i)
for j in range(site.getNumParticles()):
bondIndices.append((i, site.getParticle(j)))
drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)]
if len(drude) > 0:
drude = drude[0]
# For purposes of creating exceptions, a Drude particle is "bonded" to anything
# its parent atom is bonded to.
drudeMap = {}
for i in range(drude.getNumParticles()):
params = drude.getParticleParameters(i)
drudeMap[params[1]] = params[0]
for atom1, atom2 in bondIndices:
drude1 = drudeMap[atom1] if atom1 in drudeMap else None
drude2 = drudeMap[atom2] if atom2 in drudeMap else None
if drude1 is not None:
bondIndices.append((drude1, atom2))
if drude2 is not None:
bondIndices.append((drude1, drude2))
if drude2 is not None:
bondIndices.append((atom1, drude2))
nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)
parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement
## @private
class CustomGBGenerator:
"""A CustomGBGenerator constructs a CustomGBForce."""
......@@ -1493,7 +1591,6 @@ class CustomGBGenerator:
self.typeMap = {}
self.globalParams = {}
self.perParticleParams = []
self.paramValues = []
self.computedValues = []
self.energyTerms = []
self.functions = []
......
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