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Commit 8167c79b authored by leeping's avatar leeping
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Merge branch 'master' of github.com:leeping/openmm

parents 855ece90 99ef4344
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Showing with 377 additions and 152 deletions
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 8167c79b
......@@ -1563,6 +1563,28 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( const std::ve
return energy;
}
void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles) {
// setup, including calculating induced dipoles
std::vector<MultipoleParticleData> particleData;
setup( particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData );
outputInducedDipoles = _inducedDipole;
}
void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments( const std::vector<RealOpenMM>& masses,
const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 8167c79b
......@@ -471,6 +471,38 @@ public:
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<OpenMM::RealVec>& forces );
/**
* Calculate particle induced dipoles.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ... ) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
void calculateInducedDipoles(const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles);
/**
* Calculate system multipole moments.
*
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ 8167c79b
......@@ -2605,6 +2605,40 @@ static void testPMEMutualPolarizationLargeWater( FILE* log ) {
}
// test querying particle induced dipoles
static void testParticleInducedDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getInducedDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0031710288, 9.3687453e-7, -0.0006919963);
expectedDipole[1] = Vec3(8.0279737504e-5, -0.000279376, 4.778060103e-5);
expectedDipole[2] = Vec3(0.000079322, 0.0002789804, 4.8696656126e-5);
expectedDipole[3] = Vec3(-0.0001407394, 1.540638116e-6, -0.0007077775);
expectedDipole[4] = Vec3(0.0019564439, -1.0409717e-7, 0.0007332188);
expectedDipole[5] = Vec3(0.0008213891, -0.0007749618, -0.0003883865);
expectedDipole[6] = Vec3(0.0046133992, -7.2868019e-7, 0.0002500622);
expectedDipole[7] = Vec3(0.0008204731, 0.0007772727, -0.0003856176);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments( FILE* log ) {
......@@ -2778,6 +2812,10 @@ int main( int numberOfArguments, char* argv[] ) {
testMultipoleAmmoniaDirectPolarization( log );
// test querying induced dipoles
testParticleInducedDipoles();
// test mutual polarization, no cutoff
testMultipoleAmmoniaMutualPolarization( log );
......
plugins/cpupme/src/CpuPmeKernels.cpp
View file @ 8167c79b
......@@ -35,9 +35,9 @@
#include "CpuPmeKernels.h"
#include "SimTKOpenMMRealType.h"
#include "openmm/internal/hardware.h"
#include "openmm/internal/vectorize.h"
#include <cmath>
#include <cstring>
#include <smmintrin.h>
using namespace OpenMM;
using namespace std;
......@@ -47,52 +47,50 @@ static const int PME_ORDER = 5;
bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false;
int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
#define EXTRACT_FLOAT(v, element) _mm_cvtss_f32(_mm_shuffle_ps(v, v, _MM_SHUFFLE(0, 0, 0, element)))
static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
float temp[4];
__m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
__m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0]));
__m128 gridSize = _mm_set_ps(0, gridz, gridy, gridx);
__m128i gridSizeInt = _mm_set_epi32(0, gridz, gridy, gridx);
__m128 one = _mm_set1_ps(1);
__m128 scale = _mm_set1_ps(1.0f/(PME_ORDER-1));
fvec4 boxSize((float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2], 0);
fvec4 invBoxSize((float) (1/periodicBoxSize[0]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[2]), 0);
fvec4 gridSize(gridx, gridy, gridz, 0);
ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1);
fvec4 scale(1.0f/(PME_ORDER-1));
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
memset(grid, 0, sizeof(float)*gridx*gridy*gridz);
for (int i = start; i < end; i++) {
// Find the position relative to the nearest grid point.
__m128 pos = _mm_loadu_ps(&posq[4*i]);
__m128 posFloor = _mm_floor_ps(_mm_mul_ps(pos, invBoxSize));
__m128 posInBox = _mm_sub_ps(pos, _mm_mul_ps(boxSize, posFloor));
__m128 t = _mm_mul_ps(_mm_mul_ps(posInBox, invBoxSize), gridSize);
__m128i ti = _mm_cvttps_epi32(t);
__m128 dr = _mm_sub_ps(t, _mm_cvtepi32_ps(ti));
__m128i gridIndex = _mm_sub_epi32(ti, _mm_and_si128(gridSizeInt, _mm_cmpeq_epi32(ti, gridSizeInt)));
fvec4 pos(&posq[4*i]);
fvec4 posFloor = floor(pos*invBoxSize);
fvec4 posInBox = pos-boxSize*posFloor;
fvec4 t = posInBox*invBoxSize*gridSize;
ivec4 ti = t;
fvec4 dr = t-ti;
ivec4 gridIndex = ti-(gridSizeInt&ti==gridSizeInt);
// Compute the B-spline coefficients.
__m128 data[PME_ORDER];
data[PME_ORDER-1] = _mm_setzero_ps();
fvec4 data[PME_ORDER];
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
data[0] = _mm_sub_ps(one, dr);
data[0] = one-dr;
for (int j = 3; j < PME_ORDER; j++) {
__m128 div = _mm_set1_ps(1.0f/(j-1));
data[j-1] = _mm_mul_ps(_mm_mul_ps(div, dr), data[j-2]);
fvec4 div(1.0f/(j-1));
data[j-1] = div*dr*data[j-2];
for (int k = 1; k < j-1; k++)
data[j-k-1] = _mm_mul_ps(div, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(k)), data[j-k-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(j-k), dr), data[j-k-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(div, _mm_sub_ps(one, dr)), data[0]);
data[j-k-1] = div*((dr+k)*data[j-k-2]+(fvec4(j-k)-dr)*data[j-k-1]);
data[0] = div*(one-dr)*data[0];
}
data[PME_ORDER-1] = _mm_mul_ps(_mm_mul_ps(scale, dr), data[PME_ORDER-2]);
data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = _mm_mul_ps(scale, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(j)), data[PME_ORDER-j-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(PME_ORDER-j), dr), data[PME_ORDER-j-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(scale, _mm_sub_ps(one, dr)), data[0]);
data[PME_ORDER-j-1] = scale*((dr+j)*data[PME_ORDER-j-2]+(fvec4(PME_ORDER-j)-dr)*data[PME_ORDER-j-1]);
data[0] = scale*(one-dr)*data[0];
// Spread the charges.
int gridIndexX = _mm_extract_epi32(gridIndex, 0);
int gridIndexY = _mm_extract_epi32(gridIndex, 1);
int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
int gridIndexX = gridIndex[0];
int gridIndexY = gridIndex[1];
int gridIndexZ = gridIndex[2];
if (gridIndexX < 0)
return; // This happens when a simulation blows up and coordinates become NaN.
int zindex[PME_ORDER];
......@@ -101,21 +99,21 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
zindex[j] -= (zindex[j] >= gridz ? gridz : 0);
}
float charge = epsilonFactor*posq[4*i+3];
__m128 zdata0to3 = _mm_set_ps(EXTRACT_FLOAT(data[3], 2), EXTRACT_FLOAT(data[2], 2), EXTRACT_FLOAT(data[1], 2), EXTRACT_FLOAT(data[0], 2));
float zdata4 = EXTRACT_FLOAT(data[4], 2);
fvec4 zdata0to3(data[0][2], data[1][2], data[2][2], data[3][2]);
float zdata4 = data[4][2];
if (gridIndexZ+4 < gridz) {
for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float xdata = charge*EXTRACT_FLOAT(data[ix], 0);
float xdata = charge*data[ix][0];
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float multiplier = xdata*EXTRACT_FLOAT(data[iy], 1);
__m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier));
_mm_storeu_ps(&grid[ybase+gridIndexZ], _mm_add_ps(_mm_loadu_ps(&grid[ybase+gridIndexZ]), add0to3));
float multiplier = xdata*data[iy][1];
fvec4 add0to3 = zdata0to3*multiplier;
(fvec4(&grid[ybase+gridIndexZ])+add0to3).store(&grid[ybase+gridIndexZ]);
grid[ybase+zindex[4]] += multiplier*zdata4;
}
}
......@@ -125,14 +123,14 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float xdata = charge*EXTRACT_FLOAT(data[ix], 0);
float xdata = charge*data[ix][0];
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float multiplier = xdata*EXTRACT_FLOAT(data[iy], 1);
__m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier));
_mm_store_ps(temp, add0to3);
float multiplier = xdata*data[iy][1];
fvec4 add0to3 = zdata0to3*multiplier;
add0to3.store(temp);
grid[ybase+zindex[0]] += temp[0];
grid[ybase+zindex[1]] += temp[1];
grid[ybase+zindex[2]] += temp[2];
......@@ -245,51 +243,51 @@ static void reciprocalConvolution(int start, int end, fftwf_complex* grid, int g
}
static void interpolateForces(int start, int end, float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
__m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
__m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0]));
__m128 gridSize = _mm_set_ps(0, gridz, gridy, gridx);
__m128i gridSizeInt = _mm_set_epi32(0, gridz, gridy, gridx);
__m128 one = _mm_set1_ps(1);
__m128 scale = _mm_set1_ps(1.0f/(PME_ORDER-1));
fvec4 boxSize((float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2], 0);
fvec4 invBoxSize((float) (1/periodicBoxSize[0]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[2]), 0);
fvec4 gridSize(gridx, gridy, gridz, 0);
ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1);
fvec4 scale(1.0f/(PME_ORDER-1));
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
for (int i = start; i < end; i++) {
// Find the position relative to the nearest grid point.
__m128 pos = _mm_loadu_ps(&posq[4*i]);
__m128 posFloor = _mm_floor_ps(_mm_mul_ps(pos, invBoxSize));
__m128 posInBox = _mm_sub_ps(pos, _mm_mul_ps(boxSize, posFloor));
__m128 t = _mm_mul_ps(_mm_mul_ps(posInBox, invBoxSize), gridSize);
__m128i ti = _mm_cvttps_epi32(t);
__m128 dr = _mm_sub_ps(t, _mm_cvtepi32_ps(ti));
__m128i gridIndex = _mm_sub_epi32(ti, _mm_and_si128(gridSizeInt, _mm_cmpeq_epi32(ti, gridSizeInt)));
fvec4 pos(&posq[4*i]);
fvec4 posFloor = floor(pos*invBoxSize);
fvec4 posInBox = pos-boxSize*posFloor;
fvec4 t = posInBox*invBoxSize*gridSize;
ivec4 ti = t;
fvec4 dr = t-ti;
ivec4 gridIndex = ti-(gridSizeInt&ti==gridSizeInt);
// Compute the B-spline coefficients.
__m128 data[PME_ORDER];
__m128 ddata[PME_ORDER];
data[PME_ORDER-1] = _mm_setzero_ps();
fvec4 data[PME_ORDER];
fvec4 ddata[PME_ORDER];
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
data[0] = _mm_sub_ps(one, dr);
data[0] = one-dr;
for (int j = 3; j < PME_ORDER; j++) {
__m128 div = _mm_set1_ps(1.0f/(j-1));
data[j-1] = _mm_mul_ps(_mm_mul_ps(div, dr), data[j-2]);
fvec4 div(1.0f/(j-1));
data[j-1] = div*dr*data[j-2];
for (int k = 1; k < j-1; k++)
data[j-k-1] = _mm_mul_ps(div, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(k)), data[j-k-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(j-k), dr), data[j-k-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(div, _mm_sub_ps(one, dr)), data[0]);
data[j-k-1] = div*((dr+k)*data[j-k-2]+(fvec4(j-k)-dr)*data[j-k-1]);
data[0] = div*(one-dr)*data[0];
}
ddata[0] = _mm_sub_ps(_mm_set1_ps(0), data[0]);
ddata[0] = -data[0];
for (int j = 1; j < PME_ORDER; j++)
ddata[j] = _mm_sub_ps(data[j-1], data[j]);
data[PME_ORDER-1] = _mm_mul_ps(_mm_mul_ps(scale, dr), data[PME_ORDER-2]);
ddata[j] = data[j-1]-data[j];
data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = _mm_mul_ps(scale, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(j)), data[PME_ORDER-j-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(PME_ORDER-j), dr), data[PME_ORDER-j-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(scale, _mm_sub_ps(one, dr)), data[0]);
data[PME_ORDER-j-1] = scale*((dr+j)*data[PME_ORDER-j-2]+(fvec4(PME_ORDER-j)-dr)*data[PME_ORDER-j-1]);
data[0] = scale*(one-dr)*data[0];
// Compute the force on this atom.
int gridIndexX = _mm_extract_epi32(gridIndex, 0);
int gridIndexY = _mm_extract_epi32(gridIndex, 1);
int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
int gridIndexX = gridIndex[0];
int gridIndexY = gridIndex[1];
int gridIndexZ = gridIndex[2];
if (gridIndexX < 0)
return; // This happens when a simulation blows up and coordinates become NaN.
int zindex[PME_ORDER];
......@@ -297,34 +295,34 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
zindex[j] = gridIndexZ+j;
zindex[j] -= (zindex[j] >= gridz ? gridz : 0);
}
__m128 zdata[PME_ORDER];
fvec4 zdata[PME_ORDER];
for (int j = 0; j < PME_ORDER; j++)
zdata[j] = _mm_set_ps(0, EXTRACT_FLOAT(ddata[j], 2), EXTRACT_FLOAT(data[j], 2), EXTRACT_FLOAT(data[j], 2));
__m128 f = _mm_set1_ps(0);
zdata[j] = fvec4(data[j][2], data[j][2], ddata[j][2], 0);
fvec4 f = 0.0f;
for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float dx = EXTRACT_FLOAT(data[ix], 0);
float ddx = EXTRACT_FLOAT(ddata[ix], 0);
__m128 xdata = _mm_set_ps(0, dx, dx, ddx);
float dx = data[ix][0];
float ddx = ddata[ix][0];
fvec4 xdata(ddx, dx, dx, 0);
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float dy = EXTRACT_FLOAT(data[iy], 1);
float ddy = EXTRACT_FLOAT(ddata[iy], 1);
__m128 xydata = _mm_mul_ps(xdata, _mm_set_ps(0, dy, ddy, dy));
float dy = data[iy][1];
float ddy = ddata[iy][1];
fvec4 xydata = xdata*fvec4(dy, ddy, dy, 0);
for (int iz = 0; iz < PME_ORDER; iz++) {
__m128 gridValue = _mm_set1_ps(grid[ybase+zindex[iz]]);
f = _mm_add_ps(f, _mm_mul_ps(xydata, _mm_mul_ps(zdata[iz], gridValue)));
fvec4 gridValue(grid[ybase+zindex[iz]]);
f = f+xydata*zdata[iz]*gridValue;
}
}
}
f = _mm_mul_ps(invBoxSize, _mm_mul_ps(gridSize, _mm_mul_ps(f, _mm_set1_ps(-epsilonFactor*posq[4*i+3]))));
_mm_store_ps(&force[4*i], f);
f = invBoxSize*gridSize*f*(-epsilonFactor*posq[4*i+3]);
f.store(&force[4*i]);
}
}
......@@ -509,10 +507,10 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
threadWait();
int numGrids = threadData.size();
for (int i = gridStart; i < gridEnd; i += 4) {
__m128 sum = _mm_load_ps(&realGrid[i]);
fvec4 sum(&realGrid[i]);
for (int j = 1; j < numGrids; j++)
sum = _mm_add_ps(sum, _mm_load_ps(&threadData[j]->tempGrid[i]));
_mm_store_ps(&realGrid[i], sum);
sum += fvec4(&threadData[j]->tempGrid[i]);
sum.store(&realGrid[i]);
}
threadWait();
if (lastBoxSize != periodicBoxSize) {
......
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ 8167c79b
......@@ -61,6 +61,11 @@ class GBn(object):
return 'GBn'
GBn = GBn()
class GBn2(object):
def __repr__(self):
return 'GBn2'
GBn2 = GBn2()
class AmberPrmtopFile(object):
"""AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""
......@@ -69,6 +74,7 @@ class AmberPrmtopFile(object):
top = Topology()
## The Topology read from the prmtop file
self.topology = top
self.elements = []
# Load the prmtop file
......@@ -96,21 +102,30 @@ class AmberPrmtopFile(object):
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
# Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.get_by_symbol(atomName[0])
element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology
......@@ -137,7 +152,7 @@ class AmberPrmtopFile(object):
- constraints (object=None) Specifies which bonds angles should be implemented with constraints.
Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, or GBn.
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
- soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
- solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
......@@ -167,19 +182,22 @@ class AmberPrmtopFile(object):
raise ValueError('Illegal value for constraints')
if implicitSolvent is None:
implicitString = None
elif implicitSolvent == HCT:
elif implicitSolvent is HCT:
implicitString = 'HCT'
elif implicitSolvent == OBC1:
elif implicitSolvent is OBC1:
implicitString = 'OBC1'
elif implicitSolvent == OBC2:
elif implicitSolvent is OBC2:
implicitString = 'OBC2'
elif implicitSolvent == GBn:
elif implicitSolvent is GBn:
implicitString = 'GBn'
elif implicitSolvent is GBn2:
implicitString = 'GBn2'
else:
raise ValueError('Illegal value for implicit solvent model')
sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater)
soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater,
elements=self.elements)
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == elem.hydrogen:
......
wrappers/python/simtk/openmm/app/element.py
View file @ 8167c79b
......@@ -203,3 +203,8 @@ ununtrium = Element(113, "ununtrium", "Uut", 284*daltons)
ununquadium = Element(114, "ununquadium", "Uuq", 289*daltons)
ununpentium = Element(115, "ununpentium", "Uup", 288*daltons)
ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons)
# Aliases to recognize common alternative spellings. Both the '==' and 'is'
# relational operators will work with any chosen name
sulphur = sulfur
aluminium = aluminum
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 8167c79b
......@@ -52,6 +52,7 @@ except:
import simtk.unit as units
import simtk.openmm
from simtk.openmm.app import element as elem
import customgbforces as customgb
#=============================================================================================
......@@ -472,34 +473,74 @@ class PrmtopLoader(object):
self._excludedAtoms.append(atomList)
return self._excludedAtoms
def getGBParms(self, symbls=None):
def getGBParms(self, gbmodel, elements):
"""Return list giving GB params, Radius and screening factor"""
try:
return self._gb_List
except AttributeError:
pass
self._gb_List=[]
radii=self._raw_data["RADII"]
screen=self._raw_data["SCREEN"]
gb_List=[]
radii=[float(r) for r in self._raw_data["RADII"]]
screen=[float(s) for s in self._raw_data["SCREEN"]]
if gbmodel == 'GBn2':
alpha = [0 for i in self._raw_data['RADII']]
beta = [0 for i in self._raw_data['RADII']]
gamma = [0 for i in self._raw_data['RADII']]
# Update screening parameters for GBn if specified
if symbls:
for (i, symbl) in enumerate(symbls):
if symbl[0] in ('c', 'C'):
if gbmodel == 'GBn':
if elements is None:
raise Exception('GBn model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 0.48435382330
elif symbl[0] in ('h', 'H'):
elif element is elem.hydrogen:
screen[i] = 1.09085413633
elif symbl[0] in ('n', 'N'):
elif element is elem.nitrogen:
screen[i] = 0.700147318409
elif symbl[0] in ('o', 'O'):
elif element is elem.oxygen:
screen[i] = 1.06557401132
elif symbl[0] in ('s', 'S'):
elif element is elem.sulfur:
screen[i] = 0.602256336067
else:
screen[i] = 0.5
if gbmodel == 'GBn2':
if elements is None:
raise Exception('GBn2 model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 1.058554
alpha[i] = 0.733756
beta[i] = 0.506378
gamma[i] = 0.205844
elif element is elem.hydrogen:
screen[i] = 1.425952
alpha[i] = 0.788440
beta[i] = 0.798699
gamma[i] = 0.437334
elif element is elem.nitrogen:
screen[i] = 0.733599
alpha[i] = 0.503364
beta[i] = 0.316828
gamma[i] = 0.192915
elif element is elem.oxygen:
screen[i] = 1.061039
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
elif element is elem.sulfur:
screen[i] = -0.703469
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
else: # not optimized
screen[i] = 0.5
alpha[i] = 1.0
beta[i] = 0.8
gamma[i] = 4.85
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
for iAtom in range(len(radii)):
self._gb_List.append((float(radii[iAtom])*lengthConversionFactor, float(screen[iAtom])))
return self._gb_List
if gbmodel == 'GBn2':
for rad, scr, alp, bet, gam in zip(radii, screen, alpha, beta, gamma):
gb_List.append((rad*lengthConversionFactor, scr, alp, bet, gam))
else:
for rad, scr in zip(radii, screen):
gb_List.append((rad*lengthConversionFactor, scr))
return gb_List
def getBoxBetaAndDimensions(self):
"""Return periodic boundary box beta angle and dimensions"""
......@@ -516,11 +557,17 @@ class PrmtopLoader(object):
def has_scee_scnb(self):
return ("SCEE_SCALE_FACTOR" in self._raw_data and "SCNB_SCALE_FACTOR" in self._raw_data)
@property
def has_atomic_number(self):
return 'ATOMIC_NUMBER' in self._raw_data
#=============================================================================================
# AMBER System builder (based on, but not identical to, systemManager from 'zander')
#=============================================================================================
def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True):
def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5,
nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True, elements=None):
"""
Create an OpenMM System from an Amber prmtop file.
......@@ -813,15 +860,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if gbmodel is not None:
if verbose: print "Adding GB parameters..."
charges = prmtop.getCharges()
symbls = None
cutoff = None
if nonbondedMethod != 'NoCutoff':
cutoff = nonbondedCutoff
if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers)
if gbmodel == 'GBn':
symbls = prmtop.getAtomTypes()
gb_parms = prmtop.getGBParms(symbls)
gb_parms = prmtop.getGBParms(gbmodel, elements)
if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
elif gbmodel == 'OBC1':
......@@ -832,11 +876,16 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
gb.setSolventDielectric(solventDielectric)
elif gbmodel == 'GBn':
gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
elif gbmodel == 'GBn2':
gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff)
else:
raise Exception("Illegal value specified for implicit solvent model")
for iAtom in range(prmtop.getNumAtoms()):
if gbmodel == 'OBC2':
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
elif gbmodel == 'GBn2':
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
gb_parms[iAtom][2], gb_parms[iAtom][3], gb_parms[iAtom][4]])
else:
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
system.addForce(gb)
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 8167c79b
......@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts
Contributors:
Contributors: Jason M. Swails
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -29,8 +29,9 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from simtk.openmm import CustomGBForce
import sys, pdb, pickle
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
......@@ -212,11 +213,11 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
......@@ -237,11 +238,11 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
......@@ -262,11 +263,11 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
......@@ -296,12 +297,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68)
......@@ -323,3 +324,50 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom
"""
Amber Equivalents: igb = 8
"""
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.0195141)
custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom
wrappers/python/simtk/openmm/app/internal/pdbstructure.py
View file @ 8167c79b
......@@ -436,7 +436,7 @@ class Chain(object):
self._finalize()
def get_residue(self, residue_number, insertion_code=' '):
return residues_by_num_icode[str(residue_number) + insertion_code]
return self.residues_by_num_icode[str(residue_number) + insertion_code]
def __contains__(self, residue_number):
return self.residues_by_number.__contains__(residue_number)
......@@ -916,7 +916,6 @@ if __name__=='__main__':
import doctest, sys
doctest.testmod(sys.modules[__name__])
import sys
import os
import gzip
import re
......
wrappers/python/simtk/openmm/app/statedatareporter.py
View file @ 8167c79b
......@@ -31,9 +31,10 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
__author__ = "Peter Eastman"
__version__ = "1.0"
import bz2
import gzip
import simtk.openmm as mm
import simtk.unit as unit
from simtk.openmm.app import PDBFile
import math
class StateDataReporter(object):
......@@ -67,7 +68,14 @@ class StateDataReporter(object):
self._reportInterval = reportInterval
self._openedFile = isinstance(file, str)
if self._openedFile:
self._out = open(file, 'w', 0)
# Detect the desired compression scheme from the filename extension
# and open all files unbuffered
if file.endswith('.gz'):
self._out = gzip.GzipFile(fileobj=open(file, 'wb', 0))
elif file.endswith('.bz2'):
self._out = bz2.BZ2File(file, 'w', 0)
else:
self._out = open(file, 'w', 0)
else:
self._out = file
self._step = step
......@@ -109,7 +117,10 @@ class StateDataReporter(object):
self._initializeConstants(simulation)
headers = self._constructHeaders()
print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers)
self._out.flush()
try:
self._out.flush()
except AttributeError:
pass
self._hasInitialized = True
# Check for errors.
......@@ -120,7 +131,10 @@ class StateDataReporter(object):
# Write the values.
print >>self._out, self._separator.join(str(v) for v in values)
self._out.flush()
try:
self._out.flush()
except AttributeError:
pass
def _constructReportValues(self, simulation, state):
"""Query the simulation for the current state of our observables of interest.
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 8167c79b
......@@ -145,6 +145,8 @@ SKIP_METHODS = [('State',),
('IntegrateDrudeSCFStepKernel',),
('XmlSerializer', 'serialize'),
('XmlSerializer', 'deserialize'),
('fvec4',),
('ivec4',),
]
# The build script assumes method args that are non-const references are
......
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