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FFParticle.cpp
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FFParticle.cpp
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/*******************************************************************************
GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
Copyright (C) 2018 GOMC Group
A copy of the GNU General Public License can be found in the COPYRIGHT.txt
along with this program, also can be found at <http://www.gnu.org/licenses/>.
********************************************************************************/
#include "FFParticle.h"
#include "ConfigSetup.h"
#include "NumLib.h" //For Sq, Cb, and MeanA/G functions.
#ifdef GOMC_CUDA
#include "ConstantDefinitionsCUDAKernel.cuh"
#endif
FFParticle::FFParticle() : mass(NULL), nameFirst(NULL), nameSec(NULL),
n(NULL), n_1_4(NULL), sigmaSq(NULL),
sigmaSq_1_4(NULL), epsilon_cn(NULL), epsilon(NULL),
epsilon_1_4(NULL), epsilon_cn_1_4(NULL), epsilon_cn_6(NULL),
epsilon_cn_6_1_4(NULL), nOver6(NULL),
nOver6_1_4(NULL), enCorrection(NULL),
virCorrection(NULL), shiftConst(NULL),
shiftConst_1_4(NULL), An(NULL),
Bn(NULL), Cn(NULL), An_1_4(NULL), Bn_1_4(NULL),
Cn_1_4(NULL), sig6(NULL), sign(NULL),
#ifdef GOMC_CUDA
varCUDA(NULL),
#endif
sig6_1_4(NULL), sign_1_4(NULL), rCut(0), rCutSq(0),
rOnSq(0), rOn(0), A6(0), B6(0), C6(0), factor1(0),
factor2(0) {}
FFParticle::~FFParticle(void)
{
delete[] mass;
delete[] nameFirst;
delete[] nameSec;
delete[] sigmaSq;
delete[] n;
delete[] epsilon;
delete[] epsilon_cn;
delete[] epsilon_cn_6;
delete[] nOver6;
// parameter for 1-4 interaction, same one will be used for 1-3 interaction
delete[] sigmaSq_1_4;
delete[] n_1_4;
delete[] epsilon_1_4;
delete[] epsilon_cn_1_4;
delete[] epsilon_cn_6_1_4;
delete[] nOver6_1_4;
delete[] enCorrection;
delete[] virCorrection;
delete[] shiftConst;
delete[] An;
delete[] Bn;
delete[] Cn;
delete[] sig6;
delete[] sign;
// parameter for 1-4 interaction, same one will be used for 1-3 interaction
delete[] shiftConst_1_4;
delete[] An_1_4;
delete[] Bn_1_4;
delete[] Cn_1_4;
delete[] sig6_1_4;
delete[] sign_1_4;
#ifdef GOMC_CUDA
DestroyCUDAVars(varCUDA);
delete varCUDA;
#endif
}
void FFParticle::Init(ff_setup::Particle const& mie,
ff_setup::NBfix const& nbfix,
config_setup::SystemVals const& sys,
config_setup::FFKind const& ffKind)
{
#ifdef GOMC_CUDA
// Variables for GPU stored in here
varCUDA = new VariablesCUDA();
#endif
count = mie.epsilon.size(); //Get # particles read
//Size LJ particle kind arrays
mass = new double [count];
vdwKind = sys.ff.VDW_KIND;
//Size LJ-LJ pair arrays
uint size = num::Sq(count);
nameFirst = new std::string [size];
nameSec = new std::string [size];
isMartini = ffKind.isMARTINI;
#ifdef MIE_INT_ONLY
n = new uint [size];
n_1_4 = new uint [size];
#else
n = new double [size];
n_1_4 = new double [size];
#endif
epsilon = new double [size];
epsilon_cn = new double [size];
epsilon_cn_6 = new double [size];
nOver6 = new double [size];
sigmaSq = new double [size];
epsilon_1_4 = new double [size];
epsilon_cn_1_4 = new double [size];
epsilon_cn_6_1_4 = new double [size];
nOver6_1_4 = new double [size];
sigmaSq_1_4 = new double [size];
enCorrection = new double [size];
virCorrection = new double [size];
if(vdwKind == sys.ff.VDW_SHIFT_KIND) {
shiftConst = new double [size];
shiftConst_1_4 = new double [size];
}
rCut = sys.ff.cutoff;
rCutSq = rCut * rCut;
rCutLow = sys.ff.cutoffLow;
rCutLowSq = rCutLow * rCutLow;
scaling_14 = sys.elect.oneFourScale;
ewald = sys.elect.ewald;
alpha = sys.elect.alpha;
diElectric_1 = 1.0 / sys.elect.dielectric;
if(vdwKind == sys.ff.VDW_SWITCH_KIND && isMartini) {
An = new double [size];
Bn = new double [size];
Cn = new double [size];
An_1_4 = new double [size];
Bn_1_4 = new double [size];
Cn_1_4 = new double [size];
sign = new double [size];
sig6 = new double [size];
sign_1_4 = new double [size];
sig6_1_4 = new double [size];
rOn = sys.ff.rswitch;
//in Martini, Coulomb switching distance is zero
rOnCoul = 0.0;
rOnSq = rOn * rOn;
// LJ constants
A6 = 6.0 * ((6.0 + 1) * rOn - (6.0 + 4) * rCut) / (pow(rCut, 6.0 + 2) *
pow(rCut - rOn, 2));
B6 = -6.0 * ((6.0 + 1) * rOn - (6.0 + 3) * rCut) / (pow(rCut, 6.0 + 2) *
pow(rCut - rOn, 3));
C6 = 1.0 / pow(rCut, 6.0) - A6 / 3.0 * pow(rCut - rOn, 3) - B6 / 4.0 *
pow(rCut - rOn, 4);
// Coulomb constants
A1 = 1.0 * ((1.0 + 1) * rOnCoul - (1.0 + 4) * rCut) / (pow(rCut, 1.0 + 2) *
pow(rCut - rOnCoul, 2));
B1 = -1.0 * ((1.0 + 1) * rOnCoul - (1.0 + 3) * rCut) / (pow(rCut, 1.0 + 2) *
pow(rCut - rOnCoul, 3));
C1 = 1.0 / pow(rCut, 1.0) - A1 / 3.0 * pow(rCut - rOnCoul, 3) - B1 / 4.0 *
pow(rCut - rOnCoul, 4);
} else if(vdwKind == sys.ff.VDW_SWITCH_KIND && !isMartini) {
rOn = sys.ff.rswitch;
rOnSq = rOn * rOn;
factor1 = rCutSq - 3 * rOnSq;
factor2 = pow((rCutSq - rOnSq), -3);
}
Blend(mie, rCut);
AdjNBfix(mie, nbfix, rCut);
#ifdef GOMC_CUDA
InitGPUForceField(*varCUDA, sigmaSq, epsilon_cn, n, vdwKind, isMartini,
count, rCut, rCutLow, rOn, alpha, ewald, diElectric_1);
#endif
}
double FFParticle::EnergyLRC(const uint kind1, const uint kind2) const
{
return enCorrection[FlatIndex(kind1, kind2)];
}
double FFParticle::VirialLRC(const uint kind1, const uint kind2) const
{
return virCorrection[FlatIndex(kind1, kind2)];
}
void FFParticle::AdjNBfix(ff_setup::Particle const& mie,
ff_setup::NBfix const& nbfix, const double rCut)
{
uint size = num::Sq(count);
for(uint i = 0; i < nbfix.epsilon.size(); i++) {
for(uint j = 0; j < size; j++) {
if(nbfix.getname(i) == nameFirst[j] || nbfix.getname(i) == nameSec[j]) {
n[j] = nbfix.n[i];
n_1_4[j] = nbfix.n_1_4[i];
double rRat = nbfix.sigma[i] / rCut, tc = 1.0;
//calculating sig^2 and tc*sig^3
num::Cb(sigmaSq[j], tc, nbfix.sigma[i]);
sigmaSq_1_4[j] = nbfix.sigma_1_4[i] * nbfix.sigma_1_4[i];
tc *= 0.5 * 4.0 * M_PI;
double cn = n[j] / (n[j] - 6) * pow(n[j] / 6, (6 / (n[j] - 6)));
double cn_1_4 = n_1_4[j] / (n_1_4[j] - 6) *
pow(n_1_4[j] / 6, (6 / (n_1_4[j] - 6)));
epsilon[j] = nbfix.epsilon[i];
epsilon_cn[j] = cn * nbfix.epsilon[i];
epsilon_1_4[j] = nbfix.epsilon_1_4[i];
epsilon_cn_1_4[j] = cn_1_4 * nbfix.epsilon_1_4[i];
epsilon_cn_6[j] = epsilon_cn[j] * 6;
epsilon_cn_6_1_4[j] = epsilon_cn_1_4[j] * 6;
nOver6[j] = n[j] / 6;
nOver6_1_4[j] = n_1_4[j] / 6;
enCorrection[j] = tc / (n[j] - 3) * epsilon_cn[j] *
( pow(rRat, n[j] - 3) -
(double)(n[j] - 3.0) / 3.0 * pow(rRat, 3) );
virCorrection[j] = tc / (n[j] - 3) * epsilon_cn_6[j] *
( (double)(n[j]) / 6.0 * pow(rRat, n[j] - 3) -
(double)(n[j] - 3.0) / 3.0 * pow(rRat, 3) );
if(vdwKind == num::VDW_SHIFT_KIND) {
double rRat2 = sigmaSq[j] / rCutSq;
double rRat4 = rRat2 * rRat2;
double attract = rRat4 * rRat2;
//for 1-4 interaction
double rRat2_1_4 = sigmaSq_1_4[j] / rCutSq;
double rRat4_1_4 = rRat2_1_4 * rRat2_1_4;
double attract_1_4 = rRat4_1_4 * rRat2_1_4;
#ifdef MIE_INT_ONLY
double repulse = num::POW(rRat2, rRat4, attract, n[j]);
double repulse_1_4 =
num::POW(rRat2_1_4, rRat4_1_4, attract_1_4, n_1_4[j]);
#else
double repulse = pow(sqrt(rRat2), n[j]);
double repulse_1_4 = pow(sqrt(rRat2_1_4), n_1_4[j]);
#endif
shiftConst[j] = epsilon_cn[j] * (repulse - attract);
shiftConst_1_4[j] = epsilon_cn_1_4[j] *
(repulse_1_4 - attract_1_4);
}
if(vdwKind == num::VDW_SWITCH_KIND && isMartini) {
double pn = n[j];
An[j] = pn * ((pn + 1) * rOn - (pn + 4) * rCut) / (pow(rCut, pn + 2) *
pow(rCut - rOn, 2));
Bn[j] = -pn * ((pn + 1) * rOn - (pn + 3) * rCut) / (pow(rCut, pn + 2) *
pow(rCut - rOn, 3));
Cn[j] = 1.0 / pow(rCut, pn) - An[j] / 3.0 * pow(rCut - rOn, 3) -
Bn[j] / 4.0 * pow(rCut - rOn, 4);
sig6[j] = pow(nbfix.sigma[i], 6);
sign[j] = pow(nbfix.sigma[i], pn);
// for 1-4 interaction
double pn_1_4 = n_1_4[j];
An_1_4[j] = pn_1_4 * ((pn_1_4 + 1) * rOn - (pn_1_4 + 4) * rCut) /
(pow(rCut, pn_1_4 + 2) * pow(rCut - rOn, 2));
Bn_1_4[j] = -pn_1_4 * ((pn_1_4 + 1) * rOn - (pn_1_4 + 3) * rCut) /
(pow(rCut, pn_1_4 + 2) * pow(rCut - rOn, 3));
Cn_1_4[j] = 1.0 / pow(rCut, pn_1_4) - An_1_4[j] / 3.0 *
pow(rCut - rOn, 3) - Bn_1_4[j] / 4.0 * pow(rCut - rOn, 4);
sig6_1_4[j] = pow(nbfix.sigma_1_4[i], 6);
sign_1_4[j] = pow(nbfix.sigma_1_4[i], pn_1_4);
}
}
}
}
}
void FFParticle::Blend(ff_setup::Particle const& mie, const double rCut)
{
for(uint i = 0; i < count; ++i) {
for(uint j = 0; j < count; ++j) {
uint idx = FlatIndex(i, j);
//get all name combination for using in nbfix
nameFirst[idx] = mie.getname(i);
nameFirst[idx] += mie.getname(j);
nameSec[idx] = mie.getname(j);
nameSec[idx] += mie.getname(i);
n[idx] = num::MeanA(mie.n, mie.n, i, j);
n_1_4[idx] = num::MeanA(mie.n_1_4, mie.n_1_4, i, j);
double cn = n[idx] / (n[idx] - 6) * pow(n[idx] / 6, (6 / (n[idx] - 6)));
double sigma = num::MeanA(mie.sigma, mie.sigma, i, j);
double cn_1_4 = n_1_4[idx] / (n_1_4[idx] - 6) *
pow(n_1_4[idx] / 6, (6 / (n_1_4[idx] - 6)));
double sigma_1_4 = num::MeanA(mie.sigma_1_4, mie.sigma_1_4, i, j);
double tc = 1.0;
double rRat = sigma / rCut;
// calculate sig^2 and tc*sig^3
num::Cb(sigmaSq[idx], tc, sigma);
sigmaSq_1_4[idx] = sigma_1_4 * sigma_1_4;
tc *= 0.5 * 4.0 * M_PI;
epsilon[idx] = num::MeanG(mie.epsilon, mie.epsilon, i, j);
epsilon_cn[idx] = cn * epsilon[idx];
epsilon_1_4[idx] = num::MeanG(mie.epsilon_1_4, mie.epsilon_1_4, i, j);
epsilon_cn_1_4[idx] = cn * epsilon_1_4[idx];
epsilon_cn_6[idx] = epsilon_cn[idx] * 6;
epsilon_cn_6_1_4[idx] = epsilon_cn_1_4[idx] * 6;
nOver6[idx] = n[idx] / 6;
nOver6_1_4[idx] = n_1_4[idx] / 6;
enCorrection[idx] = tc / (n[idx] - 3) * epsilon_cn[idx] *
( pow(rRat, n[idx] - 3) -
(double)(n[idx] - 3.0) / 3.0 * pow(rRat, 3) );
virCorrection[idx] = tc / (n[idx] - 3) * epsilon_cn_6[idx] *
( (double)(n[idx]) / 6.0 * pow(rRat, n[idx] - 3) -
(double)(n[idx] - 3.0) / 3.0 * pow(rRat, 3) );
if(vdwKind == num::VDW_SHIFT_KIND) {
double rRat2 = sigmaSq[idx] / rCutSq;
double rRat4 = rRat2 * rRat2;
double attract = rRat4 * rRat2;
//for 1-4 interaction
double rRat2_1_4 = sigmaSq_1_4[idx] / rCutSq;
double rRat4_1_4 = rRat2_1_4 * rRat2_1_4;
double attract_1_4 = rRat4_1_4 * rRat2_1_4;
#ifdef MIE_INT_ONLY
double repulse = num::POW(rRat2, rRat4, attract, n[idx]);
double repulse_1_4 =
num::POW(rRat2_1_4, rRat4_1_4, attract_1_4, n_1_4[idx]);
#else
double repulse = pow(sqrt(rRat2), n[idx]);
double repulse_1_4 = pow(sqrt(rRat2_1_4), n_1_4[idx]);
#endif
shiftConst[idx] = epsilon_cn[idx] * (repulse - attract);
shiftConst_1_4[idx] = epsilon_cn_1_4[idx] *
(repulse_1_4 - attract_1_4);
}
if(vdwKind == num::VDW_SWITCH_KIND && isMartini) {
double pn = n[idx];
An[idx] = pn * ((pn + 1) * rOn - (pn + 4) * rCut) / (pow(rCut, pn + 2) *
pow(rCut - rOn, 2));
Bn[idx] = -pn * ((pn + 1) * rOn - (pn + 3) * rCut) / (pow(rCut, pn + 2) *
pow(rCut - rOn, 3));
Cn[idx] = 1.0 / pow(rCut, pn) - An[idx] / 3.0 * pow(rCut - rOn, 3) -
Bn[idx] / 4.0 * pow(rCut - rOn, 4);
sig6[idx] = pow(sigma, 6);
sign[idx] = pow(sigma, pn);
// for 1-4 interaction
double pn_1_4 = n_1_4[idx];
An_1_4[idx] = pn_1_4 * ((pn_1_4 + 1) * rOn - (pn_1_4 + 4) * rCut) /
(pow(rCut, pn_1_4 + 2) * pow(rCut - rOn, 2));
Bn_1_4[idx] = -pn_1_4 * ((pn_1_4 + 1) * rOn - (pn_1_4 + 3) * rCut) /
(pow(rCut, pn_1_4 + 2) * pow(rCut - rOn, 3));
Cn_1_4[idx] = 1.0 / pow(rCut, pn_1_4) - An_1_4[idx] / 3.0 *
pow(rCut - rOn, 3) - Bn_1_4[idx] / 4.0 * pow(rCut - rOn, 4);
sig6_1_4[idx] = pow(sigma_1_4, 6);
sign_1_4[idx] = pow(sigma_1_4, pn_1_4);
}
}
}
}
double FFParticle::GetEpsilon(const uint i, const uint j) const
{
uint idx = FlatIndex(i, j);
return epsilon[idx];
}
double FFParticle::GetEpsilon_1_4(const uint i, const uint j) const
{
uint idx = FlatIndex(i, j);
return epsilon_1_4[idx];
}
double FFParticle::GetSigma(const uint i, const uint j) const
{
uint idx = FlatIndex(i, j);
return sqrt(sigmaSq[idx]);
}
double FFParticle::GetSigma_1_4(const uint i, const uint j) const
{
uint idx = FlatIndex(i, j);
return sqrt(sigmaSq_1_4[idx]);
}
double FFParticle::GetN(const uint i, const uint j) const
{
uint idx = FlatIndex(i, j);
return n[idx];
}
double FFParticle::GetN_1_4(const uint i, const uint j) const
{
uint idx = FlatIndex(i, j);
return n_1_4[idx];
}