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ComputeGBISser.C
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ComputeGBISser.C
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/**
*** Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by
*** The Board of Trustees of the University of Illinois.
*** All rights reserved.
**/
/*******************************************************************************
*******************************************************************************
This serial version of GBIS is out of date and hasn't been vetted;
it is to be used as a way of testing new implicit solvent models
since all atomic coordinates are gathered into a single Compute.
*******************************************************************************
******************************************************************************/
/*
print debug
1 - once per step
2 - once per atom
3 - once per pair
*/
//#define PRINT_SERFORCES
#define BENCH_PERIOD 1000
//sum all forces
#define GBIS_DEDR_FORCE 1
#define GBIS_DEDA_FORCE 1
#define GBIS_COUL_FORCE 1
#include "Vector.h"
#include <limits>
#include "InfoStream.h"
#include "Node.h"
#include "PatchMap.h"
#include "PatchMap.inl"
#include "AtomMap.h"
#include "ComputeGBISser.h"
#include "ComputeGBISserMgr.decl.h"
#include "PatchMgr.h"
#include "Molecule.h"
#include "ReductionMgr.h"
#include "ComputeMgr.h"
#include "ComputeMgr.decl.h"
#include "ComputeGBIS.inl"
// #define DEBUGM
#define MIN_DEBUG_LEVEL 3
#include "Debug.h"
#include "SimParameters.h"
#include "WorkDistrib.h"
#include "varsizemsg.h"
#include <stdlib.h>
#include <stdio.h>
#include <errno.h>
#include <time.h>
struct vect {
BigReal x, y, z;
};
#ifndef COUL_CONST
#define COUL_CONST 332.0636 // ke [kcal*Ang/e^2]
#endif
#ifndef TA
#define TA 0.333333333333333 // 1/3
#define TB 0.4 // 2/5
#define TC 0.428571428571428 // 3/7
#define TD 0.444444444444444 // 4/9
#define TE 0.454545454545454 // 5/11
#define DA 1.333333333333333 // 4* 1/3
#define DB 2.4 // 6* 2/5
#define DC 3.428571428571428 // 8* 3/7
#define DD 4.444444444444444 // 10*4/9
#define DE 5.454545454545454 // 12*5/11
#endif
inline void Phase2_PairSer(//doesn't do self energies
//input values
BigReal r,
BigReal r2,
BigReal r_i,
BigReal qiqj,
BigReal ai,
BigReal aj,
BigReal epsilon_p_i,
BigReal epsilon_s_i,
BigReal kappa,
int exclij,
BigReal scale14,
int stat,
//return values
BigReal & coulEij,
BigReal & ddrCoulEij,
BigReal & gbEij,
BigReal & ddrGbEij,
BigReal & dEdai,
BigReal & dEdaj
);
inline void CalcHPairSer (
BigReal r,//distance
BigReal r2,
BigReal ri,
BigReal rc,//cutoff
BigReal ri0,
BigReal rjs,
BigReal rj0,
BigReal ris,
int & dij,//domain 1
int & dji,//domain 2
BigReal & dhij,
BigReal & dhji);
inline void CalcDHPairSer (
BigReal r,//distance
BigReal r2,
BigReal ri,
BigReal rc,//cutoff
BigReal ri0,
BigReal rjs,
BigReal rj0,
BigReal ris,
int & dij,//domain 1
int & dji,//domain 2
BigReal & dhij,
BigReal & dhji);
struct ComputeGBISAtom {
Position position;
Real charge;
Real rho;//coulomb radius
Real rho0;//coulomb radius
Real rhos;//coulomb radius
Mass mass;
//int type;//atom type for S scaling table
int id;
int vdwType;
};
class GBISCoordMsg : public CMessage_GBISCoordMsg {
public:
int sourceNode;
int numAtoms;
int doSlow;
ComputeGBISAtom *coord;
int sequence;
};
class GBISForceMsg : public CMessage_GBISForceMsg {
public:
BigReal gbInterEnergy;
BigReal gbSelfEnergy;
BigReal coulEnergy;
ExtForce *force;
ExtForce *slowForce;
};
class ComputeGBISserMgr : public CBase_ComputeGBISserMgr {
public:
ComputeGBISserMgr();
~ComputeGBISserMgr();
void setCompute(ComputeGBISser *c) { gbisCompute = c; }
void recvCoord(GBISCoordMsg *);
void recvForce(GBISForceMsg *);
private:
CProxy_ComputeGBISserMgr gbisProxy;
ComputeGBISser *gbisCompute;
int numSources;
int numArrived;
GBISCoordMsg **coordMsgs;
int numAtoms;
ComputeGBISAtom *coord;
ExtForce *force;
ExtForce *slowForce;
GBISForceMsg *oldmsg;
BigReal gbSelfEnergy;
BigReal gbInterEnergy;
BigReal coulEnergy;
int timestep;
clock_t t_start;
clock_t t_stop;
clock_t t1, t2;
double totalnamdtime;
double totalgbistime;
double inittime;
double psitime;
double alphatime;
double dEdrtime;
double dEdasumtime;
double dEdaprefixtime;
double dEdalooptime;
void calcGBISReg(int stat);
int blockSize;
int numBlocks;
int loop1Iter, loop2Iter, loop3Iter;
bool all2all;
BigReal MinErr;
BigReal MaxErr;
int numBins;
BigReal base;
};
ComputeGBISserMgr::ComputeGBISserMgr() :
gbisProxy(thisgroup), gbisCompute(0), numSources(0), numArrived(0),
inittime(0),
psitime(0),
alphatime(0),
dEdrtime(0),
dEdasumtime(0),
dEdaprefixtime(0),
dEdalooptime(0), slowForce(0),
coordMsgs(0), coord(0), force(0), oldmsg(0), numAtoms(0), timestep(0) {
CkpvAccess(BOCclass_group).computeGBISserMgr = thisgroup;
t_start = clock();
t_stop = clock();
all2all = false;
}
ComputeGBISserMgr::~ComputeGBISserMgr() {
for ( int i=0; i<numSources; ++i ) { delete coordMsgs[i]; }
delete [] coordMsgs;
delete [] coord;
delete [] force;
delete [] slowForce;
delete oldmsg;
}
ComputeGBISser::ComputeGBISser(ComputeID c) :
ComputeHomePatches(c)
{
CProxy_ComputeGBISserMgr::ckLocalBranch(
CkpvAccess(BOCclass_group).computeGBISserMgr)->setCompute(this);
reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);
}
ComputeGBISser::~ComputeGBISser()
{
}
/******************************************************************************
* scale from 1 to 0 between transition and cutoff
* s = 1 for [0,trans]
* s = s(r) for [trans, cutoff]
* s = 0 for [cutoff, infinity]
* meets the following 4 conditions:
* (1) s(trans) = 1
* (3) s'(trans) = 0
* (2) s(cutoff) = 0
* (4) s'(cutoff) = 0
******************************************************************************/
inline void CalcScaleSer (
BigReal r,//rij
BigReal t,//transition distance
BigReal c,//cutoff distance
BigReal & s,//output s(r)
BigReal & d ) {//output s'(r)
if (r <= t) { //[0,trans]
s = 1;
d = 0;
} else if (r < c) { //[trans,cutoff]
//precompute
BigReal ct = (c-t);
BigReal ct_i = 1/ct;
BigReal ct_i2 = ct_i*ct_i;
//BigReal ct_i4 = ct_i2*ct_i2;
BigReal rt = r - t;
BigReal rt2 = rt*rt;
BigReal omrtct2 = 1-rt2*ct_i2;
s = omrtct2*omrtct2;
BigReal rc = r - c;
d=s*4*rt/(rc*(rt+ct));
} else { //[cutoff,infinity]
s = 0;
d = 0;
}
}
/**********************************************************
*
* Regular 3 sets of nested loops
*
* supports 1-2-4 scheme
*
**********************************************************/
void ComputeGBISserMgr::calcGBISReg(int stat) {
t1 = clock();
//printf("GBIS: ComputeGBIS::serial\n");
/*********************************************************
* Initializations
********************************************************/
Molecule *molecule = Node::Object()->molecule;
SimParameters *simParams = Node::Object()->simParameters;
BigReal epsilon_s = simParams->solvent_dielectric;
BigReal epsilon_p = simParams->dielectric;
BigReal epsilon_s_i = 1/epsilon_s;
BigReal epsilon_p_i = 1/epsilon_p;
BigReal rho_0 = simParams->coulomb_radius_offset;
BigReal cutoff = simParams->cutoff;// + 1.8*0.96;//+max screen radius
BigReal trans = simParams->switchingDist;
BigReal fsMax = 1.728;
BigReal a_cut = simParams->alpha_cutoff-fsMax;//+max screen radius; partial sphere
//a_cut = 10;
BigReal a_cut2 = a_cut*a_cut;
BigReal a_cut_ps = a_cut + fsMax;//+max screen radius; partial sphere
BigReal cutoff2 = cutoff*cutoff;
BigReal a_cut_ps2 = a_cut_ps*a_cut_ps;
BigReal delta = simParams->gbis_delta;
BigReal beta = simParams->gbis_beta;
BigReal gamma = simParams->gbis_gamma;
BigReal alphaMax = simParams->alpha_max;
int exclude = simParams->exclude;
BigReal scale14 = (exclude==SCALED14) ? simParams->scale14 : 1.0;
#if PRINT > 0
//printf("cut=%e, rgbmax=%e, fsmax=%e, gbalpha=%e, gbbeta=%e, gbgamma=%e\n", cutoff, alphaMax, fsMax, delta, beta, gamma);
#endif
//calc kappa
BigReal kappa = simParams->kappa;
//debugging variables
gbInterEnergy = 0;
gbSelfEnergy = 0;
coulEnergy = 0;
BigReal fx, fy, fz;
loop1Iter = 0;
loop2Iter = 0;
loop3Iter = 0;
int loop1flops = 0;
int loop2flops = 0;
int loop3flops = 0;
BigReal loop1time = 0;
BigReal loop2time = 0;
BigReal loop3time = 0;
Position ri, rj;
BigReal rhoi, rhoi0, rhois;
BigReal rhoj, rhoj0, rhojs;
BigReal dx, dy, dz;
BigReal r, r2, r_i, qiqj;
BigReal rnx, rny, rnz;
BigReal bornRad;
BigReal aiaj, aiaj4, expr2aiaj4, fij, finv, expkappa, Dij;
BigReal rc, shift, ddrshift;
BigReal tmp_dEda, dEdai, dEdaj, gbEij;
BigReal ddrfij, ddrfinv, ddrDij, ddrGbEij;
BigReal coulEij, ddrCoulEij;
BigReal forceCoul, forcedEdr, forceAlpha;
BigReal hij, hji, ddrHij, ddrHji;
BigReal tanhi, daidr, dajdr;
BigReal nbetapsi, gammapsi2;
vect *coulForce = new vect[numAtoms];
vect *gbForceR = new vect[numAtoms];//dEdr
vect *gbForceA = new vect[numAtoms];//dEda*dadr
BigReal *a = new BigReal[numAtoms];
BigReal *psi = new BigReal[numAtoms];
BigReal *dEda = new BigReal[numAtoms];
BigReal *ddrHijPrefix = new BigReal[numAtoms];
//init arrays
for (int i = 0; i < numAtoms; i++) {
force[i].force.x =0.0;
force[i].force.y =0.0;
force[i].force.z =0.0;
slowForce[i].force.x =0.0;
slowForce[i].force.y =0.0;
slowForce[i].force.z =0.0;
dEda[i] = 0;
psi[i] = 0;
ddrHijPrefix[i] = 0;
coulForce[i].x = 0;
coulForce[i].y = 0;
coulForce[i].z = 0;
gbForceR[i].x = 0;//dEdr
gbForceR[i].y = 0;//dEdr
gbForceR[i].z = 0;//dEdr
gbForceA[i].x = 0;//dEda*dadr
gbForceA[i].y = 0;//dEda*dadr
gbForceA[i].z = 0;//dEda*dadr
}
t2 = clock();
inittime = (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
/**********************************************************
*
* Loop 1 : accumulate Hij into psi array
* cutoff = a_cut = 25A
* every 2 timesteps
*
**********************************************************/
double missTime = 0;
double hitTime = 0;
t1 = clock();
int dij, dji;//which hij domain 0123456 - for debugging only
BigReal dhij, dhji;
//int TESTITER = 1;
//for (int k = 0; k < TESTITER; k++)
for (int i = 0; i < numAtoms; i++) {
ri = coord[i].position;
for (int j = i+1; j < numAtoms; j++) {
rj = coord[j].position;
dx = (ri.x - rj.x);
dy = (ri.y - rj.y);
dz = (ri.z - rj.z);
r2 = dx*dx+dy*dy+dz*dz;
if (r2 > a_cut_ps2) continue;
r_i = 1.0/sqrt(r2);;
r = 1.0/r_i;;
loop1Iter++;
BigReal rhoi0 = coord[i].rho0;
BigReal rhojs = coord[j].rhos;
BigReal rhoj0 = coord[j].rho0;
BigReal rhois = coord[i].rhos;
CalcHPairSer(r,r2,r_i,a_cut, coord[i].rho0, coord[j].rhos,
coord[j].rho0, coord[i].rhos,dij,dji,hij,hji);
#ifdef PRINT_COMP
CkPrintf("PSI(%04i)[%04i,%04i] = %i%i % .4e % .4e\n",timestep,coord[i].id,coord[j].id,dij,dji,hij,hji);
//CkPrintf("S_Hij_%i\n",dij);
//CkPrintf("S_Hji_%i\n",dji);
#endif
psi[i] += hij;
psi[j] += hji;
}
}
t2 = clock();
psitime += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
loop1time += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
t1 = clock();
/**********************************************************
*
* Atom 1: Calculate alpha based on phi for each atom
*
**********************************************************/
BigReal totPsi = 0;
for (int i = 0; i < numAtoms; i++) {
//CkPrintf("Srho[%i] = %.3e %.3e\n",coord[i].id,coord[i].rho0,coord[i].rhos);
rhoi0 = coord[i].rho0;
rhoi = coord[i].rho;
//CkPrintf("GBIS_SER: psi[%03i] = %.4e\n",i,psi[i]);
totPsi += psi[i];
psi[i] *= rhoi0;
bornRad=1/(1/rhoi0-1/rhoi*tanh(psi[i]*(delta+psi[i]*(-beta+gamma*psi[i]))));
bornRad = (1.0/bornRad < 1.0/alphaMax) ? alphaMax : bornRad;
a[i] = bornRad;
#ifdef PRINT_COMP
CkPrintf("BORNRAD(%04i)[%04i] = % .4e\n",timestep,coord[i].id,bornRad);
#endif
}
t2 = clock();
alphatime += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
t1 = clock();
/**********************************************************
*
* Loop 2 : dEda
*
**********************************************************/
for (int i = 0; i < numAtoms; i++) {
ri = coord[i].position;
for (int j = i+1; j < numAtoms; j++) {
rj = coord[j].position;
dx = (ri.x - rj.x);//rptI
dy = (ri.y - rj.y);//rptI
dz = (ri.z - rj.z);//rptI
r2 = dx*dx+dy*dy+dz*dz;//rptI
if (r2 > cutoff2) continue;
//calculate distance
loop2Iter++;
qiqj = (-COUL_CONST*coord[i].charge);
qiqj *= coord[j].charge;
r_i = 1.0/sqrt(r2);
r = 1.0/r_i;//rptI
rnx = dx*r_i;//normalized vector
rny = dy*r_i;
rnz = dz*r_i;
//calculate scaling for energy smoothing
BigReal scale, ddrScale;
//CalcScaleSer(r, trans, cutoff, scale, ddrScale);
if ( false ) {
BigReal ratio = r2 / cutoff2;
scale = ratio - 1;
scale *= scale;
ddrScale = 4.0*r*(r2-cutoff2)/cutoff2/cutoff2;
} else {
scale = 1;
ddrScale = 0;
}
//BigReal ai = a[i];
//BigReal aj = a[j];
int exclij = 0;//molecule->checkexcl(i,j);
//CkPrintf("GBIS_SER_excl[%i,%i] %i\n",i,j,exclij);
//CkPrintf("GBIS_DOFULL = %i\n",stat);
Phase2_PairSer(r,r2,r_i,qiqj,a[i],a[j],epsilon_p_i,epsilon_s_i,kappa,exclij,
scale14,stat,coulEij,ddrCoulEij,gbEij,ddrGbEij,dEdai,dEdaj);
int id1 = coord[i].id;
int id2 = coord[j].id;
if (id1 > id2 ) {
int tmp = id2;
id2 = id1;
id1 = tmp;
}//print ids as lower index, higher index
//accumulate energies
gbInterEnergy += gbEij *scale;
forcedEdr = -(ddrGbEij)*scale-(gbEij)*ddrScale;
//add GB force
fx = rnx*forcedEdr;
fy = rny*forcedEdr;
fz = rnz*forcedEdr;
#ifdef PRINT_COMP
CkPrintf("DEDR(%04i)[%04i,%04i] = % .4e\n",timestep,i,j,forcedEdr);
CkPrintf("DASM(%04i)[%04i,%04i] = % .4e % .4e\n",timestep,i,j,dEdai*scale,dEdaj*scale);
CkPrintf("P2RM(%04i)[%04i,%04i] = % .4e % .4e % .4e % .4e % .4e\n",timestep,i,j, r, a[i],a[j],epsilon_p_i,epsilon_s_i,kappa);
#endif
gbForceR[i].x += fx;
gbForceR[i].y += fy;
gbForceR[i].z += fz;
gbForceR[j].x -= fx;
gbForceR[j].y -= fy;
gbForceR[j].z -= fz;
//add dEda
if (stat) {
dEda[i] += dEdai*scale;
dEda[j] += dEdaj*scale;
}
}//end j loop
}//end i loop
t2 = clock();
dEdasumtime += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
loop2time += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
t1 = clock();
/*******************************************************************************
*
* Atom 2 : Calculate dHij Prefix
*
*******************************************************************************/
for (int i = 0; i < numAtoms; i++) {
//add diagonal dEda term
fij = a[i];//inf
expkappa = exp(-kappa*fij);//0
Dij = epsilon_p_i - expkappa*epsilon_s_i;//dielectric term
//add diagonal GB energy term
gbEij = -COUL_CONST*coord[i].charge*coord[i].charge*Dij/fij;
gbSelfEnergy += 0.5*gbEij;//self energy
//CkPrintf("self_energy[%03i] = %e\n",i,0.5*gbEij);
//CkPrintf("gbSelfEnergy[%03i] = % e\n", coord[i].id,0.5*gbEij);
//calculate dHij prefix
if (stat) {
dEdai = -0.5*COUL_CONST*coord[i].charge*coord[i].charge
*(kappa*epsilon_s_i*expkappa-Dij/fij)/a[i];
//CkPrintf("SER_dEdai[%03i]%i = % e\n",i,timestep,dEdai);
dEda[i] += dEdai;
BigReal dedasum = dEda[i];
//CkPrintf("SER_dEdaSum[%03i]%i = % e\n",i,timestep,dEda[i]);
rhoi0 = coord[i].rho0;
rhoi = rhoi0+rho_0;
BigReal psii = psi[i];
nbetapsi = -beta*psii;
gammapsi2 = gamma*psii*psii;
tanhi = tanh(psii*(delta+nbetapsi+gammapsi2));
daidr = a[i]*a[i]*rhoi0/rhoi*(1-tanhi*tanhi)
* (delta+nbetapsi+nbetapsi+gammapsi2+gammapsi2+gammapsi2);
ddrHijPrefix[i] = daidr*dEda[i];
#ifdef PRINT_COMP
CkPrintf("DHDR(%04i)[%04i] = % .4e\n",timestep,coord[i].id, ddrHijPrefix[i]);
#endif
}
}
t2 = clock();
dEdaprefixtime += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
//gbEnergy = gbInterEnergy + gbSelfEnergy;
t1 = clock();
/**********************************************************
*
* Loop 3 : Calculate dEda*dadr Forces
*
**********************************************************/
if (stat) {
BigReal dhij, dhji;
int dij, dji;
//for (int k = 0; k < TESTITER; k++)
for (int i = 0; i < numAtoms; i++) {
ri = coord[i].position;
//CkPrintf("SER_dHdrPrefix[%i]%i = % .5e\n",coord[i].id,timestep,ddrHijPrefix[i]);
for (int j = i+1; j < numAtoms; j++) {
rj = coord[j].position;
dx = (ri.x - rj.x);//rptI
dy = (ri.y - rj.y);//rptI
dz = (ri.z - rj.z);//rptI
r2 = dx*dx+dy*dy+dz*dz;//rptI
//loop3flops += 9;
if (r2 > a_cut_ps2) continue;
r_i = 1.0/sqrt(r2);//rptI
loop3Iter++;
//calculate dHij for pair
r = 1.0/r_i;
CalcDHPairSer(r,r2,r_i,a_cut,
coord[i].rho0,coord[j].rhos,
coord[j].rho0,coord[i].rhos,
dij,dji,dhij,dhji);
//calculate and add dEijdai,j*dai,jdrij force
forceAlpha = -r_i*(ddrHijPrefix[i]*dhij+ddrHijPrefix[j]*dhji);
#ifdef PRINT_COMP
CkPrintf("DEDA(%04i)[%04i,%04i] = %i%i % .4e % .4e % .4e\n",timestep,i,j,dij,dji,dhij,dhji, forceAlpha/r_i);
#endif
fx = dx * forceAlpha;
fy = dy * forceAlpha;
fz = dz * forceAlpha;
gbForceA[i].x += fx;
gbForceA[i].y += fy;
gbForceA[i].z += fz;
gbForceA[j].x -= fx;
gbForceA[j].y -= fy;
gbForceA[j].z -= fz;
}//end inner summation loop
}//end outer summation loop
}//end if stat
t2 = clock();
dEdalooptime += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
loop3time += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
t1 = clock();
//add forces
for (int i = 0; i < numAtoms; i++) {
force[i].force.x =0.0;
force[i].force.y =0.0;
force[i].force.z =0.0;
slowForce[i].force.x =0.0;
slowForce[i].force.y =0.0;
slowForce[i].force.z =0.0;
#if GBIS_COUL_FORCE
force[i].force.x += coulForce[i].x;
force[i].force.y += coulForce[i].y;
force[i].force.z += coulForce[i].z;
#endif
#if GBIS_DEDR_FORCE
force[i].force.x += gbForceR[i].x;
force[i].force.y += gbForceR[i].y;
force[i].force.z += gbForceR[i].z;
#endif
#if GBIS_DEDA_FORCE
if (stat) {
slowForce[i].force.x += gbForceA[i].x;
slowForce[i].force.y += gbForceA[i].y;
slowForce[i].force.z += gbForceA[i].z;
//CkPrintf("SERIAL SLOW %e %e %e\n",gbForceA[i].x,gbForceA[i].y,gbForceA[i].z);
}
//force[i].force.x += gbForceA[i].x;
//force[i].force.y += gbForceA[i].y;
//force[i].force.z += gbForceA[i].z;
#endif
#ifdef PRINT_SERFORCES
BigReal fC, fR, fA;
fx = 0;
fy = 0;
fz = 0;
#if GBIS_COUL_FORCE
fx += coulForce[i].x;
fy += coulForce[i].y;
fz += coulForce[i].z;
//fC = sqrt(fx*fx+fy*fy+fz*fz);
//fprintf(stderr, "%i %e %e %e ",i,fx, fy, fz);
#endif
#if GBIS_DEDR_FORCE
fx += gbForceR[i].x;
fy += gbForceR[i].y;
fz += gbForceR[i].z;
//fR = sqrt(fx*fx+fy*fy+fz*fz);
//fprintf(stderr, "%e %e %e",fx, fy, fz);
#endif
#if GBIS_DEDA_FORCE
fx += gbForceA[i].x;
fy += gbForceA[i].y;
fz += gbForceA[i].z;
//fA = sqrt(fx*fx+fy*fy+fz*fz);
//fprintf(stderr, "%5i % .5e % .5e % .5e\n",i, fx, fy, fz);
#endif
//fprintf(stderr, "%5i % .5e % .5e % .5e\n",i, fx, fy, fz);
#endif //if print>1
}
t2 = clock();
inittime += (double)((double)t2-(double)t1)/CLOCKS_PER_SEC;
timestep++;
delete[] coulForce;
delete[] gbForceR;
delete[] gbForceA;
delete[] a;
delete[] psi;
delete[] dEda;
delete[] ddrHijPrefix;
//printf("GBIS calcReg COMPLETE!\n");
}
void ComputeGBISserMgr::recvCoord(GBISCoordMsg *msg) {
//printf("GBIS recvCoord()\n");
if ( ! numSources ) {//init receiving coord
numSources = (PatchMap::Object())->numNodesWithPatches();
coordMsgs = new GBISCoordMsg*[numSources];
for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
numArrived = 0;
numAtoms = Node::Object()->molecule->numAtoms;
coord = new ComputeGBISAtom[numAtoms];
force = new ExtForce[numAtoms];
slowForce = new ExtForce[numAtoms];
timestep = msg[0].sequence;
}
//receive coord
int i;
for ( i=0; i < msg->numAtoms; ++i ) {
coord[msg->coord[i].id] = msg->coord[i];
}
coordMsgs[numArrived] = msg;
++numArrived;
if ( numArrived < numSources ) return;
numArrived = 0;
/**********************************************************
*
* All sources arrived; calculate energy, forces
*
**********************************************************/
t_start = clock();
//how long did namd take to cycle back here
double namdtime = (double)((double)t_start-(double)t_stop)/CLOCKS_PER_SEC;
totalnamdtime += namdtime;
//choice choose
calcGBISReg(msg->doSlow);
t_stop = clock();
double gbistime = (double)((double)t_stop-(double)t_start)/CLOCKS_PER_SEC;
//printf("GBIS: elapsednamd(%i)=%f\n", timestep, namdtime);
//printf("GBIS: elapsedgbis(%i)=%f\n", timestep, gbistime);
totalgbistime += gbistime;
//printf("GBIS: total(%i)=%f\n", timestep, totaltime);
if (timestep % BENCH_PERIOD == 0) {
printf("\n");
printf("GBIS: t_GB=%f sec for %i steps\n",totalgbistime,BENCH_PERIOD);
printf("GBIS: t_MD=%f sec for %i steps\n",totalnamdtime,BENCH_PERIOD);
printf("GBIS: init=%f sec for %i steps\n", inittime, BENCH_PERIOD);
printf("GBIS: psi=%f sec for %i steps\n", psitime, BENCH_PERIOD);
printf("GBIS: alpha=%f sec for %i steps\n", alphatime, BENCH_PERIOD);
printf("GBIS: dEdasum=%f sec for %i steps\n", dEdasumtime, BENCH_PERIOD);
printf("GBIS: dEdaprefix=%f sec for %i steps\n",dEdaprefixtime,BENCH_PERIOD);
printf("GBIS: dEdaloop=%f sec for %i steps\n", dEdalooptime,BENCH_PERIOD);
printf("GBIS: loop1=%i iters\n", loop1Iter);
printf("GBIS: loop2=%i iters\n", loop2Iter);
printf("GBIS: loop3=%i iters\n", loop3Iter);
printf("\n");
totalgbistime = 0;
totalnamdtime = 0;
inittime = 0;
psitime = 0;
alphatime = 0;
dEdrtime = 0;
dEdasumtime = 0;
dEdaprefixtime = 0;
dEdalooptime = 0;
}
// distribute forces
//printf("GBIS distributing forces\n");
for ( int j=0; j < numSources; ++j ) {
GBISCoordMsg *cmsg = coordMsgs[j];
coordMsgs[j] = 0;
GBISForceMsg *fmsg = new (cmsg->numAtoms, cmsg->numAtoms, 0) GBISForceMsg;
//does this init slowForce, force?
for ( int i=0; i < cmsg->numAtoms; ++i ) {
fmsg->force[i] = force[cmsg->coord[i].id];
fmsg->slowForce[i] = slowForce[cmsg->coord[i].id];
/*
if (i == 1000 ) {
printf("%i force: <", i);
printf("%f, ", fmsg->force[i].force.x);
printf("%f, ", fmsg->force[i].force.y);
printf("%f>\n", fmsg->force[i].force.z);
printf("%i slwfr: <", i);
printf("%f, ", fmsg->slowForce[i].force.x);
printf("%f, ", fmsg->slowForce[i].force.y);
printf("%f>\n", fmsg->slowForce[i].force.z);
}
*/
}
//CkPrintf("GBISENERGY[%i] c = % e, b = % e\n",timestep,coulEnergy, gbEnergy);
if ( ! j ) {
#if GBIS_DEDR_FORCE
fmsg->gbSelfEnergy = gbSelfEnergy;
fmsg->gbInterEnergy = gbInterEnergy;
#else
fmsg->gbSelfEnergy = 0;
fmsg->gbInterEnergy = 0;
#endif
#if GBIS_COUL_FORCE
fmsg->coulEnergy = coulEnergy;
#else
fmsg->coulEnergy = 0;
#endif
} else {
fmsg->gbSelfEnergy = 0;
fmsg->gbInterEnergy = 0;
fmsg->coulEnergy = 0;
}
gbisProxy[cmsg->sourceNode].recvForce(fmsg);
delete cmsg;
}
//printf("GBIS distributing forces COMPLETE!\n");
}
void ComputeGBISserMgr::recvForce(GBISForceMsg *msg) {
//printf("GBIS recvForce()\n");
gbisCompute->saveResults(msg);
delete oldmsg;
oldmsg = msg;
}
void ComputeGBISser::saveResults(GBISForceMsg *msg) {
//printf("GBIS saveResults()\n");
ResizeArrayIter<PatchElem> ap(patchList);
ExtForce *results_ptr = msg->force;
ExtForce *results_ptr_slow = msg->slowForce;
// add in forces
for (ap = ap.begin(); ap != ap.end(); ap++) {
//CkPrintf("GBIS%i: ComputeGBIS(%i)::saveResults() openedForceBox",CkMyPe(),cid);
Results *r = (*ap).forceBox->open();
Force *f = r->f[Results::nbond];
Force *sf = r->f[Results::slow];
int numAtoms = (*ap).p->getNumAtoms();
for(int i=0; i<numAtoms; ++i) {
f[i] += results_ptr->force;
sf[i] += results_ptr_slow->force;
//CkPrintf("GBIS%i: slow[%i] = % e\n",CkMyPe(),i,sf[i].x);
++results_ptr;
++results_ptr_slow;
}
//CkPrintf("GBIS%i: ComputeGBIS(%i)::saveResults() closedForceBox",CkMyPe(),cid);
(*ap).forceBox->close(&r);
}
//reduction->item(REDUCTION_ELECT_ENERGY) += msg->coulEnergy;
reduction->item(REDUCTION_ELECT_ENERGY) += msg->gbInterEnergy;
reduction->item(REDUCTION_ELECT_ENERGY) += msg->gbSelfEnergy;
//CkPrintf("energies= % e, % e, % e\n",msg->coulEnergy, msg->gbInterEnergy, msg->gbSelfEnergy);
reduction->submit();
}
/******************************************************************************
* Send data to node 0
******************************************************************************/
void ComputeGBISser::doWork()
{
//printf("GBIS doWork()\n");
ResizeArrayIter<PatchElem> ap(patchList);
#if 1
// Skip computations if nothing to do.
if ( ! patchList[0].p->flags.doNonbonded )
{
for (ap = ap.begin(); ap != ap.end(); ap++) {
CompAtom *x = (*ap).positionBox->open();
//CkPrintf("GBIS%i: ComputeGBIS(%i)::doWork() openedForceBox",CkMyPe(),cid);
Results *r = (*ap).forceBox->open();
(*ap).positionBox->close(&x);
//CkPrintf("GBIS%i: ComputeGBIS(%i)::doWork() closedForceBox",CkMyPe(),cid);
(*ap).forceBox->close(&r);
}
reduction->submit();
return;
}
#endif
// allocate message
int numLocalAtoms = 0;
for (ap = ap.begin(); ap != ap.end(); ap++) {
numLocalAtoms += (*ap).p->getNumAtoms();
}
GBISCoordMsg *msg = new (numLocalAtoms, 0) GBISCoordMsg;
msg->sourceNode = CkMyPe();
msg->numAtoms = numLocalAtoms;
ComputeGBISAtom *data_ptr = msg->coord;
SimParameters *simParams = Node::Object()->simParameters;
msg->doSlow = patchList[0].p->flags.doFullElectrostatics;
//CkPrintf("SERIAL SLOW %i\n",msg->doSlow);
msg->sequence = sequence();
// get positions
for (ap = ap.begin(); ap != ap.end(); ap++) {
FullAtomList &atoms = (*ap).p->getAtomList();
CompAtom *x = (*ap).positionBox->open();
CompAtomExt *xExt = (*ap).p->getCompAtomExtInfo();
int numAtoms = (*ap).p->getNumAtoms();
for(int i=0; i<numAtoms; ++i)
{
data_ptr->position = x[i].position;
data_ptr->charge = x[i].charge;
data_ptr->mass = atoms[i].mass;
data_ptr->id = xExt[i].id;
data_ptr->rho = MassToRadius(data_ptr->mass);
SimParameters *simParams = Node::Object()->simParameters;
data_ptr->rho0 = data_ptr->rho - simParams->coulomb_radius_offset;
data_ptr->rhos = data_ptr->rho0 * MassToScreen(data_ptr->mass);
data_ptr->vdwType = x[i].vdwType;
++data_ptr;
}
#if 0
if ( patchList[0].p->flags.doMolly ) { (*ap).avgPositionBox->close(&x); }
else { (*ap).positionBox->close(&x); }
#endif
(*ap).positionBox->close(&x);
}
CProxy_ComputeGBISserMgr gbisProxy(CkpvAccess(BOCclass_group).computeGBISserMgr);
gbisProxy[0].recvCoord(msg);
}
#include "ComputeGBISserMgr.def.h"
/*
Piecewise screening functions Hij dHij/drij
r distance
r2 square distance
ri inverse distance
rc cutoff
r0 descreened atom radius
rs descreening atom radius
h return value
dh return value
*/
inline void h0Ser ( BigReal r, BigReal r2, BigReal ri,// 5.3%
Real rc, BigReal r0, BigReal rs, BigReal & h ) {
h = 0;
}
inline void dh0Ser ( BigReal r, BigReal r2, BigReal ri,// 5.3%
Real rc, BigReal r0, BigReal rs, BigReal & dh ) {
dh = 0;
}
inline void h1Ser ( BigReal r, BigReal r2, BigReal ri, //18.4%
BigReal rc, BigReal r0, BigReal rs, BigReal & h ) {
BigReal rci = 1.0/rc;
BigReal rmrs = r-rs;// 4 times