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Added kinetic contribution to pressure/cylinder and clang-format on all

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This commit is contained in:
Olav Galteland
2022-03-05 16:30:47 +01:00
parent 089e46a540
commit 99d29ea86a
6 changed files with 178 additions and 103 deletions
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4
src/EXTRA-COMPUTE/compute_pressure_cartesian.cpp
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@ -41,7 +41,8 @@ using namespace MathConst;
static const char cite_compute_pressure_cartesian[] =
"compute pressure/cartesian:\n\n"
"@article{ikeshoji2003molecular,\n"
"title={Molecular-level calculation scheme for pressure in inhomogeneous systems of flat and spherical layers},\n"
"title={Molecular-level calculation scheme for pressure in inhomogeneous systems of flat and "
"spherical layers},\n"
"author={Ikeshoji, Tamio and Hafskjold, Bj{\\o}rn and Furuholt, Hilde},\n"
"journal={Molecular Simulation},\n"
"volume={29},\n"
@ -247,7 +248,6 @@ void ComputePressureCartesian::compute_array()
j = bin1 + bin2 * nbins1;
tdens[j] += 1;
// TODO: Subtract streaming velocity
tpkxx[j] += mass[type[i]] * v[i][0] * v[i][0];
tpkyy[j] += mass[type[i]] * v[i][1] * v[i][1];
tpkzz[j] += mass[type[i]] * v[i][2] * v[i][2];

10
src/EXTRA-COMPUTE/compute_pressure_cartesian.h
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@ -27,11 +27,11 @@ namespace LAMMPS_NS {
class ComputePressureCartesian : public Compute {
public:
ComputePressureCartesian(class LAMMPS *, int, char **);
~ComputePressureCartesian();
void init();
void init_list(int, class NeighList *);
void compute_array();
double memory_usage();
~ComputePressureCartesian() override;
void init() override;
void init_list(int, class NeighList *) override;
void compute_array() override;
double memory_usage() override;
private:
int nbins1, nbins2, dir1, dir2, dims;

198
src/EXTRA-COMPUTE/compute_pressure_cylinder.cpp
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@ -20,6 +20,7 @@
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
@ -27,10 +28,19 @@
#include "update.h"
#include <cmath>
#include <cstring>
#include <mpi.h>
using namespace LAMMPS_NS;
using namespace MathConst;
/*-----------------------------------------------------------------------------------
Contributing authors: Cody K. Addington (North Carolina State University)
(Kinetic contribution) : Olav Galteland,
(Norwegian University of Science and Technology),
olav.galteland@ntnu.no
------------------------------------------------------------------------------------*/
static const char cite_compute_pressure_cylinder[] =
"compute pressure/cylinder:\n\n"
"@Article{Addington,\n"
@ -48,19 +58,32 @@ static const char cite_compute_pressure_cylinder[] =
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), Pvr_temp(nullptr), Pvr_all(nullptr), Pvz_temp(nullptr), Pvz_all(nullptr),
Pvphi_temp(nullptr), Pvphi_all(nullptr), R(nullptr), Rinv(nullptr), R2(nullptr), PrAinv(nullptr),
PzAinv(nullptr), R2kin(nullptr), density_temp(nullptr), invVbin(nullptr), density_all(nullptr),
tangent(nullptr), ephi_x(nullptr), ephi_y(nullptr), binz(nullptr)
Compute(lmp, narg, arg), Pvr_temp(nullptr), Pvr_all(nullptr), Pvz_temp(nullptr),
Pvz_all(nullptr), Pvphi_temp(nullptr), Pvphi_all(nullptr), R(nullptr), Rinv(nullptr),
R2(nullptr), PrAinv(nullptr), PzAinv(nullptr), R2kin(nullptr), density_temp(nullptr),
invVbin(nullptr), density_all(nullptr), tangent(nullptr), ephi_x(nullptr), ephi_y(nullptr),
binz(nullptr)
{
if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
if (narg != 7) error->all(FLERR, "Illegal compute pressure/cylinder command");
if ((narg != 7) && (narg != 9)) error->all(FLERR, "Illegal compute pressure/cylinder command");
zlo = utils::numeric(FLERR, arg[3], false, lmp);
zhi = utils::numeric(FLERR, arg[4], false, lmp);
Rmax = utils::numeric(FLERR, arg[5], false, lmp);
bin_width = utils::numeric(FLERR, arg[6], false, lmp);
// Option to include/exclude kinetic contribution. Default is to include
kinetic_flag = 1;
int iarg = 7;
if (narg > iarg) {
if (strcmp("ke", arg[iarg]) == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid compute pressure/cylinder command");
kinetic_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else
error->all(FLERR, "Unknown compute pressure/cylinder command");
}
if ((bin_width <= 0.0) || (bin_width > Rmax))
error->all(FLERR, "Illegal compute pressure/cylinder command");
if ((zhi < zlo) || ((zhi - zlo) < bin_width))
@ -80,39 +103,44 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
vector_flag = 0;
extarray = 0;
size_array_cols = 8; // r, number density, pkr, pkphi, pkz, pvr, pvphi, pz
size_array_cols = 5; // r, number density, pvr, pvphi, pz
size_array_rows = nbins;
memory->create(density_all, nbins, "density_all");
memory->create(Pkr_all, nbins, "Pkr_all");
memory->create(Pkphi_all, nbins, "Pkphi_all");
memory->create(Pkz_all, nbins, "Pkz_all");
memory->create(Pvr_all, nbins, "Pvr_all");
memory->create(Pvphi_all, nbins, "Pvphi_all");
memory->create(Pvz_all, nbins, "Pvz_all");
memory->create(density_temp, nbins, "density_temp");
memory->create(Pkr_temp, nbins, "Pkr_temp");
memory->create(Pkphi_temp, nbins, "Pkphi_temp");
memory->create(Pkz_temp, nbins, "Pkz_temp");
memory->create(Pvr_temp, nbins, "Pvr_temp");
memory->create(Pvphi_temp, nbins, "Pvphi_temp");
memory->create(Pvz_temp, nbins, "Pvz_temp");
memory->create(R,nbins, "R");
memory->create(R2,nbins, "R2");
memory->create(PrAinv,nbins, "PrAinv");
memory->create(PzAinv,nbins, "PzAinv");
memory->create(Rinv,nbins, "Rinv");
memory->create(binz,nbins, "binz");
memory->create(invVbin,nbins, "invVbin");
if (kinetic_flag == 1) {
size_array_cols = 8; // r, number density, pkr, pkphi, pkz, pvr, pvphi, pz
Pkr_temp = new double[nbins];
Pkr_all = new double[nbins];
Pkz_temp = new double[nbins];
Pkz_all = new double[nbins];
Pkphi_temp = new double[nbins];
Pkphi_all = new double[nbins];
}
Pvr_temp = new double[nbins];
Pvr_all = new double[nbins];
Pvz_temp = new double[nbins];
Pvz_all = new double[nbins];
Pvphi_temp = new double[nbins];
Pvphi_all = new double[nbins];
R = new double[nbins];
R2 = new double[nbins];
PrAinv = new double[nbins];
PzAinv = new double[nbins];
Rinv = new double[nbins];
binz = new double[nzbins];
R2kin = new double[nbins];
density_temp = new double[nbins];
invVbin = new double[nbins];
density_all = new double[nbins];
nphi = 360;
memory->create(tangent,nbins, "tangent");
memory->create(ephi_x,nbins, "ephi_x");
memory->create(ephi_y,nbins, "ephi_y");
memory->create(array, nbins, 5, "PN:array");
tangent = new double[nphi];
ephi_x = new double[nphi];
ephi_y = new double[nphi];
memory->create(array, size_array_rows, size_array_cols, "PN:array");
nktv2p = force->nktv2p;
printf("Constructor done");
}
/* ---------------------------------------------------------------------- */
@ -120,31 +148,33 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
ComputePressureCyl::~ComputePressureCyl()
{
memory->destroy(array);
memory->destroy(density_all);
memory->destroy(Pkr_all);
memory->destroy(Pkphi_all);
memory->destroy(Pkz_all);
memory->destroy(Pvr_all);
memory->destroy(Pvphi_all);
memory->destroy(Pvz_all);
memory->destroy(density_temp);
memory->destroy(Pkr_temp);
memory->destroy(Pkphi_temp);
memory->destroy(Pkz_temp);
memory->destroy(Pvr_temp);
memory->destroy(Pvphi_temp);
memory->destroy(Pvz_temp);
memory->destroy(R);
memory->destroy(R2);
memory->destroy(PrAinv);
memory->destroy(PzAinv);
memory->destroy(Rinv);
memory->destroy(binz);
memory->destroy(invVbin);
memory->destroy(tangent);
memory->destroy(ephi_x);
memory->destroy(ephi_y);
memory->destroy(array);
if (kinetic_flag == 1) {
delete[] Pkr_temp;
delete[] Pkr_all;
delete[] Pkz_temp;
delete[] Pkz_all;
delete[] Pkphi_temp;
delete[] Pkphi_all;
}
delete[] R;
delete[] Rinv;
delete[] R2;
delete[] R2kin;
delete[] invVbin;
delete[] density_temp;
delete[] density_all;
delete[] tangent;
delete[] ephi_x;
delete[] ephi_y;
delete[] Pvr_temp;
delete[] Pvr_all;
delete[] Pvz_temp;
delete[] Pvz_all;
delete[] Pvphi_temp;
delete[] Pvphi_all;
delete[] PrAinv;
delete[] PzAinv;
delete[] binz;
}
/* ---------------------------------------------------------------------- */
@ -157,14 +187,12 @@ void ComputePressureCyl::init()
error->all(FLERR, "Pair style does not support compute pressure/cylinder");
double phi;
for (int iphi = 0; iphi < nphi; iphi++) {
phi = ((double) iphi) * MY_PI / 180.0;
tangent[iphi] = tan(phi);
ephi_x[iphi] = -sin(phi);
ephi_y[iphi] = cos(phi);
}
for (int iq = 0; iq < nbins; iq++) {
R[iq] = ((double) iq + 0.5) * bin_width;
Rinv[iq] = 1.0 / R[iq];
@ -213,9 +241,16 @@ void ComputePressureCyl::compute_array()
invoked_array = update->ntimestep;
int ibin;
// clear pressures
for (ibin = 0; ibin < nbins; ibin++) {
if (kinetic_flag == 1) {
Pkr_temp[ibin] = 0.0;
Pkr_all[ibin] = 0.0;
Pkphi_temp[ibin] = 0.0;
Pkphi_all[ibin] = 0.0;
Pkz_temp[ibin] = 0.0;
Pkz_all[ibin] = 0.0;
}
density_temp[ibin] = 0.0;
density_all[ibin] = 0.0;
Pvr_temp[ibin] = 0.0;
@ -236,7 +271,10 @@ void ComputePressureCyl::compute_array()
double rsq, fpair, factor_coul, factor_lj;
int *ilist, *jlist, *numneigh, **firstneigh;
double vr, vp;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
@ -253,7 +291,7 @@ void ComputePressureCyl::compute_array()
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// calculate number density (by radius)
// calculate number density and kinetic contribution (by radius)
double temp_R2;
for (i = 0; i < nlocal; i++)
if ((x[i][2] < zhi) && (x[i][2] > zlo)) {
@ -264,6 +302,21 @@ void ComputePressureCyl::compute_array()
if (temp_R2 < R2kin[j]) break;
density_temp[j] += invVbin[j];
// Check if kinetic option is set to yes
if (kinetic_flag == 1) {
if (temp_R2 != 0) {
// Radial velocity times R
vr = (x[i][0] * v[i][0] + x[i][1] * v[i][1]);
// Azimuthal velocity divided by R
vp = (v[i][1] / x[i][0] - x[i][1] * v[i][0] / (x[i][0] * x[i][0])) /
(pow(x[i][1] / x[i][0], 2.0) + 1.0);
Pkr_temp[j] += mass[type[i]] * vr * vr / temp_R2;
Pkphi_temp[j] += mass[type[i]] * temp_R2 * vp * vp;
Pkz_temp[j] += mass[type[i]] * v[i][2] * v[i][2];
}
}
}
MPI_Allreduce(density_temp, density_all, nbins, MPI_DOUBLE, MPI_SUM, world);
for (i = 0; i < nbins; i++) array[i][1] = density_all[i]; // NEW
@ -459,12 +512,22 @@ void ComputePressureCyl::compute_array()
// calculate pressure (force over area)
for (ibin = 0; ibin < nbins; ibin++) {
if (kinetic_flag == 1) {
Pkr_temp[ibin] *= invVbin[ibin];
Pkphi_temp[ibin] *= invVbin[ibin];
Pkz_temp[ibin] *= invVbin[ibin];
}
Pvr_temp[ibin] *= PrAinv[ibin] * Rinv[ibin];
Pvphi_temp[ibin] *= PphiAinv;
Pvz_temp[ibin] *= PzAinv[ibin];
}
// communicate these values across processors
if (kinetic_flag == 1) {
MPI_Allreduce(Pkr_temp, Pkr_all, nbins, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(Pkphi_temp, Pkphi_all, nbins, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(Pkz_temp, Pkz_all, nbins, MPI_DOUBLE, MPI_SUM, world);
}
MPI_Allreduce(Pvr_temp, Pvr_all, nbins, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(Pvphi_temp, Pvphi_all, nbins, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(Pvz_temp, Pvz_all, nbins, MPI_DOUBLE, MPI_SUM, world);
@ -472,19 +535,28 @@ void ComputePressureCyl::compute_array()
// populate array
for (ibin = 0; ibin < nbins; ibin++) {
array[ibin][0] = R[ibin];
if (kinetic_flag == 1) {
array[ibin][2] = Pkr_all[ibin] * nktv2p;
array[ibin][3] = Pkphi_all[ibin] * nktv2p;
array[ibin][4] = Pkz_all[ibin] * nktv2p;
array[ibin][5] = Pvr_all[ibin] * nktv2p;
array[ibin][6] = Pvphi_all[ibin] * nktv2p;
array[ibin][7] = Pvz_all[ibin] * nktv2p;
} else {
array[ibin][2] = Pvr_all[ibin] * nktv2p;
array[ibin][3] = Pvphi_all[ibin] * nktv2p;
array[ibin][4] = Pvz_all[ibin] * nktv2p;
}
}
}
/* ----------------------------------------------------------------------
memory usage of data
------------------------------------------------------------------------- */
// TODO: update this
double ComputePressureCyl::memory_usage()
{
double bytes =
(3.0 * (double) nphi + 16.0 * (double) nbins + 5.0 * (double) nbins) * sizeof(double);
(3.0 * (double) nphi + 16.0 * (double) nbins + (5.0 + 3.0 * kinetic_flag) * (double) nbins) *
sizeof(double);
return bytes;
}

5
src/EXTRA-COMPUTE/compute_pressure_cylinder.h
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@ -17,8 +17,8 @@ ComputeStyle(pressure/cylinder,ComputePressureCyl);
// clang-format on
#else
#ifndef LMP_COMPUTE_PRESSURE_CYLINDER
#define LMP_COMPUTE_PRESSURE_CYLINDER
#ifndef LMP_COMPUTE_PRESSURE_CYLINDER_H
#define LMP_COMPUTE_PRESSURE_CYLINDER_H
#include "compute.h"
@ -34,6 +34,7 @@ class ComputePressureCyl : public Compute {
double memory_usage() override;
private:
int kinetic_flag;
int nbins, nphi, nzbins;
double *Pvr_temp, *Pvr_all, *Pvz_temp, *Pvz_all, *Pvphi_temp, *Pvphi_all;
double *Pkr_temp, *Pkr_all, *Pkz_temp, *Pkz_all, *Pkphi_temp, *Pkphi_all;

4
src/EXTRA-COMPUTE/compute_pressure_spherical.cpp
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@ -42,7 +42,8 @@ using namespace MathConst;
static const char cite_compute_pressure_sphere[] =
"compute pressure/spherical:\n\n"
"@article{ikeshoji2003molecular,\n"
"title={Molecular-level calculation scheme for pressure in inhomogeneous systems of flat and spherical layers},\n"
"title={Molecular-level calculation scheme for pressure in inhomogeneous systems of flat and "
"spherical layers},\n"
"author={Ikeshoji, Tamio and Hafskjold, Bj{\\o}rn and Furuholt, Hilde},\n"
"journal={Molecular Simulation},\n"
"volume={29},\n"
@ -130,6 +131,7 @@ void ComputePressureSpherical::init()
if (force->pair->single_enable == 0)
error->all(FLERR, "Pair style does not support compute pressure/spherical");
// Inverse volume of each spherical shell (bin)
for (int bin = 0; bin < nbins; bin++)
invV[bin] = 3.0 / (4.0 * MY_PI * (pow((bin + 1) * bin_width, 3.0) - pow(bin * bin_width, 3.0)));

10
src/EXTRA-COMPUTE/compute_pressure_spherical.h
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@ -27,11 +27,11 @@ namespace LAMMPS_NS {
class ComputePressureSpherical : public Compute {
public:
ComputePressureSpherical(class LAMMPS *, int, char **);
~ComputePressureSpherical();
void init();
void init_list(int, class NeighList *);
void compute_array();
double memory_usage();
~ComputePressureSpherical() override;
void init() override;
void init_list(int, class NeighList *) override;
void compute_array() override;
double memory_usage() override;
private:
int nbins;