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Clarifying contact penalty logic, minimizing use of std

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This commit is contained in:
jtclemm
2024-12-22 11:13:04 -07:00
parent 6abbdfd740
commit ecb0f9525b
2 changed files with 55 additions and 42 deletions
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92
src/GRANULAR/fix_granular_mdr.cpp
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@ -38,10 +38,6 @@
#include "update.h"
#include "variable.h"
#include <algorithm>
#include <iomanip>
#include <sstream>
using namespace LAMMPS_NS;
using namespace Granular_NS;
using namespace FixConst;
@ -275,12 +271,12 @@ void FixGranularMDR::end_of_step()
const double Vo = 4.0 / 3.0 * MY_PI * pow(Ro[i], 3.0);
const double Vgeoi = 4.0 / 3.0 * MY_PI * pow(R, 3.0) - Vcaps[i];
Vgeo[i] = std::min(Vgeoi, Vo);
Vgeo[i] = MIN(Vgeoi, Vo);
const double Afree = Atot[i] - Acon1[i];
psi[i] = Afree / Atot[i];
const double dR = std::max(dRnumerator[i] / (dRdenominator[i] - 4.0 * MY_PI * pow(R, 2.0)), 0.0);
const double dR = MAX(dRnumerator[i] / (dRdenominator[i] - 4.0 * MY_PI * pow(R, 2.0)), 0.0);
if (psi_b[i] < psi[i]) {
if ((radius[i] + dR) < (1.5 * Ro[i])) radius[i] += dR;
}
@ -426,6 +422,7 @@ void FixGranularMDR::calculate_contact_penalty()
k = jlist[kk];
k &= NEIGHMASK;
// QUESTION: why not start loop at jj+1?
if (kk == jj) continue;
const double delx_ik = x[k][0] - xtmp;
const double dely_ik = x[k][1] - ytmp;
@ -458,41 +455,17 @@ void FixGranularMDR::calculate_contact_penalty()
history_ik = &allhistory[size_history * kk];
double * pik = &history_ik[22]; // penalty for contact i and k
// we don't know if who owns the contact ahead of time, k might be in j'sneigbor list or vice versa,
// so we need to manually search to figure out the owner check if k is inthe neighbor list of j
double * pjk = nullptr;
int * const jklist = firstneigh[j];
const int jknum = numneigh[j];
for (int jk = 0; jk < jknum; jk++) {
const int kneigh = jklist[jk] & NEIGHMASK;
if (k == kneigh) {
allhistory_j = firsthistory[j];
history_jk = &allhistory_j[size_history * jk];
pjk = &history_jk[22]; // penalty for contact j and k
break;
}
}
// Find pair of atoms with the smallest overlap, atoms a & b, 3rd atom c is central
// if a & b are both local:
// calculate ab penalty and add to the one history entry
// if a is local & b is ghost:
// each processor has a-b in nlist and independently calculates + adds penalty
// if a & b are both ghosts:
// skip calculation since it's performed on other proc
// This process requires newon off, or nlist may not include ab, ac, & bc
// check if j is in the neighbor list of k
if (pjk == nullptr) {
int * const kjlist = firstneigh[k];
const int kjnum = numneigh[k];
for (int kj = 0; kj < kjnum; kj++) {
const int jneigh = kjlist[kj] & NEIGHMASK;
if (j == jneigh) {
allhistory_k = firsthistory[k];
history_kj = &allhistory_k[size_history * kj];
pjk = &history_kj[22]; // penalty for contact j and k
break;
}
}
}
std::vector<double> distances = {r_ij, r_ik, r_jk};
auto maxElement = std::max_element(distances.begin(), distances.end());
double maxValue = *maxElement;
int maxIndex = std::distance(distances.begin(), maxElement);
if (maxIndex == 0) { // the central particle is k
const double r_max = MAX(r_ij, MAX(r_ik, r_jk));
if (r_ij == r_max) { // the central particle is k
const double enx_ki = -delx_ik * rinv_ik;
const double eny_ki = -dely_ik * rinv_ik;
const double enz_ki = -delz_ik * rinv_ik;
@ -501,7 +474,7 @@ void FixGranularMDR::calculate_contact_penalty()
const double enz_kj = -delz_jk * rinv_jk;
const double alpha = std::acos(enx_ki * enx_kj + eny_ki * eny_kj + enz_ki * enz_kj);
pij[0] += 1.0 / (1.0 + std::exp(-50.0 * (alpha / MY_PI - 0.5)));
} else if (maxIndex == 1) { // the central particle is j
} else if (r_ik == r_max) { // the central particle is j
const double enx_ji = -delx_ij * rinv_ij;
const double eny_ji = -dely_ij * rinv_ij;
const double enz_ji = -delz_ij * rinv_ij;
@ -519,6 +492,43 @@ void FixGranularMDR::calculate_contact_penalty()
const double eny_ik = dely_ik * rinv_ik;
const double enz_ik = delz_ik * rinv_ik;
const double alpha = std::acos(enx_ij * enx_ik + eny_ij * eny_ik + enz_ij * enz_ik);
// don't know who owns the contact, k may be in j's nlist or vice versa
// need to search both to find owner
double * pjk = nullptr;
if (j < atom->nlocal) {
int * const jklist = firstneigh[j];
const int jknum = numneigh[j];
for (int jk = 0; jk < jknum; jk++) {
const int kneigh = jklist[jk] & NEIGHMASK;
if (k == kneigh) {
allhistory_j = firsthistory[j];
history_jk = &allhistory_j[size_history * jk];
pjk = &history_jk[22]; // penalty for contact j and k
break;
}
}
}
// check if j is in the neighbor list of k
if (pjk == nullptr && k < atom->nlocal) {
int * const kjlist = firstneigh[k];
const int kjnum = numneigh[k];
for (int kj = 0; kj < kjnum; kj++) {
const int jneigh = kjlist[kj] & NEIGHMASK;
if (j == jneigh) {
allhistory_k = firsthistory[k];
history_kj = &allhistory_k[size_history * kj];
pjk = &history_kj[22]; // penalty for contact j and k
break;
}
}
}
// QUESTION: is this ever supposed to happen?
if (pjk == nullptr)
error->one(FLERR, "MDR could not find atom pair in neighbor list");
pjk[0] += 1.0 / (1.0 + std::exp(-50.0 * (alpha / MY_PI - 0.5)));
}
}

5
src/GRANULAR/granular_model.cpp
View File

@ -244,7 +244,10 @@ void GranularModel::init()
// Must have valid normal, damping, and tangential models
if (normal_model->name == "none") error->all(FLERR, "Must specify normal granular model");
if (normal_model->name == "mdr") {
if (damping_model->name != "none") error->all(FLERR, "Damping model must be set to 'none' for the MDR contact model. Specify a coefficient of restitution CoR < 1 if normal damping is desired.");
if (damping_model->name != "none")
error->all(FLERR, "MDR require 'none' damping model. To damp, specify a coefficient of restitution < 1.");
if (force->newton)
error->all(FLERR, "MDR contact model requires Newton off");
} else {
if (damping_model->name == "none") error->all(FLERR, "Must specify damping granular model");
}