[WIP] Add fix cboamd for cavity Born-Oppenheimer MD #4972

Yi-FanLi · 2025-09-11T03:19:56Z

This PR is a work in progress and not ready for review right not.

This PR implements the MD framework to study vibrational strong coupling based on the cavity Born-Oppenheimer approximation. It adds a new fix style fix cboamd for DeePMD-kit's LAMMPS interface.

Copilot

Pull Request Overview

This PR implements the MD framework to study vibrational strong coupling based on the cavity Born-Oppenheimer approximation by adding a new fix style fix cboamd for DeePMD-kit's LAMMPS interface.

Adds a new LAMMPS fix implementation for cavity Born-Oppenheimer molecular dynamics
Integrates DeepMD models for computing molecular dipoles and polarizabilities
Implements photon coordinate evolution using velocity Verlet integration

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
source/lmp/plugin/deepmdplugin.cpp	Registers the new `fix cboamd` plugin with LAMMPS
source/lmp/fix_cboamd.h	Header file defining the FixCBOAMD class interface and member variables
source/lmp/fix_cboamd.cpp	Implementation of the cavity Born-Oppenheimer MD fix with DeepMD integration

Copilot · 2025-09-11T03:20:59Z

source/lmp/fix_cboamd.cpp

+    fprintf(output_file, "%d %.6f %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e",
+            current_step, update->dt * current_step,
+            dipole[0], dipole[1], dipole[2],
+            polarizability[0], polarizability[1], polarizability[2],
+            polarizability[3], polarizability[4], polarizability[5],
+            polarizability[6], polarizability[7], polarizability[8]);


The output format writes 15 values but the header comment at line 160 indicates it should write Energy which is missing. The scalar energy value from compute_scalar() is not being written to the output file, creating a mismatch between the header and data columns.

Suggested change

fprintf(output_file, "%d %.6f %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e",

current_step, update->dt * current_step,

dipole[0], dipole[1], dipole[2],

polarizability[0], polarizability[1], polarizability[2],

polarizability[3], polarizability[4], polarizability[5],

polarizability[6], polarizability[7], polarizability[8]);

double energy = compute_scalar();

fprintf(output_file, "%d %.6f %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e",

current_step, update->dt * current_step,

dipole[0], dipole[1], dipole[2],

polarizability[0], polarizability[1], polarizability[2],

polarizability[3], polarizability[4], polarizability[5],

polarizability[6], polarizability[7], polarizability[8],

energy);

Copilot · 2025-09-11T03:20:59Z

source/lmp/fix_cboamd.cpp

+  for (int i=0; i<nphoton; i++) {
+    if (n == i) return pa[i];
+    if (n == nphoton+i) return qa[i];
+    if (n == 2*nphoton+i) return ea[i];
+  }


The vector size is set to 3 at line 67, but compute_vector() attempts to return values for up to 3*nphoton indices. This will cause out-of-bounds access when n >= 3 and nphoton > 1, potentially leading to crashes or undefined behavior.

Copilot · 2025-09-11T03:21:00Z

source/lmp/fix_cboamd.cpp

+        int idx = dp * nlocal * 3 + i * 3 + di; // index in dipole_grad_deepmd: dipole component dp, atom i, coordinate di
+        for (int alpha = 0; alpha < nphoton; alpha++) {
+          // CBOA force contribution from photon alpha
+          f[i][di] -= ea[alpha] * lambda_photon[alpha] * lambda_vector[alpha][di] * dipole_grad_deepmd[idx] / EV_TO_HARTREE;


Indexing error in lambda_vector access. The code uses lambda_vector[alpha][di] but should use lambda_vector[alpha][dp] since the lambda_vector represents the coupling vector for dipole component dp, not the atomic coordinate direction di.

Suggested change

f[i][di] -= ea[alpha] * lambda_photon[alpha] * lambda_vector[alpha][di] * dipole_grad_deepmd[idx] / EV_TO_HARTREE;

f[i][di] -= ea[alpha] * lambda_photon[alpha] * lambda_vector[alpha][dp] * dipole_grad_deepmd[idx] / EV_TO_HARTREE;

Copilot · 2025-09-11T03:21:00Z

source/lmp/fix_cboamd.h

+  static constexpr double EV_TO_HARTREE = 0.0367493;
+  static constexpr double ANGSTROM_TO_BOHR = 1.88973;
+  static constexpr double EV_PER_ANGSTROM_TO_HARTREE_PER_BOHR = 0.0194467;
+  static constexpr double PS_TO_AU = 41.3413745758e3; // 1 fs = 41.3413745758 a.u. of time


The comment incorrectly states '1 fs' when the constant name indicates picoseconds (PS). The comment should read '1 ps = 41.3413745758e3 a.u. of time' to match the PS_TO_AU constant name.

Suggested change

static constexpr double PS_TO_AU = 41.3413745758e3; // 1 fs = 41.3413745758 a.u. of time

static constexpr double PS_TO_AU = 41.3413745758e3; // 1 ps = 41.3413745758 a.u. of time

for more information, see https://pre-commit.ci

coderabbitai · 2025-09-11T03:23:41Z

Caution

Review failed

The head commit changed during the review from 031f9c0 to 2f88d06.

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source/lmp/fix_cboamd.cpp

+        FLERR,
+        "fix cboamd: lambda_vector must be specified when photons enabled");
+  }
+  // if (dt <= 0.0) error->all(FLERR,"fix cboamd: dt must be > 0");


source/lmp/fix_cboamd.cpp

+  init_deepmd_models();
+
+  // Open output file
+  output_file = fopen("cboamd_output.dat", "w");


source/lmp/fix_cboamd.cpp

+  // // Initialize DeepMD calculations
+  // convert_coordinates_to_deepmd_format();
+  // compute_deepmd_dipole();
+  // // compute_deepmd_polarizability();


source/lmp/fix_cboamd.cpp

+  // if (photons_enabled) {
+  //   compute_cboa_forces();
+  // }


source/lmp/fix_cboamd.cpp

+  // Update photon coordinates if enabled
+  // if (photons_enabled) {
+  // update_photon_coordinates();
+  // }


source/lmp/fix_cboamd.cpp

+  // Compute DeepMD properties
+  convert_coordinates_to_deepmd_format();
+  compute_deepmd_dipole();
+  // compute_deepmd_polarizability();


source/lmp/fix_cboamd.cpp

+    // Extract dipole components (DeepMD returns in eV/A, convert to a.u.)
+    // dipole[0] = dipole_deepmd[0] * ANGSTROM_TO_BOHR;
+    // dipole[1] = dipole_deepmd[1] * ANGSTROM_TO_BOHR;
+    // dipole[2] = dipole_deepmd[2] * ANGSTROM_TO_BOHR;


source/lmp/fix_cboamd.cpp

+void FixCBOAMD::write_output() {
+  // Write output to file
+  if (comm->me == 0) {
+    fprintf(output_file,


codecov · 2025-09-11T04:16:17Z

Codecov Report

❌ Patch coverage is 1.81818% with 324 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.82%. Comparing base (40f0b1c) to head (61c7289).

Files with missing lines	Patch %	Lines
source/lmp/fix_cboamd.cpp	0.00%	323 Missing ⚠️
source/lmp/plugin/deepmdplugin.cpp	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #4972      +/-   ##
==========================================
- Coverage   84.27%   83.82%   -0.46%     
==========================================
  Files         705      706       +1     
  Lines       69209    69548     +339     
  Branches     3573     3646      +73     
==========================================
- Hits        58325    58297      -28     
- Misses       9743    10112     +369     
+ Partials     1141     1139       -2

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add fix cboamd for cavity Born-Oppenheimer MD

031f9c0

Copilot AI review requested due to automatic review settings September 11, 2025 03:19

github-actions bot added the LAMMPS label Sep 11, 2025

Yi-FanLi marked this pull request as draft September 11, 2025 03:20

Copilot AI reviewed Sep 11, 2025

View reviewed changes

[pre-commit.ci] auto fixes from pre-commit.com hooks

2f88d06

for more information, see https://pre-commit.ci

github-advanced-security bot found potential problems Sep 11, 2025

View reviewed changes

delete potential-model-related lines

61c7289

	f[i][di] -= ea[alpha] * lambda_photon[alpha] * lambda_vector[alpha][di] * dipole_grad_deepmd[idx] / EV_TO_HARTREE;
	f[i][di] -= ea[alpha] * lambda_photon[alpha] * lambda_vector[alpha][dp] * dipole_grad_deepmd[idx] / EV_TO_HARTREE;

	static constexpr double PS_TO_AU = 41.3413745758e3; // 1 fs = 41.3413745758 a.u. of time
	static constexpr double PS_TO_AU = 41.3413745758e3; // 1 ps = 41.3413745758 a.u. of time

[WIP] Add fix cboamd for cavity Born-Oppenheimer MD #4972

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