Add NonbondedInteractionGroup potential, rename existing nonbonded po…

…tentials (#578)

tests/test_parameter_interpolation.py

@@ -2,22 +2,13 @@
 
 config.update("jax_enable_x64", True)
 import copy
-import functools
 
 import jax.numpy as jnp
 import numpy as np
 from common import GradientTest, prepare_water_system
 
 from timemachine.lib import potentials
-
-
-def interpolated_potential(conf, params, box, lamb, u_fn):
-    assert params.size % 2 == 0
-
-    CP = params.shape[0] // 2
-    new_params = (1 - lamb) * params[:CP] + lamb * params[CP:]
-
-    return u_fn(conf, new_params, box, lamb)
+from timemachine.potentials import nonbonded
 
 
 class TestInterpolatedPotential(GradientTest):
@@ -57,7 +48,7 @@ def test_nonbonded(self):
 
                 print("lambda", lamb, "cutoff", cutoff, "precision", precision, "xshape", coords.shape)
 
-                ref_interpolated_potential = functools.partial(interpolated_potential, u_fn=ref_potential)
+                ref_interpolated_potential = nonbonded.interpolated(ref_potential)
 
                 test_interpolated_potential = potentials.NonbondedInterpolated(*test_potential.args)
 

timemachine/cpp/CMakeLists.txt

@@ -42,8 +42,9 @@ pybind11_add_module(${LIBRARY_NAME} SHARED NO_EXTRAS
   src/gpu_utils.cu
   src/vendored/hilbert.cpp
   src/nonbonded.cu
-  src/nonbonded_dense.cu
-  src/nonbonded_pairs.cu
+  src/nonbonded_all_pairs.cu
+  src/nonbonded_pair_list.cu
+  src/nonbonded_interaction_group.cu
   src/neighborlist.cu
   src/harmonic_bond.cu
   src/harmonic_angle.cu
@@ -54,6 +55,7 @@ pybind11_add_module(${LIBRARY_NAME} SHARED NO_EXTRAS
   src/rmsd_align.cpp
   src/summed_potential.cu
   src/device_buffer.cu
+  src/kernels/k_nonbonded.cu
   src/kernels/nonbonded_common.cu
 )
 

timemachine/cpp/src/kernels/k_nonbonded.cu

@@ -0,0 +1,91 @@
+#include "k_nonbonded.cuh"
+
+void __global__ k_coords_to_kv(
+    const int N,
+    const double *coords,
+    const double *box,
+    const unsigned int *bin_to_idx,
+    unsigned int *keys,
+    unsigned int *vals) {
+
+    const int atom_idx = blockIdx.x * blockDim.x + threadIdx.x;
+
+    if (atom_idx >= N) {
+        return;
+    }
+
+    // these coords have to be centered
+    double bx = box[0 * 3 + 0];
+    double by = box[1 * 3 + 1];
+    double bz = box[2 * 3 + 2];
+
+    double binWidth = max(max(bx, by), bz) / 255.0;
+
+    double x = coords[atom_idx * 3 + 0];
+    double y = coords[atom_idx * 3 + 1];
+    double z = coords[atom_idx * 3 + 2];
+
+    x -= bx * floor(x / bx);
+    y -= by * floor(y / by);
+    z -= bz * floor(z / bz);
+
+    unsigned int bin_x = x / binWidth;
+    unsigned int bin_y = y / binWidth;
+    unsigned int bin_z = z / binWidth;
+
+    keys[atom_idx] = bin_to_idx[bin_x * 256 * 256 + bin_y * 256 + bin_z];
+    // uncomment below if you want to preserve the atom ordering
+    // keys[atom_idx] = atom_idx;
+    vals[atom_idx] = atom_idx;
+}
+
+// TODO: DRY with k_coords_to_kv
+void __global__ k_coords_to_kv_gather(
+    const int N,
+    const unsigned int *atom_idxs,
+    const double *coords,
+    const double *box,
+    const unsigned int *bin_to_idx,
+    unsigned int *keys,
+    unsigned int *vals) {
+
+    const int idx = blockIdx.x * blockDim.x + threadIdx.x;
+
+    if (idx >= N) {
+        return;
+    }
+
+    const int atom_idx = atom_idxs[idx];
+
+    // these coords have to be centered
+    double bx = box[0 * 3 + 0];
+    double by = box[1 * 3 + 1];
+    double bz = box[2 * 3 + 2];
+
+    double binWidth = max(max(bx, by), bz) / 255.0;
+
+    double x = coords[atom_idx * 3 + 0];
+    double y = coords[atom_idx * 3 + 1];
+    double z = coords[atom_idx * 3 + 2];
+
+    x -= bx * floor(x / bx);
+    y -= by * floor(y / by);
+    z -= bz * floor(z / bz);
+
+    unsigned int bin_x = x / binWidth;
+    unsigned int bin_y = y / binWidth;
+    unsigned int bin_z = z / binWidth;
+
+    keys[idx] = bin_to_idx[bin_x * 256 * 256 + bin_y * 256 + bin_z];
+    // uncomment below if you want to preserve the atom ordering
+    // keys[idx] = atom_idx;
+    vals[idx] = atom_idx;
+}
+
+void __global__ k_arange(int N, unsigned int *arr) {
+    const int atom_idx = blockIdx.x * blockDim.x + threadIdx.x;
+    if (atom_idx >= N) {
+        return;
+    }
+    arr[atom_idx] = atom_idx;
+}

timemachine/cpp/src/kernels/k_nonbonded_dense.cuh → timemachine/cpp/src/kernels/k_nonbonded.cuh

@@ -5,45 +5,26 @@
 #include "nonbonded_common.cuh"
 #include "surreal.cuh"
 
+void __global__ k_arange(int N, unsigned int *arr);
+
 // generate kv values from coordinates to be radix sorted
 void __global__ k_coords_to_kv(
     const int N,
     const double *coords,
     const double *box,
     const unsigned int *bin_to_idx,
     unsigned int *keys,
-    unsigned int *vals) {
-
-    const int atom_idx = blockIdx.x * blockDim.x + threadIdx.x;
-
-    if (atom_idx >= N) {
-        return;
-    }
-
-    // these coords have to be centered
-    double bx = box[0 * 3 + 0];
-    double by = box[1 * 3 + 1];
-    double bz = box[2 * 3 + 2];
-
-    double binWidth = max(max(bx, by), bz) / 255.0;
+    unsigned int *vals);
 
-    double x = coords[atom_idx * 3 + 0];
-    double y = coords[atom_idx * 3 + 1];
-    double z = coords[atom_idx * 3 + 2];
-
-    x -= bx * floor(x / bx);
-    y -= by * floor(y / by);
-    z -= bz * floor(z / bz);
-
-    unsigned int bin_x = x / binWidth;
-    unsigned int bin_y = y / binWidth;
-    unsigned int bin_z = z / binWidth;
-
-    keys[atom_idx] = bin_to_idx[bin_x * 256 * 256 + bin_y * 256 + bin_z];
-    // uncomment below if you want to preserve the atom ordering
-    // keys[atom_idx] = atom_idx;
-    vals[atom_idx] = atom_idx;
-}
+// variant of k_coords_to_kv allowing the selection of a subset of coordinates
+void __global__ k_coords_to_kv_gather(
+    const int N,                   // number of atoms in selection
+    const unsigned int *atom_idxs, // [N] indices of atoms to select
+    const double *coords,
+    const double *box,
+    const unsigned int *bin_to_idx,
+    unsigned int *keys,
+    unsigned int *vals);
 
 template <typename RealType>
 void __global__ k_check_rebuild_box(const int N, const double *new_box, const double *old_box, int *rebuild) {
@@ -282,7 +263,8 @@ template <
     bool COMPUTE_DU_DP>
 // void __device__ __forceinline__ v_nonbonded_unified(
 void __device__ v_nonbonded_unified(
-    const int N,
+    const int NC,
+    const int NR,
     const double *__restrict__ coords,
     const double *__restrict__ params, // [N]
     const double *__restrict__ box,
@@ -316,6 +298,12 @@ void __device__ v_nonbonded_unified(
     // int lambda_offset_i = atom_i_idx < N ? lambda_offset_idxs[atom_i_idx] : 0;
     // int lambda_plane_i = atom_i_idx < N ? lambda_plane_idxs[atom_i_idx] : 0;
 
+    const int N = NC + NR;
+
+    if (NR != 0) {
+        atom_i_idx += NC;
+    }
+
     RealType ci_x = atom_i_idx < N ? coords[atom_i_idx * 3 + 0] : 0;
     RealType ci_y = atom_i_idx < N ? coords[atom_i_idx * 3 + 1] : 0;
     RealType ci_z = atom_i_idx < N ? coords[atom_i_idx * 3 + 2] : 0;
@@ -348,15 +336,15 @@ void __device__ v_nonbonded_unified(
     // int lambda_offset_j = atom_j_idx < N ? lambda_offset_idxs[atom_j_idx] : 0;
     // int lambda_plane_j = atom_j_idx < N ? lambda_plane_idxs[atom_j_idx] : 0;
 
-    RealType cj_x = atom_j_idx < N ? coords[atom_j_idx * 3 + 0] : 0;
-    RealType cj_y = atom_j_idx < N ? coords[atom_j_idx * 3 + 1] : 0;
-    RealType cj_z = atom_j_idx < N ? coords[atom_j_idx * 3 + 2] : 0;
-    RealType cj_w = atom_j_idx < N ? coords_w[atom_j_idx] : 0;
+    RealType cj_x = atom_j_idx < NC ? coords[atom_j_idx * 3 + 0] : 0;
+    RealType cj_y = atom_j_idx < NC ? coords[atom_j_idx * 3 + 1] : 0;
+    RealType cj_z = atom_j_idx < NC ? coords[atom_j_idx * 3 + 2] : 0;
+    RealType cj_w = atom_j_idx < NC ? coords_w[atom_j_idx] : 0;
 
-    RealType dq_dl_j = atom_j_idx < N ? dp_dl[atom_j_idx * 3 + 0] : 0;
-    RealType dsig_dl_j = atom_j_idx < N ? dp_dl[atom_j_idx * 3 + 1] : 0;
-    RealType deps_dl_j = atom_j_idx < N ? dp_dl[atom_j_idx * 3 + 2] : 0;
-    RealType dw_dl_j = atom_j_idx < N ? dw_dl[atom_j_idx] : 0;
+    RealType dq_dl_j = atom_j_idx < NC ? dp_dl[atom_j_idx * 3 + 0] : 0;
+    RealType dsig_dl_j = atom_j_idx < NC ? dp_dl[atom_j_idx * 3 + 1] : 0;
+    RealType deps_dl_j = atom_j_idx < NC ? dp_dl[atom_j_idx * 3 + 2] : 0;
+    RealType dw_dl_j = atom_j_idx < NC ? dw_dl[atom_j_idx] : 0;
 
     unsigned long long gj_x = 0;
     unsigned long long gj_y = 0;
@@ -366,9 +354,9 @@ void __device__ v_nonbonded_unified(
     int lj_param_idx_sig_j = atom_j_idx * 3 + 1;
     int lj_param_idx_eps_j = atom_j_idx * 3 + 2;
 
-    RealType qj = atom_j_idx < N ? params[charge_param_idx_j] : 0;
-    RealType sig_j = atom_j_idx < N ? params[lj_param_idx_sig_j] : 0;
-    RealType eps_j = atom_j_idx < N ? params[lj_param_idx_eps_j] : 0;
+    RealType qj = atom_j_idx < NC ? params[charge_param_idx_j] : 0;
+    RealType sig_j = atom_j_idx < NC ? params[lj_param_idx_sig_j] : 0;
+    RealType eps_j = atom_j_idx < NC ? params[lj_param_idx_eps_j] : 0;
 
     unsigned long long g_qj = 0;
     unsigned long long g_sigj = 0;
@@ -403,11 +391,17 @@ void __device__ v_nonbonded_unified(
             d2ij += delta_w * delta_w;
         }
 
+        const bool valid_ij =
+            atom_i_idx < N &&
+            ((NR == 0) ? atom_i_idx < atom_j_idx && atom_j_idx < N // all-pairs case, only compute the upper tri
+                                                                   //   0  <= i < N, i < j < N
+                       : atom_j_idx < NC);                         // ixn groups case, compute all pairwise ixns
+                                                                   //   NC <= i < N, 0 <= j < NC
+
         // (ytz): note that d2ij must be *strictly* less than cutoff_squared. This is because we set the
         // non-interacting atoms to exactly real_cutoff*real_cutoff. This ensures that atoms who's 4th dimension
         // is set to cutoff are non-interacting.
-        if (d2ij < cutoff_squared && atom_j_idx > atom_i_idx && atom_j_idx < N && atom_i_idx < N) {
-
+        if (d2ij < cutoff_squared && valid_ij) {
             // electrostatics
             RealType u;
             RealType es_prefactor;
@@ -547,7 +541,8 @@ void __device__ v_nonbonded_unified(
 
 template <typename RealType, bool COMPUTE_U, bool COMPUTE_DU_DX, bool COMPUTE_DU_DL, bool COMPUTE_DU_DP>
 void __global__ k_nonbonded_unified(
-    const int N,
+    const int NC,
+    const int NR,
     const double *__restrict__ coords,
     const double *__restrict__ params, // [N]
     const double *__restrict__ box,
@@ -567,6 +562,12 @@ void __global__ k_nonbonded_unified(
     int row_block_idx = ixn_tiles[tile_idx];
     int atom_i_idx = row_block_idx * 32 + threadIdx.x;
 
+    const int N = NC + NR;
+
+    if (NR != 0) {
+        atom_i_idx += NC;
+    }
+
     RealType dq_dl_i = atom_i_idx < N ? dp_dl[atom_i_idx * 3 + 0] : 0;
     RealType dsig_dl_i = atom_i_idx < N ? dp_dl[atom_i_idx * 3 + 1] : 0;
     RealType deps_dl_i = atom_i_idx < N ? dp_dl[atom_i_idx * 3 + 2] : 0;
@@ -587,7 +588,8 @@ void __global__ k_nonbonded_unified(
 
     if (tile_is_vanilla) {
         v_nonbonded_unified<RealType, 0, COMPUTE_U, COMPUTE_DU_DX, COMPUTE_DU_DL, COMPUTE_DU_DP>(
-            N,
+            NC,
+            NR,
             coords,
             params,
             box,
@@ -604,7 +606,8 @@ void __global__ k_nonbonded_unified(
             u_buffer);
     } else {
         v_nonbonded_unified<RealType, 1, COMPUTE_U, COMPUTE_DU_DX, COMPUTE_DU_DL, COMPUTE_DU_DP>(
-            N,
+            NC,
+            NR,
             coords,
             params,
             box,

timemachine/cpp/src/kernels/k_nonbonded_pairs.cuh → timemachine/cpp/src/kernels/k_nonbonded_pair_list.cuh

@@ -14,7 +14,7 @@ void __device__ __forceinline__ accumulate(unsigned long long *__restrict acc, u
 }
 
 template <typename RealType, bool Negated>
-void __global__ k_nonbonded_pairs(
+void __global__ k_nonbonded_pair_list(
     const int M, // number of pairs
     const double *__restrict__ coords,
     const double *__restrict__ params,

timemachine/cpp/src/nonbonded.hpp

@@ -1,7 +1,7 @@
 #pragma once
 
-#include "nonbonded_dense.hpp"
-#include "nonbonded_pairs.hpp"
+#include "nonbonded_all_pairs.hpp"
+#include "nonbonded_pair_list.hpp"
 #include "potential.hpp"
 #include <vector>
 
@@ -10,10 +10,10 @@ namespace timemachine {
 template <typename RealType, bool Interpolated> class Nonbonded : public Potential {
 
 private:
-    NonbondedDense<RealType, Interpolated> dense_;
+    NonbondedAllPairs<RealType, Interpolated> dense_;
 
     static const bool Negated = true;
-    NonbondedPairs<RealType, Negated, Interpolated> exclusions_; // implement exclusions as negated NonbondedPairs
+    NonbondedPairList<RealType, Negated, Interpolated> exclusions_; // implement exclusions as negated NonbondedPairList
 
 public:
     // these are marked public but really only intended for testing.