Refactor general weight DPD potential (#81)

* Refactor Filenames DPDGeneralWeight * Rename parameters, add parameter struct * Add python class * Add test for DPDGeneralWeight * Fix typo and formatting * Move potentials to be alphabetical in pair.py * Remove unneccessary files * Fix whitespace * Fix docstring * Remove trailing whitespace * More whitespaces * Fix missing GPU in module.cc * configure whitespace settings * EOF fix? * more whitespace? * Add blank line * Applied clang-format * Remove whitespace from test py file * Apply formatting pre-commit :wq * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add DPD framework - rename files for consistency * add template class * Fix infrastructure * Fix wrong import GPU * More wrong imports * kT = 0 for potential test * Change RNG identifier * Add system test for DPD temperature * remove termalize momenta for just testing termostat * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix formatting * attempt to fix mpi in dpd test * Update unit-test.yaml * Simplify and fix DPD thermostat test * Follow azplugins naming conventions for DPD potential * Simplify pair potential special case * Cleanup DPD documentation * Don't execute GPU tests on GitHub Actions --------- Co-authored-by: Antonia Statt <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Michael Howard <[email protected]>
mphowardlab · Jul 16, 2024 · 0c520e0 · 0c520e0
1 parent b32e900
commit 0c520e0
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diff --git a/.github/workflows/unit-test.yaml b/.github/workflows/unit-test.yaml
@@ -22,7 +22,7 @@ env:
   # skip running the CPU tests in GPU builds
   _HOOMD_SKIP_CPU_TESTS_WHEN_GPUS_PRESENT_: 1
   # Require GPU tests in GPU builds.
-  _HOOMD_REQUIRE_GPU_TESTS_IN_GPU_BUILDS_: 1
+  # _HOOMD_REQUIRE_GPU_TESTS_IN_GPU_BUILDS_: 1
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

diff --git a/README.md b/README.md
@@ -24,7 +24,7 @@ python -m pytest --pyargs hoomd.azplugins
 Contributions are welcomed and appreciated! Fork and create a pull request on
 [GitHub][4]. Be sure to follow the [HOOMD-blue guidelines for developers][5]! We
 value the input and experiences all users and contributors bring to
-`relentless`.
+`azplugins`.
 
 ## History
 

diff --git a/doc/module-azplugins-pair.rst b/doc/module-azplugins-pair.rst
@@ -13,6 +13,7 @@ azplugins.pair
     :nosignatures:
 
     Colloid
+    DPDGeneralWeight
     Hertz
     PerturbedLennardJones
     TwoPatchMorse
@@ -22,6 +23,7 @@ azplugins.pair
 .. automodule:: hoomd.azplugins.pair
     :synopsis: Pair potentials.
     :members: Colloid,
+        DPDGeneralWeight,
         Hertz,
         PerturbedLennardJones,
         TwoPatchMorse

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -27,13 +27,18 @@ set(_bond_evaluators
     DoubleWell
     )
 
-# TODO: Add names of all pair evaluators`
+# TODO: Add names of all pair evaluators
 set(_pair_evaluators
     Colloid
     Hertz
     PerturbedLennardJones
     )
 
+# TODO: Add names of all dpd evaluators
+set(_dpd_evaluators
+    GeneralWeight
+    )
+
 # TODO: Add names of all anisotropic pair evaluators
 set(_aniso_pair_evaluators
     TwoPatchMorse
@@ -77,6 +82,25 @@ foreach(_evaluator ${_pair_evaluators})
     endif()
 endforeach()
 
+# process DPD potentials
+foreach(_evaluator ${_dpd_evaluators})
+    configure_file(export_PotentialPairDPDThermo.cc.inc
+                   export_PotentialPairDPDThermo${_evaluator}.cc
+                   @ONLY)
+    set(_${COMPONENT_NAME}_sources ${_${COMPONENT_NAME}_sources}  export_PotentialPairDPDThermo${_evaluator}.cc)
+
+    if (ENABLE_HIP)
+        configure_file(export_PotentialPairDPDThermoGPU.cc.inc
+                       export_PotentialPairDPDThermo${_evaluator}GPU.cc
+                       @ONLY)
+        configure_file(PotentialPairDPDThermoGPUKernel.cu.inc
+                       PotentialPairDPDThermo${_evaluator}GPUKernel.cu
+                       @ONLY)
+        set(_${COMPONENT_NAME}_sources ${_${COMPONENT_NAME}_sources} export_PotentialPairDPDThermo${_evaluator}GPU.cc)
+        set(_${COMPONENT_NAME}_cu_sources ${_${COMPONENT_NAME}_cu_sources} PotentialPairDPDThermo${_evaluator}GPUKernel.cu)
+    endif()
+endforeach()
+
 # process anisotropic pair potentials
 foreach(_evaluator ${_aniso_pair_evaluators})
     configure_file(export_AnisoPotentialPair.cc.inc

diff --git a/src/DPDEvaluatorGeneralWeight.h → src/DPDPairEvaluatorGeneralWeight.h b/src/DPDEvaluatorGeneralWeight.h → src/DPDPairEvaluatorGeneralWeight.h
@@ -3,31 +3,64 @@
 // Part of azplugins, released under the BSD 3-Clause License.
 
 /*!
- * \file DPDEvaluatorGeneralWeight.h
+ * \file DPDPairEvaluatorGeneralWeight.h
  * \brief Defines the dpd force evaluator using generalized weight functions.
  */
 
-#ifndef AZPLUGINS_DPD_EVALUATOR_GENERAL_WEIGHT_H_
-#define AZPLUGINS_DPD_EVALUATOR_GENERAL_WEIGHT_H_
+#ifndef AZPLUGINS_DPD_PAIR_EVALUATOR_GENERAL_WEIGHT_H_
+#define AZPLUGINS_DPD_PAIR_EVALUATOR_GENERAL_WEIGHT_H_
 
 #include "PairEvaluator.h"
 
 #include "RNGIdentifiers.h"
 #include "hoomd/HOOMDMath.h"
 #include "hoomd/RandomNumbers.h"
 
-#ifdef NVCC
+#ifdef __HIPCC__
 #define DEVICE __device__
 #else
 #define DEVICE
-#include <string>
 #endif
 
+namespace hoomd
+    {
 namespace azplugins
     {
 namespace detail
     {
 
+struct PairParametersDPDGeneralWeight : public PairParameters
+    {
+#ifndef __HIPCC__
+    PairParametersDPDGeneralWeight() : A(0), gamma(0), s(0) { }
+
+    PairParametersDPDGeneralWeight(pybind11::dict v, bool managed = false)
+        {
+        A = v["A"].cast<Scalar>();
+        gamma = v["gamma"].cast<Scalar>();
+        s = v["s"].cast<Scalar>();
+        }
+
+    pybind11::dict asDict()
+        {
+        pybind11::dict v;
+        v["A"] = A;
+        v["gamma"] = gamma;
+        v["s"] = s;
+        return v;
+        }
+#endif // __HIPCC__
+
+    Scalar A;
+    Scalar gamma;
+    Scalar s;
+    }
+#if HOOMD_LONGREAL_SIZE == 32
+    __attribute__((aligned(16)));
+#else
+    __attribute__((aligned(32)));
+#endif
+
 //! Evaluator for DPD generalized dissipative / random weight functions
 /*!
  * Implements the generalized weight functions described in;
@@ -57,21 +90,25 @@ namespace detail
  * where \a s is usually 2 for the "standard" DPD method. Refer to the original paper for more
  * details.
  */
-class DPDEvaluatorGeneralWeight : public PairEvaluator
+class DPDPairEvaluatorGeneralWeight : public PairEvaluator
     {
     public:
     //! Three parameters are used by this DPD potential evaluator
-    typedef Scalar3 param_type;
+    typedef PairParametersDPDGeneralWeight param_type;
 
     //! Constructs the DPD potential evaluator
     /*!
      * \param _rsq Squared distance beteen the particles
      * \param _rcutsq Sqauared distance at which the potential goes to 0
      * \param _params Per type pair parameters of this potential
      */
-    DEVICE DPDEvaluatorGeneralWeight(Scalar _rsq, Scalar _rcutsq, const param_type& _params)
-        : PairEvaluator(_rsq, _rcutsq), a(_params.x), gamma(_params.y), s(_params.z)
+    DEVICE
+    DPDPairEvaluatorGeneralWeight(Scalar _rsq, Scalar _rcutsq, const param_type& _params)
+        : PairEvaluator(_rsq, _rcutsq)
         {
+        A = _params.A;
+        gamma = _params.gamma;
+        s = _params.s;
         }
 
     //! Set seed, i and j (particle tags), and the timestep
@@ -82,7 +119,7 @@ class DPDEvaluatorGeneralWeight : public PairEvaluator
      * \param timestep Timestep to evaluate forces at
      */
     DEVICE void
-    set_seed_ij_timestep(unsigned int seed, unsigned int i, unsigned int j, unsigned int timestep)
+    set_seed_ij_timestep(uint16_t seed, unsigned int i, unsigned int j, unsigned int timestep)
         {
         m_seed = seed;
         m_i = i;
@@ -136,8 +173,8 @@ class DPDEvaluatorGeneralWeight : public PairEvaluator
             Scalar rcut = Scalar(1.0) / rcutinv;
 
             // force is easy to calculate
-            force_divr = a * (rinv - rcutinv);
-            pair_eng = a * (rcut - r) - Scalar(0.5) * a * rcutinv * (rcutsq - rsq);
+            force_divr = A * (rinv - rcutinv);
+            pair_eng = A * (rcut - r) - Scalar(0.5) * A * rcutinv * (rcutsq - rsq);
 
             return true;
             }
@@ -187,15 +224,16 @@ class DPDEvaluatorGeneralWeight : public PairEvaluator
                 }
 
             // Generate a single random number
-            hoomd::RandomGenerator rng(azplugins::RNGIdentifier::DPDEvaluatorGeneralWeight,
-                                       m_seed,
-                                       m_oi,
-                                       m_oj,
-                                       m_timestep);
+            hoomd::RandomGenerator rng(
+                hoomd::Seed(hoomd::azplugins::detail::RNGIdentifier::DPDEvaluatorGeneralWeight,
+                            m_timestep,
+                            m_seed),
+                hoomd::Counter(m_oi, m_oj));
+
             Scalar alpha = hoomd::UniformDistribution<Scalar>(-1, 1)(rng);
 
             // conservative dpd
-            force_divr = a * (rinv - rcutinv);
+            force_divr = A * (rinv - rcutinv);
 
             //  conservative force only
             force_divr_cons = force_divr;
@@ -208,7 +246,7 @@ class DPDEvaluatorGeneralWeight : public PairEvaluator
             force_divr += fast::rsqrt(m_deltaT / (m_T * gamma * Scalar(6.0))) * wR * alpha;
 
             // conservative energy only
-            pair_eng = a * (rcut - r) - Scalar(0.5) * a * rcutinv * (rcutsq - rsq);
+            pair_eng = A * (rcut - r) - Scalar(0.5) * A * rcutinv * (rcutsq - rsq);
 
             return true;
             }
@@ -225,11 +263,11 @@ class DPDEvaluatorGeneralWeight : public PairEvaluator
 #endif
 
     protected:
-    Scalar a;     //!< Strength of repulsion
+    Scalar A;     //!< Strength of repulsion
     Scalar gamma; //!< Drag term
     Scalar s;     //!< Exponent for the dissipative weight function
 
-    unsigned int m_seed;     //!< User set seed for PRNG
+    uint16_t m_seed;         //!< User set seed for PRNG
     unsigned int m_i;        //!< Tag of first particle for PRNG
     unsigned int m_j;        //!< Tag of second particle for PRNG
     unsigned int m_timestep; //!< timestep for use in PRNG
@@ -241,7 +279,8 @@ class DPDEvaluatorGeneralWeight : public PairEvaluator
 
     } // end namespace detail
     } // end namespace azplugins
+    } // end namespace hoomd
 
 #undef DEVICE
 
-#endif // AZPLUGINS_DPD_EVALUATOR_GENERAL_WEIGHT_H_
+#endif // AZPLUGINS_DPD_PAIR_EVALUATOR_GENERAL_WEIGHT_H_
diff --git a/src/DPDPotentialGeneralWeight.cu b/src/DPDPotentialGeneralWeight.cu
diff --git a/src/DPDPotentials.cuh b/src/DPDPotentials.cuh
diff --git a/src/DPDPotentials.h b/src/DPDPotentials.h