ipi: remove normalize_coord (#3257)

(1) Remove `normalize_coord` and add a test to confirm it still works; (2) Remove the include of `SimulationRegion.h` and the direct link to `libdeepmd.so`; (3) Allow using a pre-compiled C library to build `dp_ipi`. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
deepmodeling · Feb 11, 2024 · c131c8f · c131c8f
1 parent dc63793
commit c131c8f
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diff --git a/doc/install/install-from-c-library.md b/doc/install/install-from-c-library.md
@@ -14,7 +14,7 @@ tar xzf libdeepmd_c.tar.gz
 
 The library is built in Linux (GLIBC 2.17) with CUDA 12.2 (`libdeepmd_c.tar.gz`) or 11.8 (`libdeepmd_c_cu11.tar.gz`). It's noted that this package does not contain CUDA Toolkit and cuDNN, so one needs to download them from the NVIDIA website.
 
-## Use Pre-compiled C Library to build the LAMMPS plugin and GROMACS patch
+## Use Pre-compiled C Library to build the LAMMPS plugin, i-PI driver, and GROMACS patch
 
 When one [installs DeePMD-kit's C++ interface](./install-from-source.md#install-deepmd-kits-c-interface), one can use the CMake argument `DEEPMD_C_ROOT` to the path `libdeepmd_c`.
 
@@ -27,4 +27,5 @@ make -j8
 make install
 ```
 
-Then one can follow the manual [Install LAMMPS](./install-lammps.md) and/or [Install GROMACS](./install-gromacs.md).
+Then the i-PI driver `dp_ipi` will be built and installed.
+One can also follow the manual [Install LAMMPS](./install-lammps.md) and/or [Install GROMACS](./install-gromacs.md).
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
@@ -297,10 +297,7 @@ if(BUILD_CPP_IF)
   endif()
   if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 4.8)
     # add_subdirectory (md/)
-    if(ENABLE_IPI
-       OR NOT BUILD_PY_IF
-       AND NOT DEEPMD_C_ROOT)
-      # ipi has a dependency on libdeepmd
+    if(ENABLE_IPI OR NOT BUILD_PY_IF)
       add_subdirectory(ipi/)
     endif()
     if(NOT BUILD_PY_IF)

diff --git a/source/ipi/CMakeLists.txt b/source/ipi/CMakeLists.txt
@@ -14,7 +14,7 @@ add_executable(${ipiname} ${DRIVER_SOURCE_FILES})
 # link: libdeepmd_cc
 if(DP_USING_C_API)
   # SimulationRegion.h
-  target_link_libraries(${ipiname} PRIVATE ${LIB_DEEPMD_C} ${LIB_DEEPMD})
+  target_link_libraries(${ipiname} PRIVATE ${LIB_DEEPMD_C})
   target_precompile_headers(${ipiname} PRIVATE [["deepmd.hpp"]])
   remove_definitions(-D_GLIBCXX_USE_CXX11_ABI=${OP_CXX_ABI})
 else()

diff --git a/source/ipi/driver.cc b/source/ipi/driver.cc
@@ -12,7 +12,6 @@ namespace deepmd_compat = deepmd;
 #include "deepmd.hpp"
 namespace deepmd_compat = deepmd::hpp;
 #endif
-#include "SimulationRegion.h"
 #include "XyzFileManager.h"
 #include "json.hpp"
 #include "sockets.h"
@@ -49,25 +48,6 @@ char *trimwhitespace(char *str) {
   return str;
 }
 
-void normalize_coord(std::vector<double> &coord,
-                     const SimulationRegion<double> &region) {
-  int natoms = coord.size() / 3;
-
-  for (int ii = 0; ii < natoms; ++ii) {
-    double inter[3];
-    region.phys2Inter(inter, &coord[3 * ii]);
-    for (int dd = 0; dd < 3; ++dd) {
-      inter[dd] -= int(floor(inter[dd]));
-      if (inter[dd] < 0) {
-        inter[dd] += 1.;
-      } else if (inter[dd] >= 1) {
-        inter[dd] -= 1.;
-      }
-    }
-    region.inter2Phys(&coord[3 * ii], inter);
-  }
-}
-
 int main(int argc, char *argv[]) {
   if (argc == 1) {
     std::cerr << "usage " << std::endl;
@@ -122,7 +102,6 @@ int main(int argc, char *argv[]) {
   std::vector<double> dcoord_tmp;
   std::vector<int> dtype = cvt.get_type();
   std::vector<double> dbox(9, 0);
-  SimulationRegion<double> region;
   double *msg_buff = NULL;
   double ener;
   double virial[9];
@@ -179,7 +158,6 @@ int main(int argc, char *argv[]) {
       for (int dd = 0; dd < 9; ++dd) {
         dbox[dd] = cell_h[(dd % 3) * 3 + (dd / 3)] * cvt_len;
       }
-      region.reinitBox(&dbox[0]);
 
       // get number of atoms
       readbuffer_(&socket, (char *)(&cbuf), sizeof(int32_t));
@@ -203,7 +181,6 @@ int main(int argc, char *argv[]) {
         dcoord_tmp[ii] = msg_buff[ii] * cvt_len;
       }
       cvt.forward(dcoord, dcoord_tmp, 3);
-      normalize_coord(dcoord, region);
 
       // nnp over writes ener, force and virial
       nnp_inter.compute(dener, dforce_tmp, dvirial, dcoord, dtype, dbox);

diff --git a/source/ipi/tests/test_driver.py b/source/ipi/tests/test_driver.py
@@ -53,7 +53,7 @@ def write_input(self, atoms, **kwargs):
         atoms.write(self.xyz_file, format="xyz")
 
 
-class TestDeepPotALargeBoxNoPBC(unittest.TestCase):
+class TestDPIPI(unittest.TestCase):
     # copy from test_deeppot_a.py
     @classmethod
     def setUpClass(cls):
@@ -193,8 +193,8 @@ def test_ase_unix(self):
                 cell=self.box.reshape((3, 3)),
                 calculator=calc,
             )
-        ee = water.get_potential_energy()
-        ff = water.get_forces()
+            ee = water.get_potential_energy()
+            ff = water.get_forces()
         nframes = 1
         np.testing.assert_almost_equal(
             ff.ravel(), self.expected_f.ravel(), default_places
@@ -213,8 +213,38 @@ def test_ase_nounix(self):
                 cell=self.box.reshape((3, 3)),
                 calculator=calc,
             )
-        ee = water.get_potential_energy()
-        ff = water.get_forces()
+            ee = water.get_potential_energy()
+            ff = water.get_forces()
+        nframes = 1
+        np.testing.assert_almost_equal(
+            ff.ravel(), self.expected_f.ravel(), default_places
+        )
+        expected_se = np.sum(self.expected_e.reshape([nframes, -1]), axis=1)
+        np.testing.assert_almost_equal(ee.ravel(), expected_se.ravel(), default_places)
+
+    def test_normalize_coords(self):
+        # coordinate nomarlization should happen inside the interface
+        cell = self.box.reshape((3, 3))
+        coord = self.coords.reshape((-1, 3))
+        # random unwrap coords
+        coord[0] += np.array([3, 0, 0]) @ cell
+        coord[1] += np.array([0, -3, 0]) @ cell
+        coord[2] += np.array([0, 0, 3]) @ cell
+        coord[3] += np.array([-3, 0, 0]) @ cell
+        coord[4] += np.array([0, 3, 0]) @ cell
+        coord[5] += np.array([0, 0, -3]) @ cell
+        with SocketIOCalculator(
+            DPiPICalculator(self.model_file, use_unix=False),
+            log=sys.stdout,
+        ) as calc:
+            water = Atoms(
+                "OHHOHH",
+                positions=coord,
+                cell=cell,
+                calculator=calc,
+            )
+            ee = water.get_potential_energy()
+            ff = water.get_forces()
         nframes = 1
         np.testing.assert_almost_equal(
             ff.ravel(), self.expected_f.ravel(), default_places