add support for set_vector for fix external in c-library, python and unittest

.gitignore

@@ -44,6 +44,7 @@ Thumbs.db
 /build*
 /CMakeCache.txt
 /CMakeFiles/
+/Testing
 /Makefile
 /cmake_install.cmake
 /lmp

doc/src/Library_utility.rst

@@ -8,7 +8,11 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_decode_image_flags`
 - :cpp:func:`lammps_set_fix_external_callback`
 - :cpp:func:`lammps_fix_external_set_energy_global`
+- :cpp:func:`lammps_fix_external_set_energy_peratom`
 - :cpp:func:`lammps_fix_external_set_virial_global`
+- :cpp:func:`lammps_fix_external_set_virial_peratom`
+- :cpp:func:`lammps_fix_external_set_vector_length`
+- :cpp:func:`lammps_fix_external_set_vector`
 - :cpp:func:`lammps_free`
 - :cpp:func:`lammps_is_running`
 - :cpp:func:`lammps_force_timeout`
@@ -43,11 +47,31 @@ where such memory buffers were allocated that require the use of
 
 -----------------------
 
+.. doxygenfunction:: lammps_fix_external_set_energy_peratom
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_fix_external_set_virial_global
    :project: progguide
 
 -----------------------
 
+.. doxygenfunction:: lammps_fix_external_set_virial_peratom
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_fix_external_set_vector_length
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_fix_external_set_vector
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_free
    :project: progguide
 

python/lammps/core.py

@@ -303,6 +303,9 @@ class lammps(object):
     self.lib.lammps_fix_external_set_energy_peratom.argtypes = [c_void_p, c_char_p, POINTER(c_double)]
     self.lib.lammps_fix_external_set_virial_peratom.argtypes = [c_void_p, c_char_p, POINTER(POINTER(c_double))]
 
+    self.lib.lammps_fix_external_set_vector_length.argtypes = [c_void_p, c_char_p, c_int]
+    self.lib.lammps_fix_external_set_vector.argtypes = [c_void_p, c_char_p, c_int, c_double]
+
     # detect if Python is using a version of mpi4py that can pass communicators
     # only needed if LAMMPS has been compiled with MPI support.
     self.has_mpi4py = False
@@ -1806,6 +1809,40 @@ class lammps(object):
     with ExceptionCheck(self):
       return self.lib.lammps_fix_external_set_energy_global(self.lmp, fix_id.encode(), eng)
 
+  # -------------------------------------------------------------------------
+  def fix_external_set_vector_length(self, fix_id, length):
+    """Set the vector length for a global vector stored with fix external for analysis
+
+    This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
+    of the C-library interface.
+
+    :param fix_id:  Fix-ID of a fix external instance
+    :type: string
+    :param length:  length of the global vector
+    :type: int
+    """
+
+    with ExceptionCheck(self):
+      return self.lib.lammps_fix_external_set_vector_length(self.lmp, fix_id.encode(), length)
+
+  # -------------------------------------------------------------------------
+  def fix_external_set_vector(self, fix_id, idx, val):
+    """Store a global vector value for a fix external instance with the given ID.
+
+    This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
+    of the C-library interface.
+
+    :param fix_id:  Fix-ID of a fix external instance
+    :type: string
+    :param idx:     1-based index of the value in the global vector
+    :type: int
+    :param val:     value to be stored in the global vector
+    :type: float
+    """
+
+    with ExceptionCheck(self):
+      return self.lib.lammps_fix_external_set_vector(self.lmp, fix_id.encode(), idx, val)
+
   # -------------------------------------------------------------------------
 
   def get_neighlist(self, idx):

src/library.cpp

@@ -4821,7 +4821,7 @@ mode. The function has to have C language bindings with the prototype:
 
    void func(void *ptr, bigint timestep, int nlocal, tagint *ids, double **x, double **fexternal);
 
-This is an alternative to the array mechanism set up by :cpp:func:`lammps_fix_external_set_force`.
+This is an alternative to the array mechanism set up by :cpp:func:`lammps_fix_external_get_force`.
 
 Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
@@ -4913,7 +4913,7 @@ double **lammps_fix_external_get_force(void *handle, const char *id)
 \verbatim embed:rst
 
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
-:cpp:func:`lammps_fix_external_set_force` to also set the contribution
+:cpp:func:`lammps_fix_external_get_force` to also set the contribution
 to the global energy from the external code.
 
 Please see the documentation for :doc:`fix external <fix_external>` for
@@ -4952,7 +4952,7 @@ void lammps_fix_external_set_energy_global(void *handle, const char *id, double
 \verbatim embed:rst
 
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
-:cpp:func:`lammps_fix_external_set_force` to also set the contribution
+:cpp:func:`lammps_fix_external_get_force` to also set the contribution
 to the global virial from the external code.
 
 Please see the documentation for :doc:`fix external <fix_external>` for
@@ -4991,7 +4991,7 @@ void lammps_fix_external_set_virial_global(void *handle, const char *id, double
 \verbatim embed:rst
 
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
-:cpp:func:`lammps_fix_external_set_force` to also set the contribution
+:cpp:func:`lammps_fix_external_get_force` to also set the contribution
 to the per-atom energy from the external code.
 
 Please see the documentation for :doc:`fix external <fix_external>` for
@@ -5030,7 +5030,7 @@ void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double
 \verbatim embed:rst
 
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
-:cpp:func:`lammps_fix_external_set_force` to also set the contribution
+:cpp:func:`lammps_fix_external_get_force` to also set the contribution
 to the per-atom virial from the external code.
 
 Please see the documentation for :doc:`fix external <fix_external>` for
@@ -5064,6 +5064,86 @@ void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double
   END_CAPTURE
 }
 
+/** Set the vector length for a global vector stored with fix external for analysis
+
+\verbatim embed:rst
+
+This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
+:cpp:func:`lammps_fix_external_get_force` to set the length of a global vector of
+properties that will be stored with the fix via :cpp:func:`lammps_fix_external_set_vector`.
+
+Please see the documentation for :doc:`fix external <fix_external>` for
+more information about how to use the fix and how to couple it with an
+external code.
+
+\endverbatim
+ *
+ * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
+ * \param  id       fix ID of fix external instance
+ * \param  len      length of the global vector to be stored with the fix */
+
+void lammps_fix_external_set_vector_length(void *handle, const char *id, int len)
+{
+  LAMMPS *lmp = (LAMMPS *) handle;
+
+  BEGIN_CAPTURE
+  {
+    int ifix = lmp->modify->find_fix(id);
+    if (ifix < 0)
+      lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id);
+
+    Fix *fix = lmp->modify->fix[ifix];
+
+    if (strcmp("external",fix->style) != 0)
+      lmp->error->all(FLERR,"Fix '{}' is not of style external!", id);
+
+    FixExternal *fext = (FixExternal*) fix;
+    fext->set_vector_length(len);
+  }
+  END_CAPTURE
+}
+
+/** Store global vector for a fix external instance with the given ID.
+
+\verbatim embed:rst
+
+This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
+:cpp:func:`lammps_fix_external_get_force` to set the values of a global vector of
+properties that will be stored with the fix. The length of the vector
+must be set beforehand with :cpp:func:`lammps_fix_external_set_vector_length`.
+
+Please see the documentation for :doc:`fix external <fix_external>` for
+more information about how to use the fix and how to couple it with an
+external code.
+
+\endverbatim
+ *
+ * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
+ * \param  id       fix ID of fix external instance
+ * \param  idx      1 based index of in global vector
+ * \param  val      value to be stored in global vector */
+
+void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val)
+{
+  LAMMPS *lmp = (LAMMPS *) handle;
+
+  BEGIN_CAPTURE
+  {
+    int ifix = lmp->modify->find_fix(id);
+    if (ifix < 0)
+      lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id);
+
+    Fix *fix = lmp->modify->fix[ifix];
+
+    if (strcmp("external",fix->style) != 0)
+      lmp->error->all(FLERR,"Fix '{}' is not of style external!", id);
+
+    FixExternal * fext = (FixExternal*) fix;
+    fext->set_vector(idx, val);
+  }
+  END_CAPTURE
+}
+
 /* ---------------------------------------------------------------------- */
 
 /** Free memory buffer allocated by LAMMPS.

src/library.h

@@ -240,7 +240,7 @@ void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double
 void lammps_fix_external_set_virial_global(void *handle, const char *id, double *virial);
 void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **virial);
 void lammps_fix_external_set_vector_length(void *handle, const char *id, int len);
-void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double **val);
+void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val);
 
 void lammps_free(void *ptr);
 

unittest/c-library/test_library_external.cpp

@@ -28,12 +28,20 @@ static void callback_one(void *handle, step_t timestep, int nlocal, tag_t *, dou
 {
     for (int i = 0; i < nlocal; ++i)
         f[i][0] = f[i][1] = f[i][2] = (double)timestep;
-    if (timestep < 10)
+
-        lammps_fix_external_set_energy_global(handle, "ext", 0.0);
-    else
-        lammps_fix_external_set_energy_global(handle, "ext", 1.0);
     double v[6] = {1.0, 1.0, 1.0, 0.0, 0.0, 0.0};
     lammps_fix_external_set_virial_global(handle, "ext", v);
+    if (timestep < 10) {
+        lammps_fix_external_set_energy_global(handle, "ext", 0.5);
+        lammps_fix_external_set_vector(handle, "ext", 1, timestep);
+        lammps_fix_external_set_vector(handle, "ext", 3, 1.0);
+        lammps_fix_external_set_vector(handle, "ext", 4, -0.25);
+    } else {
+        lammps_fix_external_set_energy_global(handle, "ext", 1.0);
+        lammps_fix_external_set_vector(handle, "ext", 2, timestep);
+        lammps_fix_external_set_vector(handle, "ext", 5, -1.0);
+        lammps_fix_external_set_vector(handle, "ext", 6, 0.25);
+    }
 }
 }
 
@@ -57,11 +65,12 @@ TEST(lammps_external, callback)
                                    "pair_style zero 0.1\n"
                                    "pair_coeff 1 1\n"
                                    "velocity all set 0.1 0.0 -0.1\n"
-                                   "thermo 5\n"
                                    "fix 1 all nve\n"
                                    "fix ext all external pf/callback 5 1\n"
+                                   "thermo_style custom step temp pe ke etotal press\n"
+                                   "thermo 5\n"
                                    "fix_modify ext energy yes virial yes\n");
-
+    lammps_fix_external_set_vector_length(handle, "ext", 6);
     output = ::testing::internal::GetCapturedStdout();
     if (verbose) std::cout << output;
 
@@ -71,11 +80,19 @@ TEST(lammps_external, callback)
     double temp  = lammps_get_thermo(handle, "temp");
     double pe    = lammps_get_thermo(handle, "pe");
     double press = lammps_get_thermo(handle, "press");
-    output       = ::testing::internal::GetCapturedStdout();
+    double val   = 0.0;
+    double *valp;
+    for (int i = 0; i < 6; ++i) {
+        valp = (double *)lammps_extract_fix(handle, "ext", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, i, 0);
+        val += *valp;
+        lammps_free(valp);
+    }
+    output = ::testing::internal::GetCapturedStdout();
     if (verbose) std::cout << output;
     EXPECT_DOUBLE_EQ(temp, 1.0 / 30.0);
     EXPECT_DOUBLE_EQ(pe, 1.0 / 8.0);
     EXPECT_DOUBLE_EQ(press, 0.15416666666666667);
+    EXPECT_DOUBLE_EQ(val, 15);
 
     ::testing::internal::CaptureStdout();
     lammps_close(handle);

unittest/python/python-fix-external.py

@@ -1,6 +1,6 @@
 import sys,os,unittest
 from ctypes import *
-from lammps import lammps
+from lammps import lammps, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR
 
 # add timestep dependent force
 def callback_one(lmp, ntimestep, nlocal, tag, x, f):
@@ -9,9 +9,15 @@ def callback_one(lmp, ntimestep, nlocal, tag, x, f):
         f[i][1] = float(ntimestep)
         f[i][2] = float(ntimestep)
     if ntimestep < 10:
-        lmp.fix_external_set_energy_global("ext",0.5)
+        lmp.fix_external_set_energy_global("ext", 0.5)
+        lmp.fix_external_set_vector("ext", 1, ntimestep)
+        lmp.fix_external_set_vector("ext", 3, 1.0)
+        lmp.fix_external_set_vector("ext", 4, -0.25)
     else:
-        lmp.fix_external_set_energy_global("ext",1.0)
+        lmp.fix_external_set_energy_global("ext", 1.0)
+        lmp.fix_external_set_vector("ext", 2, ntimestep)
+        lmp.fix_external_set_vector("ext", 5, -1.0)
+        lmp.fix_external_set_vector("ext", 6, 0.25)
 
 class PythonExternal(unittest.TestCase):
     def testExternalCallback(self):
@@ -31,15 +37,22 @@ class PythonExternal(unittest.TestCase):
                         pair_style zero 0.1
                         pair_coeff 1 1
                         velocity all set 0.1 0.0 -0.1
+                        thermo_style custom step temp pe ke etotal press
                         thermo 5
                         fix 1 all nve
                         fix ext all external pf/callback 5 1
+                        fix_modify ext energy yes virial yes
 """
         lmp.commands_string(basic_system)
+        lmp.fix_external_set_vector_length("ext",6);
         lmp.set_fix_external_callback("ext",callback_one,lmp)
         lmp.command("run 10 post no")
         self.assertAlmostEqual(lmp.get_thermo("temp"),1.0/30.0,14)
         self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/8.0,14)
+        val = 0.0
+        for i in range(0,6):
+            val += lmp.extract_fix("ext",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=i)
+        self.assertAlmostEqual(val,15.0,14)
 
     def testExternalArray(self):
         """Test fix external from Python with pf/array"""