DecohesionEnergy + Lat_param_T (property+report + unittest) update 27 Aug

.github/workflows/mirror_gitee.yml

@@ -0,0 +1,13 @@
+name: Mirror to Gitee Repository
+
+on: [ push, delete, create ]
+
+# Ensures that only one mirror task will run at a time.
+concurrency:
+  group: git-mirror
+
+jobs:
+  git-mirror:
+    uses: deepmodeling/workflows/.github/workflows/mirror_gitee.yml@main
+    secrets:
+      SYNC_GITEE_PRIVATE_KEY: ${{ secrets.SYNC_GITEE_PRIVATE_KEY }}

apex/core/calculator/Lammps.py

@@ -518,13 +518,17 @@ def _prepare_result_dict(self, atom_numbs, type_map_list, type_list, box, coord,
     def forward_files(self, property_type="relaxation"):
         if self.inter_type in ["meam", "snap"]:
             return ["conf.lmp", "in.lammps"] + list(map(os.path.basename, self.model))
+        elif property_type == "Lat_param_T":
+            return ["in.lammps", "variable_Lat_param_T.in", os.path.basename(self.model)]
         else:
             return ["conf.lmp", "in.lammps", os.path.basename(self.model)]
 
     def forward_common_files(self, property_type="relaxation"):
         if property_type not in ["eos"]:
             if self.inter_type in ["meam", "snap"]:
                 return ["in.lammps"] + list(map(os.path.basename, self.model))
+            elif property_type == "Lat_param_T":
+                return ["in.lammps", "variable_Lat_param_T.in", os.path.basename(self.model)]
             else:
                 return ["in.lammps", os.path.basename(self.model)]
         else:
@@ -536,6 +540,8 @@ def forward_common_files(self, property_type="relaxation"):
     def backward_files(self, property_type="relaxation"):
         if property_type == "phonon":
             return ["outlog", "FORCE_CONSTANTS"]
+        elif property_type == "Lat_param_T":
+            return ["log.lammps", "outlog", "dump.relax", "average_box.txt"]
         else:
             return ["log.lammps", "outlog", "dump.relax"]
 

apex/core/calculator/lib/lammps_utils.py

@@ -418,6 +418,63 @@ def make_lammps_elastic(
     ret += 'print "Final Stress (xx yy zz xy xz yz) = ${Pxx} ${Pyy} ${Pzz} ${Pxy} ${Pxz} ${Pyz}"\n'
     return ret
 
+def make_lammps_Lat_param_T(conf, type_map, interaction, param):
+    type_map_list = element_list(type_map)
+    deepmd_version = param.get("deepmd_version", None)
+    dump_step = 100
+    # detour sychronizing problem of dumping in new version of deepmd-kit >=2.1.5
+    tdamp = 100
+    ret = ""
+    ret += "include  variable_Lat_param_T.in\n"
+    ret += "clear\n"
+    ret += "units 	metal\n"
+    ret += "dimension	3\n"
+    ret += "boundary	p p p\n"
+    ret += "atom_style	atomic\n"
+    ret += "box         tilt large\n"
+    ret += "read_data   %s\n" % conf
+    ret += "replicate   ${nx} ${ny} ${nz}\n"
+    for ii in range(len(type_map)):
+        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)
+    ret += "neigh_modify    every 1 delay 0 check no\n"
+    ret += interaction(param)
+    ret += "compute         mype all pe\n"
+    ret += "thermo          100\n"
+    ret += (
+        "thermo_style    custom step pe pxx pyy pzz pxy pxz pyz lx ly lz vol c_mype\n"
+    )
+    ret += "velocity all create ${temperature} 12345 mom yes rot yes dist gaussian\n"
+    ret += f"fix 1 all npt temp ${{temperature}} ${{temperature}} {tdamp} x 1.0 1.0 1000 y 1.0 1.0 1000 xy 1.0 1.0 1000\n"
+    ret += "run ${equi_step}\n"
+    ret += "reset_timestep 0 \n"
+    ret += f"dump            1 all custom  {dump_step} dump.relax id type xs ys zs fx fy fz\n"
+    ret += "variable lx equal lx \n"
+    ret += "variable ly equal ly \n"
+    ret += "variable lz equal lz \n"
+    ret += "fix 2 all ave/time ${N_every} ${N_repeat} ${N_freq}  v_lx v_ly v_lz  ave running file average_box.txt\n"
+    ret += "run ${ave_step} \n"
+    ret += "variable        N equal count(all)\n"
+    ret += "variable        V equal vol\n"
+    ret += "variable        E equal \"c_mype\"\n"
+    ret += "variable        tmplx equal lx\n"
+    ret += "variable        tmply equal ly\n"
+    ret += "variable        Pxx equal pxx\n"
+    ret += "variable        Pyy equal pyy\n"
+    ret += "variable        Pzz equal pzz\n"
+    ret += "variable        Pxy equal pxy\n"
+    ret += "variable        Pxz equal pxz\n"
+    ret += "variable        Pyz equal pyz\n"
+    ret += "variable        Epa equal ${E}/${N}\n"
+    ret += "variable        Vpa equal ${V}/${N}\n"
+    ret += "variable        AA equal (${tmplx}*${tmply})\n"
+    ret += "print \"All done\"\n"
+    ret += "print \"Total number of atoms = ${N}\"\n"
+    ret += "print \"Final energy per atoms = ${Epa}\"\n"
+    ret += "print \"Final volume per atoms = ${Vpa}\"\n"
+    ret += "print \"Final Base area = ${AA}\"\n"
+    ret += "print \"Final Stress (xx yy zz xy xz yz) = ${Pxx} ${Pyy} ${Pzz} ${Pxy} ${Pxz} ${Pyz}\"\n"
+    ret += "print \"Final Length (box_x box_y box_z) = ${lx} ${ly} ${lz}\"\n"
+    return ret
 
 def make_lammps_press_relax(
     conf,

apex/core/common_prop.py

@@ -11,6 +11,8 @@
 from apex.core.property.Surface import Surface
 from apex.core.property.Vacancy import Vacancy
 from apex.core.property.Phonon import Phonon
+from apex.core.property.DecohesionEnergy import DecohesionEnergy
+from apex.core.property.Lat_param_T import Lat_param_T
 from apex.core.lib.utils import create_path
 from apex.core.lib.util import collect_task
 from apex.core.lib.dispatcher import make_submission
@@ -39,6 +41,10 @@ def make_property_instance(parameters, inter_param):
         return Gamma(parameters, inter_param)
     elif prop_type == "phonon":
         return Phonon(parameters, inter_param)
+    elif prop_type == "DecohesionEnergy":
+        return DecohesionEnergy(parameters, inter_param)
+    elif prop_type == "Lat_param_T":
+        return Lat_param_T(parameters, inter_param)
     else:
         raise RuntimeError(f"unknown APEX type {prop_type}")