cleanup, fix wrong type definition in imported json data

.gitignore

@@ -39,3 +39,5 @@ TAGS
 .idea
 notebook/FF-fit_adam.bkr
 notebook/FF-fit_aldo.bkr
+
+main.py
\ No newline at end of file

python-module/ML_of_Forces/DataModel/ForceConfs.py

@@ -56,8 +56,8 @@ class ForceConfs(DataModel):
         with open(filename, 'r') as jsonfile:
             data = json.load(jsonfile)['data']
 
-        confs = [np.array(timestep['confs']) for timestep in data]
-        force = [np.array(timestep['force']) for timestep in data]
+        confs = [np.array(timestep['confs'], dtype=np.float) for timestep in data]
+        force = [np.array(timestep['force'], dtype=np.float) for timestep in data]
 
         self.confs = np.asarray(confs)
         self.force = np.asarray(force)

read_lammps_data.py

+import json
 
 class TimeStep(object):
     def __init__(self):
@@ -24,10 +25,6 @@ class TimeStep(object):
         )
 
 
-        # N = 207
-        # num_lines = sum(1 for line in open('disloiron.xyz'))
-        # steps = 100  # num_lines/(N+2)
-
         N = len(self.confs)
 
         r_cut = 5  # 3.5  4.4
@@ -49,52 +46,51 @@ class TimeStep(object):
         for i, (a2, offset) in enumerate(zip(indices, offsets)):
             d = atoms.positions[a2] + offset - atoms.positions[0]
             conf[i] = d
-        confs.append(conf)
-
-
-
-        print(confs)
-
-
-
 
-        cutoffs = np.ones(N) * r_cut / 2.
-        print(cutoffs)
-        nl = NeighborList(cutoffs, skin=0., sorted=False, self_interaction=False, bothways=True)
-
-        confs = []
-        forces = np.zeros((np.round(steps / every), 1, 3))
-
-        for n in np.arange(np.round(steps / every)):
-            atoms = extxyz.read_extxyz('disloiron.xyz', index=n * every)
-            forces[n] = atoms.get_array('force')[0]
-
-            cutoffs = np.ones(len(atoms)) * r_cut / 2.
-            nl = NeighborList(cutoffs, skin=0., sorted=False, self_interaction=False,
-                              bothways=True)
-            nl.build(atoms)
-
-            cell = atoms.get_cell()
-
-            indices, offsets = nl.get_neighbors(0)
-            offsets = np.dot(offsets, cell)
-            conf = np.zeros((len(indices), 3))
-
-            for i, (a2, offset) in enumerate(zip(indices, offsets)):
-                d = atoms.positions[a2] + offset - atoms.positions[0]
-                conf[i] = d
-            confs.append(conf)
-
-        np.save("confst.npy", confs)
-        np.save("forcest.npy", forces)
-
-        lens = []
-        for i in np.arange(len(confs)):
-            lens.append(len(confs[i]))
-
-        print(max(lens))
-        print(min(lens))
-        print(np.mean(lens))
+        return conf, self.force[0]
+
+
+
+
+
+        #
+        # cutoffs = np.ones(N) * r_cut / 2.
+        # print(cutoffs)
+        # nl = NeighborList(cutoffs, skin=0., sorted=False, self_interaction=False, bothways=True)
+        #
+        # confs = []
+        # forces = np.zeros((np.round(steps / every), 1, 3))
+        #
+        # for n in np.arange(np.round(steps / every)):
+        #     atoms = extxyz.read_extxyz('disloiron.xyz', index=n * every)
+        #     forces[n] = atoms.get_array('force')[0]
+        #
+        #     cutoffs = np.ones(len(atoms)) * r_cut / 2.
+        #     nl = NeighborList(cutoffs, skin=0., sorted=False, self_interaction=False,
+        #                       bothways=True)
+        #     nl.build(atoms)
+        #
+        #     cell = atoms.get_cell()
+        #
+        #     indices, offsets = nl.get_neighbors(0)
+        #     offsets = np.dot(offsets, cell)
+        #     conf = np.zeros((len(indices), 3))
+        #
+        #     for i, (a2, offset) in enumerate(zip(indices, offsets)):
+        #         d = atoms.positions[a2] + offset - atoms.positions[0]
+        #         conf[i] = d
+        #     confs.append(conf)
+        #
+        # np.save("confst.npy", confs)
+        # np.save("forcest.npy", forces)
+        #
+        # lens = []
+        # for i in np.arange(len(confs)):
+        #     lens.append(len(confs[i]))
+        #
+        # print(max(lens))
+        # print(min(lens))
+        # print(np.mean(lens))
 
 
 class ReadLammpsDumpFile():
@@ -103,32 +99,32 @@ class ReadLammpsDumpFile():
         self.counter = 0  # type: int
 
     def __enter__(self):
-        print('enter')
+        # print('enter')
         self.fid = open(self.filename, 'r')
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
-        print('exit')
+        # print('exit')
         self.fid.close()
         pass
 
     def __iter__(self):
-        print("iter")
+        # print("iter")
         return self
 
     def __next__(self):
         try:
             timestep = self.readtimestep()
 
-            print('next')
+            # print('next')
 
         except:
             raise StopIteration
 
-        if self.counter > 1:
-            raise StopIteration
-        else:
-            self.counter += 1
+        # if self.counter > 1:
+        #     raise StopIteration
+        # else:
+        #     self.counter += 1
 
         return timestep
 
@@ -137,7 +133,7 @@ class ReadLammpsDumpFile():
         item = self.fid.readline()
         words = item.split()[2:]
 
-        print(words)
+        # print(words)
 
         confs = []
         force = []
@@ -184,24 +180,44 @@ class JsonWriter():
         pass
 
 
-if __name__ == '__main__':
+def write_json(output, confs, forces):
+
+    # print(json.dumps({'confs': confs[0].tolist()}))
+    # print(json.dumps({'force': forces}))
+    # print(json.dumps({'confs': confs[0].tolist(), 'force': forces[0].tolist()}))
 
-    filename='data-lammps/Silic_300/Si_300_dump.atom'
+    out = []
+    for c, f in zip(confs, forces):
+        out.append({'confs': c.tolist(), 'force': f})
 
+    with open(output, 'w') as outfile:
+        json.dump({'data': out}, outfile)
 
 
 
+if __name__ == '__main__':
+
+    filename='data-lammps/Silic_2000/Si_2000_dump.atom'
+    output = 'Si_2000K.json'
+
+
+    confs = []
+    forces = []
+
     with ReadLammpsDumpFile(filename) as file:
 
         for timestep in file:
             conf, force = timestep.convert()
 
+            confs.append(conf)
+            forces.append(force)
 
-            print(timestep)
-            print(timestep.confs)
-            print(timestep.force)
+            # print(timestep)
+            # print(timestep.confs)
+            # print(timestep.force)
 
 
+    write_json(output, confs, forces)