Fix virial (#324)

* fix a bug, now ck2p/aimd_output can generate virial.raw

* Delete test.py

* Update output.py

Signed-off-by: HuangJiameng <[email protected]>

* Update output.py

Signed-off-by: HuangJiameng <[email protected]>

* add unittest for aimd_output with stress

* add cp2k.log

Co-authored-by: Han Wang <[email protected]>

Author: HuangJiameng

dpdata/cp2k/output.py

@@ -120,7 +120,22 @@ def handle_single_log_frame(self, lines):
         print_level_flag = 0
         atomic_kinds_pattern = re.compile(r'\s+\d+\. Atomic kind:\s+(?P<akind>\S+)')
         atomic_kinds = [] 
+        stress_sign = 'STRESS'
+        stress_flag = 0
+        stress = []
+
         for line in lines:
+            if stress_flag == 3 :
+                if (line == '\n') :
+                    stress_flag = 0
+                else :
+                    stress.append(line.split()[1:4])
+            if stress_flag == 2 :
+                stress_flag = 3
+            if stress_flag == 1 :
+                stress_flag = 2
+            if (stress_sign in line):
+                stress_flag = 1
             if force_start_pattern.match(line):
                 force_flag=True
             if force_end_pattern.match(line):
@@ -214,7 +229,18 @@ def handle_single_log_frame(self, lines):
         #atom_names=list(element_dict.keys())
         atom_names=self.atomic_kinds
         atom_numbs=[]
-        
+
+        GPa = PressureConversion("eV/angstrom^3", "GPa").value()
+        if stress:
+            stress = np.array(stress)
+            stress = stress.astype('float32')
+            stress = stress[np.newaxis, :, :]
+            # stress to virial conversion, default unit in cp2k is GPa
+            # note the stress is virial = stress * volume
+            virial = stress * np.linalg.det(self.cell)/GPa
+            virial = virial.squeeze()
+        else:
+            virial = None
         for ii in element_dict.keys():
             atom_numbs.append(element_dict[ii][1])
         #print(atom_numbs)
@@ -225,6 +251,8 @@ def handle_single_log_frame(self, lines):
         info_dict['cells'] = np.asarray([self.cell]).astype('float32')
         info_dict['energies'] = np.asarray([energy]).astype('float32')
         info_dict['forces'] = np.asarray([forces_list]).astype('float32')
+        if(virial is not None ): 
+            info_dict['virials'] = np.asarray([virial]).astype('float32')
         return info_dict
 
     def handle_single_xyz_frame(self, lines):

tests/cp2k/aimd_stress/DPGEN-pos-1.xyz

@@ -0,0 +1,7 @@
+     5
+ i =        0, time =        0.000, E =      -8.07218972206
+  H 5.70191 3.8096  4.38845
+  H 4.44601 4.65681 5.38195
+  H 4.49216 4.90991 3.57756
+  H 5.83825 5.62228 4.61068
+  C 5.11666 4.75533 4.46123

tests/cp2k/aimd_stress/cp2k.log

@@ -0,0 +1 @@
+1.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.000000000000000000e+01

tests/cp2k/aimd_stress/deepmd/box.raw

@@ -0,0 +1 @@
+5.701910018920898438e+00 3.809600114822387695e+00 4.388450145721435547e+00 4.446010112762451172e+00 4.656809806823730469e+00 5.381949901580810547e+00 4.492159843444824219e+00 4.909910202026367188e+00 3.577559947967529297e+00 5.838250160217285156e+00 5.622280120849609375e+00 4.610680103302001953e+00 5.116660118103027344e+00 4.755330085754394531e+00 4.461229801177978516e+00

tests/cp2k/aimd_stress/deepmd/coord.raw

@@ -0,0 +1 @@
+-2.196554718017578125e+02

tests/cp2k/aimd_stress/deepmd/energy.raw

@@ -0,0 +1 @@
+-2.743706703186035156e-01 4.712709188461303711e-01 -1.367179006338119507e-01 7.652513980865478516e-01 2.514204978942871094e-01 -1.059429287910461426e+00 2.538656070828437805e-02 1.183478906750679016e-02 -1.267343163490295410e-01 -8.532900810241699219e-01 -9.029597043991088867e-01 -1.871660351753234863e-01 3.367811143398284912e-01 1.687173396348953247e-01 1.509592533111572266e+00

tests/cp2k/aimd_stress/deepmd/force.raw

@@ -0,0 +1,5 @@
+0
+0
+0
+0
+1

tests/cp2k/aimd_stress/deepmd/type.raw

@@ -0,0 +1,2 @@
+H
+C

tests/cp2k/aimd_stress/deepmd/type_map.raw

@@ -0,0 +1 @@
+-1.305763244628906250e+00 -5.517681837081909180e-01 5.745944380760192871e-01 -5.517681837081909180e-01 -1.251762151718139648e+00 5.180240049958229065e-02 5.745944380760192871e-01 5.180240049958229065e-02 -8.817730545997619629e-01