Merge branch 'devel' into feat/set-force-label-optional

deepmodeling · Jan 13, 2025 · 9a58fd4 · 9a58fd4
2 parents 2fcbf45 + 2905792
commit 9a58fd4
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Showing 6 changed files with 13 additions and 13 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.8.4
+    rev: v0.8.6
     hooks:
     - id: ruff
       args: ["--fix"]

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 
 ## Installation
 
-DP-GEN only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
+dpdata only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install dpdata:
 
 - Install via pip: `pip install dpdata`
 - Install via conda: `conda install -c conda-forge dpdata`

diff --git a/dpdata/xyz/quip_gap_xyz.py b/dpdata/xyz/quip_gap_xyz.py
@@ -161,7 +161,7 @@ def handle_single_xyz_frame(lines):
                         list(filter(bool, field_dict["virial"].split(" ")))
                     ).reshape(3, 3)
                 ]
-            ).astype("float32")
+            ).astype(np.float64)
         else:
             virials = None
 
@@ -175,10 +175,10 @@ def handle_single_xyz_frame(lines):
                     3, 3
                 )
             ]
-        ).astype("float32")
-        info_dict["coords"] = np.array([coords_array]).astype("float32")
-        info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
-        info_dict["forces"] = np.array([force_array]).astype("float32")
+        ).astype(np.float64)
+        info_dict["coords"] = np.array([coords_array]).astype(np.float64)
+        info_dict["energies"] = np.array([field_dict["energy"]]).astype(np.float64)
+        info_dict["forces"] = np.array([force_array]).astype(np.float64)
         if virials is not None:
             info_dict["virials"] = virials
         info_dict["orig"] = np.zeros(3)

diff --git a/tests/xyz/xyz_unittest.field.xyz b/tests/xyz/xyz_unittest.field.xyz
@@ -16,7 +16,7 @@ energy=0.2397023e+01    virial="159.582203018    1.23282341824e-05    0.18783516
 
 
   10   
-virial=" -3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091 "    Lattice=" 9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915 "  Properties='species:S:1:pos:R:3:Z:I:1:force:R:3 ' energy='-58.342497      '
+virial=" -3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091 "    Lattice=" 9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915 "  Properties='species:S:1:pos:R:3:Z:I:1:force:R:3 ' energy='-5.834249877929687500e+01      '
 B   12.38023000000   3.21563000000   2.13103000000   5    -9.35551000000  -0.00000000000  -0.22364600000
 C   12.96783000000   4.32879000000   2.14172000000   6     7.05653600000  11.19171000000   1.80087100000
 C   12.96783000000   2.10247000000   2.14172000000   6     7.05653500000 -11.19171000000   1.80087100000
@@ -28,7 +28,7 @@ C    2.71900000000   1.71197000000   0.17210000000   6    -3.43041200000   0.056
 C    2.71900000000   4.71930000000   0.17210000000   6    -3.43041200000  -0.05665700000  -0.44035700000
 C    9.69981000000   3.21563000000   0.55395000000   6    -2.18778000000  -0.00000000000  -1.00760300000
 10
-energy=-56.397425    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.639742660522460938e+01    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B    4.08581000000   4.57623000000   2.94238000000   5     0.03989300000  -1.87257900000   0.97202400000
 C    1.42627000000   0.93584000000   2.94238000000   5    -0.03989300000   1.87257900000   0.97202400000
 C    0.93584000000   4.08581000000   2.94238000000   5     1.87257900000   0.03989300000   0.97202400000

diff --git a/tests/xyz/xyz_unittest.sort.xyz b/tests/xyz/xyz_unittest.sort.xyz
@@ -13,7 +13,7 @@ B    3.19567000000   7.85111000000   1.52250000000   5    -7.25565700000   8.829
 C    2.27564000000   0.00000000000   1.03309000000   6    -0.00000000000  -0.00000000000   0.00000000000
 B    2.27564000000   4.41538000000   1.03309000000   5    -0.00000000000  -0.00000000000   0.00000000000
 10
-energy=-58.342497    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.834249877929687500e+01    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 C   12.96783000000   4.32879000000   2.14172000000   6     7.05653600000  11.19171000000   1.80087100000
 C   12.96783000000   2.10247000000   2.14172000000   6     7.05653500000 -11.19171000000   1.80087100000
 C    7.95424000000   1.03482000000   2.10290000000   6     1.71010500000  -3.80357800000  -0.12402100000
@@ -25,7 +25,7 @@ C    2.71900000000   1.71197000000   0.17210000000   6    -3.43041200000   0.056
 C    2.71900000000   4.71930000000   0.17210000000   6    -3.43041200000  -0.05665700000  -0.44035700000
 C    9.69981000000   3.21563000000   0.55395000000   6    -2.18778000000  -0.00000000000  -1.00760300000
 10
-energy=-56.397425    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.639742660522460938e+01    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B    4.08581000000   4.57623000000   2.94238000000   5     0.03989300000  -1.87257900000   0.97202400000
 C    1.42627000000   0.93584000000   2.94238000000   5    -0.03989300000   1.87257900000   0.97202400000
 C    0.93584000000   4.08581000000   2.94238000000   5     1.87257900000   0.03989300000   0.97202400000

diff --git a/tests/xyz/xyz_unittest.xyz b/tests/xyz/xyz_unittest.xyz
@@ -13,7 +13,7 @@ C    2.27564000000   1.56002000000   1.03309000000   6    -0.00000000000  -4.519
 C    2.27564000000   7.27074000000   1.03309000000   6     0.00000000000   4.51935800000   0.00000000000
 C    2.27564000000   0.00000000000   1.03309000000   6    -0.00000000000  -0.00000000000   0.00000000000
 10
-energy=-58.342497    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.834249877929687500e+01    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B   12.38023000000   3.21563000000   2.13103000000   5    -9.35551000000  -0.00000000000  -0.22364600000
 C   12.96783000000   4.32879000000   2.14172000000   6     7.05653600000  11.19171000000   1.80087100000
 C   12.96783000000   2.10247000000   2.14172000000   6     7.05653500000 -11.19171000000   1.80087100000
@@ -25,7 +25,7 @@ C    2.71900000000   1.71197000000   0.17210000000   6    -3.43041200000   0.056
 C    2.71900000000   4.71930000000   0.17210000000   6    -3.43041200000  -0.05665700000  -0.44035700000
 C    9.69981000000   3.21563000000   0.55395000000   6    -2.18778000000  -0.00000000000  -1.00760300000
 10
-energy=-56.397425    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.639742660522460938e+01    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B    4.08581000000   4.57623000000   2.94238000000   5     0.03989300000  -1.87257900000   0.97202400000
 C    1.42627000000   0.93584000000   2.94238000000   5    -0.03989300000   1.87257900000   0.97202400000
 C    0.93584000000   4.08581000000   2.94238000000   5     1.87257900000   0.03989300000   0.97202400000