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Merge branch 'develop' into fix-mdi-aimd-enhance

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# Conflicts:
#	doc/src/fix_mdi_aimd.rst
This commit is contained in:
Axel Kohlmeyer
2022-06-28 13:38:43 -04:00
parent 7aabbba7ff f65bc76326
commit 141d09ab9b
134 changed files with 3841 additions and 1191 deletions
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1
unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml
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@ -1,6 +1,5 @@
---
lammps_version: 4 May 2022
tags: generated
date_generated: Wed Jun 1 15:17:22 2022
epsilon: 1e-12
skip_tests: single

1
unittest/force-styles/tests/atomic-pair-threebody_table.yaml
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@ -1,6 +1,5 @@
---
lammps_version: 4 May 2022
tags: generated
date_generated: Wed Jun 1 15:28:13 2022
epsilon: 1e-05
skip_tests: single

2
unittest/force-styles/tests/manybody-pair-pace_product.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:48 2022
epsilon: 5e-13
epsilon: 5e-12
skip_tests:
prerequisites: ! |
pair pace

2
unittest/force-styles/tests/manybody-pair-pace_recursive.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Mar 2021
date_generated: Wed Apr 7 19:30:07 2021
epsilon: 5e-13
epsilon: 5e-12
prerequisites: ! |
pair pace
pre_commands: ! |

12
unittest/python/python-commands.py
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@ -1,6 +1,8 @@
import sys,os,unittest,ctypes
from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL
from lammps import LMP_TYPE_VECTOR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
from lammps import LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
has_manybody=False
try:
@ -311,6 +313,14 @@ create_atoms 1 single &
self.assertEqual(minval,1.0)
self.assertEqual(maxval,2.1)
ndist1 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_VECTOR)
ndist2 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_ROWS)
ndist3 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_COLS)
self.assertEqual(ndist1,21)
self.assertEqual(ndist2,21)
self.assertEqual(ndist3,0)
self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1)
self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1)

38
unittest/python/python-numpy.py
View File

@ -93,17 +93,39 @@ class PythonNumpy(unittest.TestCase):
# TODO
pass
def testExtractComputeLocalScalar(self):
# TODO
pass
def testExtractComputeLocalVector(self):
# TODO
pass
self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
self.lmp.command("mass 1 1.0")
self.lmp.command("pair_style lj/cut 1.9")
self.lmp.command("pair_coeff 1 1 1.0 1.0")
self.lmp.command("compute r0 all pair/local dist")
self.lmp.command("run 0 post no")
values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_VECTOR)
self.assertEqual(values.ndim, 1)
self.assertEqual(values.size, 2)
self.assertEqual(values[0], 0.5)
self.assertEqual(values[1], 1.5)
def testExtractComputeLocalArray(self):
# TODO
pass
self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
self.lmp.command("mass 1 1.0")
self.lmp.command("pair_style lj/cut 1.9")
self.lmp.command("pair_coeff 1 1 1.0 1.0")
self.lmp.command("compute r0 all pair/local dist dx dy dz")
self.lmp.command("run 0 post no")
values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY)
self.assertEqual(values.ndim, 2)
self.assertEqual(values.size, 8)
self.assertEqual(values[0,0], 0.5)
self.assertEqual(values[0,3], -0.5)
self.assertEqual(values[1,0], 1.5)
self.assertEqual(values[1,3], 1.5)
def testExtractAtomDeprecated(self):
self.lmp.command("units lj")