From 3970942028d6964957e556d11bb5e8d9870649c8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 7 Apr 2022 02:43:39 -0400
Subject: [PATCH] add test for yaml dump style

---
 examples/yaml/in.yaml             |  8 ++---
 python/lammps/formats.py          |  2 +-
 unittest/python/python-formats.py | 55 +++++++++++++++++++++++++++++++
 3 files changed, 60 insertions(+), 5 deletions(-)

diff --git a/examples/yaml/in.yaml b/examples/yaml/in.yaml
index 28660751c8..f682f39776 100644
--- a/examples/yaml/in.yaml
+++ b/examples/yaml/in.yaml
@@ -29,9 +29,9 @@ fix             1 all nve
 thermo_style    yaml
 thermo 10
 
-dump            1 all yaml 25 dump.yaml id type x y z ix iy iz vx vy vz
-dump_modify     1 sort id thermo yes units yes time yes format 1 %5d format float "% 12.8e" format int %2d
+#dump            1 all yaml 25 dump.yaml id type x y z ix iy iz vx vy vz
+#dump_modify     1 sort id thermo yes units yes time yes format 1 %5d format float "% 12.8e" format int %2d
 
-run             100
+run             100 post no
 
-run             100
+run             100 post no
diff --git a/python/lammps/formats.py b/python/lammps/formats.py
index 83d05dd9f7..a311867253 100644
--- a/python/lammps/formats.py
+++ b/python/lammps/formats.py
@@ -21,7 +21,7 @@ import re, yaml
 try:
   from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
 except ImportError:
-    from yaml import SafeLoader as Loader, SafeDumper as Dumper
+  from yaml import SafeLoader as Loader, SafeDumper as Dumper
 
 class LogFile:
   """Reads LAMMPS log files and extracts the thermo information
diff --git a/unittest/python/python-formats.py b/unittest/python/python-formats.py
index 9e7863e198..4d6aa7e2cd 100644
--- a/unittest/python/python-formats.py
+++ b/unittest/python/python-formats.py
@@ -2,6 +2,12 @@ import os
 import unittest
 from lammps.formats import LogFile, AvgChunkFile
 
+import yaml
+try:
+    from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
+except ImportError:
+    from yaml import SafeLoader, SafeDumper
+
 EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
 
 DEFAULT_STYLE_EXAMPLE_LOG="melt/log.8Apr21.melt.g++.1"
@@ -109,5 +115,54 @@ class AvgChunkFiles(unittest.TestCase):
         self.assertEqual(len(chunk['coord'][0]), 1)
 
 
+from lammps import lammps
+has_full = False
+try:
+    machine=None
+    if 'LAMMPS_MACHINE_NAME' in os.environ:
+        machine=os.environ['LAMMPS_MACHINE_NAME']
+    lmp=lammps(name=machine)
+    has_full = lmp.has_style("atom","full")
+    lmp.close()
+except:
+    pass
+
+@unittest.skipIf(not has_full, "atom_style full is not available")
+class PythonDump(unittest.TestCase):
+    def setUp(self):
+        machine = None
+        if 'LAMMPS_MACHINE_NAME' in os.environ:
+            machine=os.environ['LAMMPS_MACHINE_NAME']
+        self.lmp = lammps(name=machine,  cmdargs=['-nocite', '-log','none', '-echo','screen'])
+
+    def tearDown(self):
+        del self.lmp
+
+    def testDumpYaml(self):
+        dumpfile = os.path.join(os.path.abspath('.'), 'dump.yaml')
+        self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
+        self.lmp.command("newton on on")
+        self.lmp.file("in.fourmol")
+        self.lmp.command("dump 1 all yaml 2 " + dumpfile + " id type mol q x y z vx vy vz")
+        self.lmp.command("dump_modify 1 time yes sort id units yes")
+        self.lmp.command("run 4 post no")
+        with open(dumpfile) as d:
+            traj = tuple(yaml.load_all(d, Loader=Loader))
+        self.assertEqual(len(traj), 3)
+        self.assertEqual(traj[0]['timestep'], 0)
+        self.assertEqual(traj[0]['time'], 0)
+        self.assertEqual(traj[0]['natoms'], 29)
+        self.assertEqual(traj[0]['units'], 'real')
+        self.assertEqual(len(traj[0]['boundary']), 6)
+        self.assertEqual(traj[0]['boundary'][0], 'p')
+        self.assertEqual(traj[1]['timestep'], 2)
+        self.assertEqual(traj[1]['time'], 0.2)
+        self.assertEqual(traj[2]['timestep'], 4)
+        self.assertEqual(traj[2]['time'], 0.4)
+        self.assertEqual(traj[0]['keywords'],['id', 'type', 'mol', 'q', 'x', 'y', 'z',
+                                              'vx', 'vy', 'vz'])
+        self.assertEqual(traj[0]['data'][0],[1, 3, 1, -0.47, -0.279937, 2.47266, -0.172009,
+                                             0.000778678, 0.000589703, -0.000221795])
+
 if __name__ == "__main__":
     unittest.main()