add unit test for yaml style thermo output and updated logfile class

examples/README

@@ -118,6 +118,7 @@ ttm:      two-temeperature model examples
 vashishta: models using the Vashishta potential
 voronoi:  Voronoi tesselation via compute voronoi/atom command
 wall:     use of reflective walls with different stochastic models
+yaml:     demonstrates use of yaml thermo and dump styles
 
 Here is how you might run and visualize one of the sample problems:
 

examples/yaml/in.yaml

@@ -0,0 +1,37 @@
+# 3d Lennard-Jones melt
+
+variable        x index 1
+variable        y index 1
+variable        z index 1
+
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
+
+units           lj
+atom_style      atomic
+
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
+
+velocity        all create 1.44 87287 loop geom
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
+
+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
+
+run             100
+
+run             100

examples/yaml/log.7Apr22.yaml.g++.1

@@ -0,0 +1,151 @@
+LAMMPS (24 Mar 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+variable        x index 1
+variable        y index 1
+variable        z index 1
+
+variable        xx equal 20*$x
+variable        xx equal 20*1
+variable        yy equal 20*$y
+variable        yy equal 20*1
+variable        zz equal 20*$z
+variable        zz equal 20*1
+
+units           lj
+atom_style      atomic
+
+lattice         fcc 0.8442
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+region          box block 0 20 0 ${yy} 0 ${zz}
+region          box block 0 20 0 20 0 ${zz}
+region          box block 0 20 0 20 0 20
+create_box      1 box
+Created orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 32000 atoms
+  using lattice units in orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
+  create_atoms CPU = 0.003 seconds
+mass            1 1.0
+
+velocity        all create 1.44 87287 loop geom
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
+
+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
+
+run             100
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 20.56 | 20.56 | 20.56 Mbytes
+---
+keywords: [Step, Temp, KinEng, PotEng, E_bond, E_angle, E_dihed, E_impro, E_vdwl, E_coul, E_long, Press, ]
+data:
+  - [0, 1.44000000000001, 2.15993250000001, -6.77336805323422, 0, 0, 0, 0, -6.77336805323422, 0, 0, -5.01970725908556, ]
+  - [10, 1.12539487029313, 1.68803955255514, -6.30005271976029, 0, 0, 0, 0, -6.30005271976029, 0, 0, -2.55968522600129, ]
+  - [20, 0.625793798302192, 0.938661363368992, -5.55655653922756, 0, 0, 0, 0, -5.55655653922756, 0, 0, 0.973517658007722, ]
+  - [30, 0.745927295413064, 1.11885597777762, -5.73951278150759, 0, 0, 0, 0, -5.73951278150759, 0, 0, 0.339284096694852, ]
+  - [40, 0.731026217827733, 1.09650505988764, -5.71764564663628, 0, 0, 0, 0, -5.71764564663628, 0, 0, 0.388973418756238, ]
+  - [50, 0.740091517740786, 1.11010258482128, -5.73150426762886, 0, 0, 0, 0, -5.73150426762886, 0, 0, 0.335273324523691, ]
+  - [60, 0.750500641591031, 1.12571578266897, -5.74713299283555, 0, 0, 0, 0, -5.74713299283555, 0, 0, 0.26343139026926, ]
+  - [70, 0.755436366857812, 1.13311913920702, -5.75480059117447, 0, 0, 0, 0, -5.75480059117447, 0, 0, 0.224276619217515, ]
+  - [80, 0.759974280364828, 1.13992579675285, -5.76187162670983, 0, 0, 0, 0, -5.76187162670983, 0, 0, 0.191626237124102, ]
+  - [90, 0.760464250735042, 1.14066072934081, -5.76280209529731, 0, 0, 0, 0, -5.76280209529731, 0, 0, 0.189478083345243, ]
+  - [100, 0.757453103239936, 1.13614414924569, -5.75850548601596, 0, 0, 0, 0, -5.75850548601596, 0, 0, 0.207261053624723, ]
+...
+Loop time of 1.89046 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 22851.622 tau/day, 52.897 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.2896     | 1.2896     | 1.2896     |   0.0 | 68.22
+Neigh   | 0.17687    | 0.17687    | 0.17687    |   0.0 |  9.36
+Comm    | 0.014543   | 0.014543   | 0.014543   |   0.0 |  0.77
+Output  | 0.37678    | 0.37678    | 0.37678    |   0.0 | 19.93
+Modify  | 0.028638   | 0.028638   | 0.028638   |   0.0 |  1.51
+Other   |            | 0.003975   |            |       |  0.21
+
+Nlocal:          32000 ave       32000 max       32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          19657 ave       19657 max       19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.588531
+Neighbor list builds = 5
+Dangerous builds not checked
+
+run             100
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 20.57 | 20.57 | 20.57 Mbytes
+---
+keywords: [Step, Temp, KinEng, PotEng, E_bond, E_angle, E_dihed, E_impro, E_vdwl, E_coul, E_long, Press, ]
+data:
+  - [100, 0.757453103239935, 1.13614414924569, -5.7585054860159, 0, 0, 0, 0, -5.7585054860159, 0, 0, 0.207261053624721, ]
+  - [110, 0.759322359337036, 1.13894794576996, -5.7614668389562, 0, 0, 0, 0, -5.7614668389562, 0, 0, 0.194314975399602, ]
+  - [120, 0.759372342462676, 1.13902291811546, -5.76149365656489, 0, 0, 0, 0, -5.76149365656489, 0, 0, 0.191600048851267, ]
+  - [130, 0.756833027516501, 1.13521406472659, -5.75777334823494, 0, 0, 0, 0, -5.75777334823494, 0, 0, 0.208792327853067, ]
+  - [140, 0.759725426691298, 1.13955252790757, -5.76208910746081, 0, 0, 0, 0, -5.76208910746081, 0, 0, 0.193895435346637, ]
+  - [150, 0.760545839455106, 1.14078310859643, -5.7633284876011, 0, 0, 0, 0, -5.7633284876011, 0, 0, 0.187959630462945, ]
+  - [160, 0.758404626168493, 1.13757138903589, -5.76023198892283, 0, 0, 0, 0, -5.76023198892283, 0, 0, 0.19692107984108, ]
+  - [170, 0.758880300638885, 1.13828487844424, -5.76103232235402, 0, 0, 0, 0, -5.76103232235402, 0, 0, 0.197653518549842, ]
+  - [180, 0.753691827878246, 1.13050241251294, -5.75304767384283, 0, 0, 0, 0, -5.75304767384283, 0, 0, 0.237041776410937, ]
+  - [190, 0.757361226563721, 1.13600633853809, -5.75852399133222, 0, 0, 0, 0, -5.75852399133222, 0, 0, 0.219529562657488, ]
+  - [200, 0.759531750132731, 1.13926202214831, -5.76188923485725, 0, 0, 0, 0, -5.76188923485725, 0, 0, 0.209105747192796, ]
+...
+Loop time of 1.93916 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 22277.687 tau/day, 51.569 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.3292     | 1.3292     | 1.3292     |   0.0 | 68.55
+Neigh   | 0.18317    | 0.18317    | 0.18317    |   0.0 |  9.45
+Comm    | 0.013626   | 0.013626   | 0.013626   |   0.0 |  0.70
+Output  | 0.38206    | 0.38206    | 0.38206    |   0.0 | 19.70
+Modify  | 0.027034   | 0.027034   | 0.027034   |   0.0 |  1.39
+Other   |            | 0.004028   |            |       |  0.21
+
+Nlocal:          32000 ave       32000 max       32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          19570 ave       19570 max       19570 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.19982e+06 ave 1.19982e+06 max 1.19982e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1199821
+Ave neighs/atom = 37.494406
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:04

python/lammps/formats.py

@@ -14,14 +14,19 @@
 ################################################################################
 # LAMMPS output formats
 # Written by Richard Berger <richard.berger@temple.edu>
+# and Axel Kohlmeyer <akohlmey@gmail.com>
 ################################################################################
 
-import re
+import re, yaml
+try:
+  from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
+except ImportError:
+    from yaml import SafeLoader as Loader, SafeDumper as Dumper
 
 class LogFile:
   """Reads LAMMPS log files and extracts the thermo information
 
-  It supports both the default thermo output style (including custom) and multi.
+  It supports the line, multi, and yaml thermo output styles.
 
   :param filename: path to log file
   :type  filename: str
@@ -33,11 +38,13 @@ class LogFile:
 
   STYLE_DEFAULT = 0
   STYLE_MULTI   = 1
+  STYLE_YAML    = 2
 
   def __init__(self, filename):
     alpha = re.compile(r'[a-df-zA-DF-Z]') # except e or E for floating-point numbers
     kvpairs = re.compile(r'([a-zA-Z_0-9]+)\s+=\s*([0-9\.eE\-]+)')
     style = LogFile.STYLE_DEFAULT
+    yamllog = ""
     self.runs = []
     self.errors = []
     with open(filename, 'rt') as f:
@@ -54,6 +61,24 @@ class LogFile:
                 current_run = {}
                 for k in keys:
                     current_run[k] = []
+
+            elif re.match(r'^(keywords:.*$|data:$|---$|  - \[.*\]$)', line):
+                style = LogFile.STYLE_YAML
+                yamllog += line;
+                current_run = {}
+
+            elif re.match(r'^\.\.\.$', line):
+                thermo = yaml.load(yamllog, Loader=Loader)
+                for k in thermo['keywords']:
+                    current_run[k] = []
+                for step in thermo['data']:
+                    icol = 0
+                    for k in thermo['keywords']:
+                        current_run[k].append(step[icol])
+                        icol += 1
+                self.runs.append(current_run)
+                yamllog = ""
+
             elif re.match(r'^------* Step ', line):
                 if not in_thermo:
                    current_run = {'Step': [], 'CPU': []}
@@ -65,28 +90,29 @@ class LogFile:
                 cpu  = float(str_cpu.split('=')[1].split()[0])
                 current_run["Step"].append(step)
                 current_run["CPU"].append(cpu)
+
             elif line.startswith('Loop time of'):
                 in_thermo = False
+                if style != LogFile.STYLE_YAML:
                     self.runs.append(current_run)
+
             elif in_thermo and in_data_section:
                 if style == LogFile.STYLE_DEFAULT:
                     if alpha.search(line):
                         continue
-
                     for k, v in zip(keys, map(float, line.split())):
                         current_run[k].append(v)
+
                 elif style == LogFile.STYLE_MULTI:
                     if '=' not in line:
                         in_data_section = False
                         continue
-
                     for k,v in kvpairs.findall(line):
                         if k not in current_run:
                             current_run[k] = [float(v)]
                         else:
                             current_run[k].append(float(v))
 
-
 class AvgChunkFile:
   """Reads files generated by fix ave/chunk
 

unittest/python/python-formats.py

@@ -7,6 +7,7 @@ EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'
 DEFAULT_STYLE_EXAMPLE_LOG="melt/log.8Apr21.melt.g++.1"
 MULTI_STYLE_EXAMPLE_LOG="peptide/log.27Nov18.peptide.g++.1"
 AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1"
+YAML_STYLE_EXAMPLE_LOG="yaml/log.7Apr22.yaml.g++.1"
 
 class Logfiles(unittest.TestCase):
     def testLogFileNotFound(self):
@@ -58,6 +59,27 @@ class Logfiles(unittest.TestCase):
 
         self.assertEqual(run0["Step"], list(range(0,350, 50)))
 
+    def testYamlLogFile(self):
+        log = LogFile(os.path.join(EXAMPLES_DIR, YAML_STYLE_EXAMPLE_LOG))
+        self.assertEqual(len(log.runs), 2)
+        run = log.runs[0]
+        self.assertEqual(len(run.keys()), 12)
+        self.assertIn("Step", run)
+        self.assertIn("Temp", run)
+        self.assertIn("E_vdwl", run)
+        self.assertIn("E_coul", run)
+        self.assertIn("E_bond", run)
+        self.assertIn("E_angle", run)
+        self.assertIn("Press", run)
+        self.assertEqual(len(run["Step"]), 11)
+        self.assertEqual(len(run["Temp"]), 11)
+        self.assertEqual(len(run["E_vdwl"]), 11)
+        self.assertEqual(len(run["E_coul"]), 11)
+        self.assertEqual(len(run["E_bond"]), 11)
+        self.assertEqual(len(run["E_angle"]), 11)
+        self.assertEqual(len(run["Press"]), 11)
+        self.assertEqual(log.runs[0]["Step"], [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
+
 
 class AvgChunkFiles(unittest.TestCase):
     def testAvgChunkFileNotFound(self):