Merge pull request #3197 from akohlmey/custom-thermo-headers

add support for custom header keywords with thermo output and dump styles

doc/src/Howto_structured_data.rst

@@ -79,6 +79,10 @@ This data can be extracted and parsed from a log file using python with:
 .. code-block:: python
 
    import re, yaml
+   try:
+       from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
+   except ImportError:
+       from yaml import SafeLoader as Loader, SafeDumper as Dumper
 
    docs = ""
    with open("log.lammps") as f:
@@ -86,7 +90,7 @@ This data can be extracted and parsed from a log file using python with:
            m = re.search(r"^(keywords:.*$|data:$|---$|\.\.\.$|  - \[.*\]$)", line)
            if m: docs += m.group(0) + '\n'
 
-   thermo = list(yaml.load_all(docs, Loader=yaml.SafeLoader))
+   thermo = list(yaml.load_all(docs, Loader=Loader))
 
    print("Number of runs: ", len(thermo))
    print(thermo[1]['keywords'][4], ' = ', thermo[1]['data'][2][4])

doc/src/dump_modify.rst

@@ -26,6 +26,10 @@ Syntax
          N = index of frame written upon first dump
        *balance* arg = *yes* or *no*
        *buffer* arg = *yes* or *no*
+       *colname* values =  ID string, or *default*
+         string = new column header name
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a custom dump keyword or reference to compute, fix, property or variable.
        *delay* arg = Dstep
          Dstep = delay output until this timestep
        *element* args = E1 E2 ... EN, where N = # of atom types
@@ -40,9 +44,10 @@ Syntax
          Np = write one file for every this many processors
        *first* arg = *yes* or *no*
        *flush* arg = *yes* or *no*
-       *format* args = *line* string, *int* string, *float* string, M string, or *none*
+       *format* args = *line* string, *int* string, *float* string, ID string, or *none*
          string = C-style format string
-         M = integer from 1 to N, where N = # of per-atom quantities being output
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a custom dump keyword or reference to compute, fix, property or variable.
        *header* arg = *yes* or *no*
          *yes* to write the header
          *no* to not write the header
@@ -375,6 +380,29 @@ performed with dump style *xtc*\ .
 
 ----------
 
+The *colname* keyword can be used to change the default header keyword
+for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
+and MPIIO variants.  The setting for *ID string* replaces the default
+text with the provided string.  *ID* can be a positive integer when it
+represents the column number counting from the left, a negative integer
+when it represents the column number from the right (i.e. -1 is the last
+column/keyword), or a custom dump keyword (or compute, fix, property, or
+variable reference) and then it replaces the string for that specific
+keyword. For *atom* dump styles only the keywords "id", "type", "x",
+"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
+whether scaled or unwrapped coordinates were enabled or disabled, and
+it always assumes 8 columns for indexing regardless of whether image
+flags are enabled or not.  For dump style *cfg* only the "auxiliary"
+keywords (6th or later keyword) may be changed and the column indexing
+considers only them (i.e. the 6th keyword is the the 1st column).
+
+The *colname* keyword can be used multiple times. If multiple *colname*
+settings refer to the same keyword, the last setting has precedence.  A
+setting of *default* clears all previous settings, reverting all values
+to their default names.
+
+----------
+
 The *format* keyword can be used to change the default numeric format output
 by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
 *xyz* styles, and their MPIIO variants. Only the *line* or *none*

doc/src/package.rst

@@ -474,7 +474,7 @@ list on GPUs. This can be faster in some cases (e.g. ReaxFF HNS
 benchmark) but slower in others (e.g. Lennard Jones benchmark). The
 copy between different memory layouts is done out of place and
 therefore doubles the memory overhead of the neigh list, which can be
-signicant.
+significant.
 
 The *newton* keyword sets the Newton flags for pairwise and bonded
 interactions to *off* or *on*, the same as the :doc:`newton <newton>`

doc/src/thermo_modify.rst

@@ -21,9 +21,14 @@ Syntax
        *norm* value = *yes* or *no*
        *flush* value = *yes* or *no*
        *line* value = *one* or *multi* or *yaml*
-       *format* values = *line* string, *int* string, *float* string, M string, or *none*
+       *colname* values =  ID string, or *default*
+         string = new column header name
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a thermo keyword or reference to compute, fix, property or variable.
+       *format* values = *line* string, *int* string, *float* string, ID string, or *none*
          string = C-style format string
-         M = integer from 1 to N, where N = # of quantities being output
+         ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* a thermo keyword or reference to compute, fix, property or variable.
        *temp* value = compute ID that calculates a temperature
        *press* value = compute ID that calculates a pressure
 
@@ -36,7 +41,8 @@ Examples
    thermo_modify temp myTemp format 3 %15.8g
    thermo_modify temp myTemp format line "%ld %g %g %15.8g"
    thermo_modify line multi format float %g
-   themos_modify line yaml format none
+   thermo_modify line yaml format none
+   thermo_modify colname 1 Timestep colname -2 Pressure colname f_1[1] AvgDensity
 
 Description
 """""""""""
@@ -147,6 +153,20 @@ containing the timestep and CPU time ("multi"), or in a YAML format
 block ("yaml").  This modify option overrides the *one*, *multi*, or
 *yaml* thermo_style settings.
 
+The *colname* keyword can be used to change the default header keyword
+for a column or field of thermodynamic output.  The setting for *ID
+string* replaces the default text with the provided string.  *ID* can be
+a positive integer when it represents the column number counting from
+the left, a negative integer when it represents the column number from
+the right (i.e. -1 is the last column/keyword), or a thermo keyword (or
+compute, fix, property, or variable reference) and then it replaces the
+string for that specific thermo keyword.
+
+The *colname* keyword can be used multiple times. If multiple *colname*
+settings refer to the same keyword, the last setting has precedence.  A
+setting of *default* clears all previous settings, reverting all values
+to their default values.
+
 The *format* keyword can be used to change the default numeric format of
 any of quantities the :doc:`thermo_style <thermo_style>` command
 outputs.  All the specified format strings are C-style formats, e.g. as
@@ -155,12 +175,16 @@ argument which is the format string for the entire line of thermo
 output, with N fields, which you must enclose in quotes if it is more
 than one field.  The *int* and *float* keywords take a single format
 argument and are applied to all integer or floating-point quantities
-output.  The setting for *M string* also takes a single format argument
+output.  The setting for *ID string* also takes a single format argument
-which is used for the Mth value output in each line, e.g. the fifth
+which is used for the indexed value in each line.  The interpretation is
-column is output in high precision for "format 5 %20.15g".
+the same as for *colname*, i.e. a positive integer is the n-th value
+corresponding to the n-th thermo keyword, a negative integer is counting
+backwards, and a string matches the entry with the thermo keyword.,
+e.g. the fifth column is output in high precision for "format 5 %20.15g"
+and the pair energy for "format epair %20.15g".
 
 The *format* keyword can be used multiple times.  The precedence is
-that for each value in a line of output, the *M* format (if specified)
+that for each value in a line of output, the *ID* format (if specified)
 is used, else the *int* or *float* setting (if specified) is used,
 else the *line* setting (if specified) for that value is used, else
 the default setting is used.  A setting of *none* clears all previous
@@ -173,9 +197,10 @@ settings, reverting all values to their default format.
    When specifying the *format int* option you can use a "%d"-style
    format identifier in the format string and LAMMPS will convert this
    to the corresponding 8-byte form when it is applied to those
-   keywords.  However, when specifying the *line* option or *format M
+   keywords.  However, when specifying the *line* option or *format ID
    string* option for *step* and *natoms*, you should specify a format
-   string appropriate for an 8-byte signed integer, e.g. one with "%ld".
+   string appropriate for an 8-byte signed integer, e.g. one with "%ld"
+   or "%lld" depending on the platform.
 
 The *temp* keyword is used to determine how thermodynamic temperature is
 calculated, which is used by all thermo quantities that require a

doc/utils/sphinx-config/false_positives.txt

@@ -1789,6 +1789,7 @@ Liu
 Livermore
 lj
 llammps
+lld
 LLVM
 lm
 lmp

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:
@@ -46,14 +53,33 @@ class LogFile:
         for line in f:
             if "ERROR" in line or "exited on signal" in line:
                 self.errors.append(line)
-            elif line.startswith('Step '):
+
+            elif re.match(r'^ *Step ', line):
                 in_thermo = True
                 in_data_section = True
                 keys = line.split()
                 current_run = {}
                 for k in keys:
                     current_run[k] = []
-            elif line.startswith('---------------- Step'):
+
+            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': []}
                 in_thermo = True
@@ -64,28 +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
-                self.runs.append(current_run)
+                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
 

src/ADIOS/dump_atom_adios.cpp

@@ -238,6 +238,9 @@ void DumpAtomADIOS::init_style()
     columnNames = {"id", "type", "xs", "ys", "zs", "ix", "iy", "iz"};
   }
 
+  for (int icol = 0; icol < (int)columnNames.size(); ++icol)
+    if (keyword_user[icol].size()) columnNames[icol] = keyword_user[icol];
+
   // setup function ptrs
 
   if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0)

src/ADIOS/dump_custom_adios.cpp

@@ -214,6 +214,19 @@ void DumpCustomADIOS::write()
 
 void DumpCustomADIOS::init_style()
 {
+  // assemble column string from defaults and user values
+
+  delete[] columns;
+  std::string combined;
+  int icol = 0;
+  for (auto item : utils::split_words(columns_default)) {
+    if (combined.size()) combined += " ";
+    if (keyword_user[icol].size()) combined += keyword_user[icol];
+    else combined += item;
+    ++icol;
+  }
+  columns = utils::strdup(combined);
+
   // setup boundary string
 
   domain->boundary_string(boundstr);

src/MPIIO/dump_atom_mpiio.cpp

@@ -234,14 +234,25 @@ void DumpAtomMPIIO::init_style()
 
   // setup column string
 
+  std::string default_columns;
+
   if (scale_flag == 0 && image_flag == 0)
-    columns = (char *) "id type x y z";
+    default_columns = "id type x y z";
   else if (scale_flag == 0 && image_flag == 1)
-    columns = (char *) "id type x y z ix iy iz";
+    default_columns = "id type x y z ix iy iz";
   else if (scale_flag == 1 && image_flag == 0)
-    columns = (char *) "id type xs ys zs";
+    default_columns = "id type xs ys zs";
   else if (scale_flag == 1 && image_flag == 1)
-    columns = (char *) "id type xs ys zs ix iy iz";
+    default_columns = "id type xs ys zs ix iy iz";
+
+  int icol = 0;
+  columns.clear();
+  for (auto item : utils::split_words(default_columns)) {
+    if (columns.size()) columns += " ";
+    if (keyword_user[icol].size()) columns += keyword_user[icol];
+    else columns += item;
+    ++icol;
+  }
 
   // setup function ptrs
 

src/MPIIO/dump_custom_mpiio.cpp

@@ -39,17 +39,6 @@ using namespace LAMMPS_NS;
 #define DUMP_BUF_CHUNK_SIZE 16384
 #define DUMP_BUF_INCREMENT_SIZE 4096
 
-// clang-format off
-enum{ ID, MOL, TYPE, ELEMENT, MASS,
-  X, Y, Z, XS, YS, ZS, XSTRI, YSTRI, ZSTRI, XU, YU, ZU, XUTRI, YUTRI, ZUTRI,
-  XSU, YSU, ZSU, XSUTRI, YSUTRI, ZSUTRI,
-  IX, IY, IZ, VX, VY, VZ, FX, FY, FZ,
-  Q, MUX, MUY, MUZ, MU, RADIUS, DIAMETER,
-  OMEGAX, OMEGAY, OMEGAZ, ANGMOMX, ANGMOMY, ANGMOMZ,
-  TQX, TQY, TQZ, SPIN, ERADIUS, ERVEL, ERFORCE,
-  COMPUTE, FIX, VARIABLE };
-enum{ LT, LE, GT, GE, EQ, NEQ };
-// clang-format on
 /* ---------------------------------------------------------------------- */
 
 DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg)
@@ -216,6 +205,19 @@ void DumpCustomMPIIO::write()
 
 void DumpCustomMPIIO::init_style()
 {
+  // assemble ITEMS: column string from defaults and user values
+
+  delete[] columns;
+  std::string combined;
+  int icol = 0;
+  for (auto item : utils::split_words(columns_default)) {
+    if (combined.size()) combined += " ";
+    if (keyword_user[icol].size()) combined += keyword_user[icol];
+    else combined += item;
+    ++icol;
+  }
+  columns = utils::strdup(combined);
+
   // format = copy of default or user-specified line format
 
   delete[] format;

src/MPIIO/dump_xyz_mpiio.cpp

@@ -38,17 +38,6 @@ using namespace LAMMPS_NS;
 #define DUMP_BUF_CHUNK_SIZE 16384
 #define DUMP_BUF_INCREMENT_SIZE 4096
 
-enum{ID,MOL,TYPE,ELEMENT,MASS,
-     X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,
-     XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
-     IX,IY,IZ,
-     VX,VY,VZ,FX,FY,FZ,
-     Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
-     OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
-     TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
-     COMPUTE,FIX,VARIABLE};
-enum{LT,LE,GT,GE,EQ,NEQ};
-
 /* ---------------------------------------------------------------------- */
 
 DumpXYZMPIIO::DumpXYZMPIIO(LAMMPS *lmp, int narg, char **arg) :

src/POEMS/fix_poems.cpp

@@ -356,7 +356,9 @@ void FixPOEMS::init()
     for (auto ifix : modify->get_fix_list()) {
       if (utils::strmatch(ifix->style, "^poems")) pflag = true;
       if (pflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
-        if (comm->me == 0) error->warning(FLERR, "Fix {} alters forces after fix poems", ifix->id);
+        if (comm->me == 0)
+          error->warning(FLERR,"Fix {} with ID {} alters forces after fix poems",
+                         ifix->style, ifix->id);
     }
   }
 

src/RIGID/fix_rigid.cpp

@@ -693,7 +693,8 @@ void FixRigid::init()
     for (auto ifix : modify->get_fix_list()) {
       if (ifix->rigid_flag) rflag = true;
       if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
-        error->warning(FLERR,"Fix {} alters forces after fix rigid", ifix->id);
+        error->warning(FLERR,"Fix {} with ID {} alters forces after fix rigid",
+                       ifix->style, ifix->id);
     }
   }
 

src/RIGID/fix_rigid_small.cpp

@@ -538,7 +538,8 @@ void FixRigidSmall::init()
     for (auto ifix : modify->get_fix_list()) {
       if (ifix->rigid_flag) rflag = true;
       if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
-        error->warning(FLERR,"Fix {} alters forces after fix rigid", ifix->id);
+        error->warning(FLERR,"Fix {} with ID {} alters forces after fix rigid/small",
+                       ifix->style, ifix->id);
     }
   }
 

src/dump.cpp

@@ -150,19 +150,19 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
 
 Dump::~Dump()
 {
-  delete [] id;
+  delete[] id;
-  delete [] style;
+  delete[] style;
-  delete [] filename;
+  delete[] filename;
-  delete [] multiname;
+  delete[] multiname;
 
-  delete [] format;
+  delete[] format;
-  delete [] format_default;
+  delete[] format_default;
-  delete [] format_line_user;
+  delete[] format_line_user;
-  delete [] format_float_user;
+  delete[] format_float_user;
-  delete [] format_int_user;
+  delete[] format_int_user;
-  delete [] format_bigint_user;
+  delete[] format_bigint_user;
 
-  delete [] refresh;
+  delete[] refresh;
 
   // format_column_user is deallocated by child classes that use it
 
@@ -1019,7 +1019,7 @@ void Dump::balance()
   memory->destroy(tmp);
   memory->destroy(proc_offsets);
   memory->destroy(proc_new_offsets);
-  delete [] request;
+  delete[] request;
 }
 
 /* ----------------------------------------------------------------------
@@ -1059,7 +1059,7 @@ void Dump::modify_params(int narg, char **arg)
         if (strcmp(id,output->dump[idump]->id) == 0) break;
       int n;
       if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
-        delete [] output->var_dump[idump];
+        delete[] output->var_dump[idump];
         output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
         n = 0;
       } else {
@@ -1077,7 +1077,7 @@ void Dump::modify_params(int narg, char **arg)
         if (strcmp(id,output->dump[idump]->id) == 0) break;
       double delta;
       if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
-        delete [] output->var_dump[idump];
+        delete[] output->var_dump[idump];
         output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
         delta = 0.0;
       } else {
@@ -1107,7 +1107,7 @@ void Dump::modify_params(int narg, char **arg)
       MPI_Comm_free(&clustercomm);
       MPI_Comm_split(world,icluster,0,&clustercomm);
 
-      delete [] multiname;
+      delete[] multiname;
       char *ptr = strchr(filename,'%');
       *ptr = '\0';
       multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
@@ -1124,14 +1124,38 @@ void Dump::modify_params(int narg, char **arg)
       flush_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"colname") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (strcmp(arg[iarg+1],"default") == 0) {
+        for (auto item : keyword_user) item.clear();
+        iarg += 2;
+      } else {
+        if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
+        int icol = -1;
+        if (utils::is_integer(arg[iarg + 1])) {
+          icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
+          if (icol < 0) icol = keyword_user.size() + icol + 1;
+          icol--;
+        } else {
+          try {
+            icol = key2col.at(arg[iarg + 1]);
+          } catch (std::out_of_range &) {
+            icol = -1;
+          }
+        }
+        if ((icol < 0) || (icol >= (int)keyword_user.size()))
+          error->all(FLERR, "Illegal thermo_modify command");
+        keyword_user[icol] = arg[iarg+2];
+        iarg += 3;
+      }
     } else if (strcmp(arg[iarg],"format") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
 
       if (strcmp(arg[iarg+1],"none") == 0) {
-        delete [] format_line_user;
+        delete[] format_line_user;
-        delete [] format_int_user;
+        delete[] format_int_user;
-        delete [] format_bigint_user;
+        delete[] format_bigint_user;
-        delete [] format_float_user;
+        delete[] format_float_user;
         format_line_user = nullptr;
         format_int_user = nullptr;
         format_bigint_user = nullptr;
@@ -1146,7 +1170,7 @@ void Dump::modify_params(int narg, char **arg)
       if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
 
       if (strcmp(arg[iarg+1],"line") == 0) {
-        delete [] format_line_user;
+        delete[] format_line_user;
         format_line_user = utils::strdup(arg[iarg+2]);
         iarg += 3;
       } else {   // pass other format options to child classes
@@ -1204,7 +1228,7 @@ void Dump::modify_params(int narg, char **arg)
       MPI_Comm_free(&clustercomm);
       MPI_Comm_split(world,icluster,0,&clustercomm);
 
-      delete [] multiname;
+      delete[] multiname;
       char *ptr = strchr(filename,'%');
       *ptr = '\0';
       multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));

src/dump.h

@@ -16,6 +16,8 @@
 
 #include "pointers.h"    // IWYU pragma: export
 
+#include <map>
+
 namespace LAMMPS_NS {
 
 class Dump : protected Pointers {
@@ -100,6 +102,8 @@ class Dump : protected Pointers {
   char *format_bigint_user;
   char **format_column_user;
   enum { INT, DOUBLE, STRING, BIGINT };
+  std::map<std::string, int> key2col;
+  std::vector<std::string> keyword_user;
 
   FILE *fp;        // file to write dump to
   int size_one;    // # of quantities for one atom

src/dump_atom.cpp

@@ -38,6 +38,9 @@ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
   buffer_allow = 1;
   buffer_flag = 1;
   format_default = nullptr;
+  key2col = { { "id", 0 }, { "type", 1 }, { "x", 2 }, { "y", 3 },
+              { "z", 4 }, { "ix", 5 }, { "iy", 6 }, { "iz", 7 } };
+  keyword_user = { "", "", "", "", "", "", "", "" };
 }
 
 /* ---------------------------------------------------------------------- */
@@ -64,14 +67,25 @@ void DumpAtom::init_style()
 
   // setup column string
 
+  std::string default_columns;
+
   if (scale_flag == 0 && image_flag == 0)
-    columns = (char *) "id type x y z";
+    default_columns = "id type x y z";
   else if (scale_flag == 0 && image_flag == 1)
-    columns = (char *) "id type x y z ix iy iz";
+    default_columns = "id type x y z ix iy iz";
   else if (scale_flag == 1 && image_flag == 0)
-    columns = (char *) "id type xs ys zs";
+    default_columns = "id type xs ys zs";
   else if (scale_flag == 1 && image_flag == 1)
-    columns = (char *) "id type xs ys zs ix iy iz";
+    default_columns = "id type xs ys zs ix iy iz";
+
+  int icol = 0;
+  columns.clear();
+  for (auto item : utils::split_words(default_columns)) {
+    if (columns.size()) columns += " ";
+    if (keyword_user[icol].size()) columns += keyword_user[icol];
+    else columns += item;
+    ++icol;
+  }
 
   // setup function ptrs
 
@@ -201,9 +215,9 @@ void DumpAtom::header_unit_style_binary()
 
 void DumpAtom::header_columns_binary()
 {
-  int len = strlen(columns);
+  int len = columns.size();
   fwrite(&len, sizeof(int), 1, fp);
-  fwrite(columns, sizeof(char), len, fp);
+  fwrite(columns.c_str(), sizeof(char), len, fp);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -301,7 +315,7 @@ void DumpAtom::header_item(bigint ndump)
   fprintf(fp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
   fprintf(fp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
   fprintf(fp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
-  fprintf(fp,"ITEM: ATOMS %s\n",columns);
+  fprintf(fp,"ITEM: ATOMS %s\n",columns.c_str());
 }
 
 /* ---------------------------------------------------------------------- */
@@ -322,7 +336,7 @@ void DumpAtom::header_item_triclinic(bigint ndump)
   fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
   fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
   fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
-  fprintf(fp,"ITEM: ATOMS %s\n",columns);
+  fprintf(fp,"ITEM: ATOMS %s\n",columns.c_str());
 }
 
 /* ---------------------------------------------------------------------- */

src/dump_atom.h

@@ -36,7 +36,7 @@ class DumpAtom : public Dump {
   int scale_flag;    // 1 if atom coords are scaled, 0 if no
   int image_flag;    // 1 if append box count to atom coords, 0 if no
 
-  char *columns;    // column labels
+  std::string columns;    // column labels
 
   void init_style() override;
   int modify_param(int, char **) override;

src/dump_cfg.cpp

@@ -53,26 +53,26 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
 
   if (strcmp(earg[2],"xs") == 0) {
     if (strcmp(earg[3],"ysu") == 0 || strcmp(earg[4],"zsu") == 0)
-      error->all(FLERR,
+      error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
-                 "Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
     unwrapflag = 0;
   } else {
     if (strcmp(earg[3],"ys") == 0 || strcmp(earg[4],"zs") == 0)
-      error->all(FLERR,
+      error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
-                 "Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
     unwrapflag = 1;
   }
 
   // setup auxiliary property name strings
   // convert 'X_ID[m]' (X=c,f,v) to 'X_ID_m'
 
-  if (nfield > 5) auxname = new char*[nfield];
+  if (nfield > 5) auxname = new char*[nfield-5];
   else auxname = nullptr;
 
   int i = 0;
+  key2col.clear();
+  keyword_user.resize(nfield-5);
   for (int iarg = 5; iarg < nfield; iarg++, i++) {
-    ArgInfo argi(earg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
+    ArgInfo argi(earg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE|
-                 |ArgInfo::DNAME|ArgInfo::INAME);
+                 ArgInfo::DNAME|ArgInfo::INAME);
 
     if (argi.get_dim() == 1) {
       std::string newarg = fmt::format("{}_{}_{}", earg[iarg][0], argi.get_name(), argi.get_index1());
@@ -80,6 +80,8 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
     } else {
       auxname[i] = utils::strdup(earg[iarg]);
     }
+    key2col[earg[iarg]] = i;
+    keyword_user[i].clear();
   }
 }
 
@@ -88,8 +90,8 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
 DumpCFG::~DumpCFG()
 {
   if (auxname) {
-    for (int i = 0; i < nfield-5; i++) delete [] auxname[i];
+    for (int i = 0; i < nfield-5; i++) delete[] auxname[i];
-    delete [] auxname;
+    delete[] auxname;
   }
 }
 
@@ -136,8 +138,12 @@ void DumpCFG::write_header(bigint n)
   fprintf(fp,"H0(3,3) = %g A\n",domain->zprd);
   fprintf(fp,".NO_VELOCITY.\n");
   fprintf(fp,"entry_count = %d\n",nfield-2);
-  for (int i = 0; i < nfield-5; i++)
+  for (int i = 0; i < nfield-5; i++) {
-    fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
+    if (keyword_user[i].size())
+      fprintf(fp,"auxiliary[%d] = %s\n",i,keyword_user[i].c_str());
+    else
+      fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
+  }
 }
 
 /* ----------------------------------------------------------------------

src/dump_custom.cpp

@@ -55,14 +55,11 @@ enum{LT,LE,GT,GE,EQ,NEQ,XOR};
 DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   Dump(lmp, narg, arg),
   idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr), thresh_value(nullptr),
-  thresh_last(nullptr), thresh_fix(nullptr),
+  thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr), thresh_first(nullptr),
-  thresh_fixID(nullptr), thresh_first(nullptr),
+  earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), columns_default(nullptr),
-  earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), choose(nullptr),
+  choose(nullptr), dchoose(nullptr), clist(nullptr), field2index(nullptr), argindex(nullptr),
-  dchoose(nullptr), clist(nullptr), field2index(nullptr),
+  id_compute(nullptr), compute(nullptr), id_fix(nullptr), fix(nullptr), id_variable(nullptr),
-  argindex(nullptr), id_compute(nullptr),
+  variable(nullptr), vbuf(nullptr), id_custom(nullptr), custom(nullptr), custom_flag(nullptr),
-  compute(nullptr), id_fix(nullptr), fix(nullptr),
-  id_variable(nullptr), variable(nullptr),
-  vbuf(nullptr), id_custom(nullptr), custom(nullptr), custom_flag(nullptr),
   typenames(nullptr), pack_choice(nullptr)
 {
   if (narg == 5) error->all(FLERR,"No dump custom arguments specified");
@@ -180,13 +177,14 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   // setup column string
 
   cols.clear();
+  keyword_user.resize(nfield);
   for (int iarg = 0; iarg < nfield; iarg++) {
+    key2col[earg[iarg]] = iarg;
+    keyword_user[iarg].clear();
+    if (cols.size()) cols += " ";
     cols += earg[iarg];
-    cols += " ";
   }
-  // remove trailing blank and copy
+  columns_default = utils::strdup(cols);
-  cols.resize(cols.size()-1);
-  columns = utils::strdup(cols);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -257,6 +255,7 @@ DumpCustom::~DumpCustom()
     delete[] format_column_user;
   }
 
+  delete[] columns_default;
   delete[] columns;
 }
 
@@ -264,6 +263,19 @@ DumpCustom::~DumpCustom()
 
 void DumpCustom::init_style()
 {
+  // assemble ITEMS: column string from defaults and user values
+
+  delete[] columns;
+  std::string combined;
+  int icol = 0;
+  for (auto item : utils::split_words(columns_default)) {
+    if (combined.size()) combined += " ";
+    if (keyword_user[icol].size()) combined += keyword_user[icol];
+    else combined += item;
+    ++icol;
+  }
+  columns = utils::strdup(combined);
+
   // format = copy of default or user-specified line format
 
   delete[] format;

src/dump_custom.h

@@ -60,6 +60,7 @@ class DumpCustom : public Dump {
   char **vformat;     // format string for each vector element
                       //
   char *columns;      // column labels
+  char *columns_default;
                       //
   int nchoose;        // # of selected atoms
   int maxlocal;       // size of atom selection and variable arrays

src/modify.cpp

@@ -249,11 +249,11 @@ void Modify::init()
 
   for (i = 0; i < nfix; i++)
     if (!fix[i]->dynamic_group_allow && group->dynamic[fix[i]->igroup])
-      error->all(FLERR, "Fix {} does not allow use with a dynamic group", fix[i]->id);
+      error->all(FLERR, "Fix {} does not allow use with a dynamic group", fix[i]->style);
 
   for (i = 0; i < ncompute; i++)
     if (!compute[i]->dynamic_group_allow && group->dynamic[compute[i]->igroup])
-      error->all(FLERR, "Compute {} does not allow use with a dynamic group", compute[i]->id);
+      error->all(FLERR, "Compute {} does not allow use with a dynamic group", compute[i]->style);
 
   // warn if any particle is time integrated more than once
 

src/thermo.cpp

@@ -252,8 +252,12 @@ void Thermo::init()
       format[i] += format_this + " ";
     else if (lineflag == YAMLLINE)
       format[i] += format_this + ", ";
-    else
+    else {
-      format[i] += fmt::format("{:<8} = {} ", keyword[i], format_this);
+      if (keyword_user[i].size())
+        format[i] += fmt::format("{:<8} = {} ", keyword_user[i], format_this);
+      else
+        format[i] += fmt::format("{:<8} = {} ", keyword[i], format_this);
+    }
   }
 
   // chop off trailing blank or add closing bracket if needed and then add newline
@@ -324,11 +328,13 @@ void Thermo::header()
   std::string hdr;
   if (lineflag == YAMLLINE) hdr = "---\nkeywords: [";
   for (int i = 0; i < nfield; i++) {
+    auto head = keyword[i];
+    if (keyword_user[i].size()) head = keyword_user[i];
     if (lineflag == ONELINE) {
       if (vtype[i] == FLOAT)
-        hdr += fmt::format("{:^14} ", keyword[i]);
+        hdr += fmt::format("{:^14} ", head);
       else if ((vtype[i] == INT) || (vtype[i] == BIGINT))
-        hdr += fmt::format("{:^11} ", keyword[i]);
+        hdr += fmt::format("{:^11} ", head);
     } else if (lineflag == YAMLLINE) {
       hdr += keyword[i];
       hdr += ", ";
@@ -622,6 +628,29 @@ void Thermo::modify_params(int narg, char **arg)
         error->all(FLERR, "Illegal thermo_modify command");
       iarg += 2;
 
+    } else if (strcmp(arg[iarg], "colname") == 0) {
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal thermo_modify command");
+      if (strcmp(arg[iarg + 1], "default") == 0) {
+        for (auto item : keyword_user) item.clear();
+        iarg += 2;
+      } else {
+        if (iarg + 3 > narg) error->all(FLERR, "Illegal thermo_modify command");
+        int icol = -1;
+        if (utils::is_integer(arg[iarg + 1])) {
+          icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
+          if (icol < 0) icol = nfield_initial + icol + 1;
+          icol--;
+        } else {
+          try {
+            icol = key2col.at(arg[iarg + 1]);
+          } catch (std::out_of_range &) {
+            icol = -1;
+          }
+        }
+        if ((icol < 0) || (icol >= nfield_initial)) error->all(FLERR, "Illegal thermo_modify command");
+        keyword_user[icol] = arg[iarg+2];
+        iarg += 3;
+      }
     } else if (strcmp(arg[iarg], "format") == 0) {
       if (iarg + 2 > narg) error->all(FLERR, "Illegal thermo_modify command");
 
@@ -630,7 +659,7 @@ void Thermo::modify_params(int narg, char **arg)
         format_int_user.clear();
         format_bigint_user.clear();
         format_float_user.clear();
-        for (int i = 0; i < nfield_initial + 1; ++i) format_column_user[i].clear();
+        for (auto item : format_column_user) item.clear();
         iarg += 2;
         continue;
       }
@@ -646,14 +675,24 @@ void Thermo::modify_params(int narg, char **arg)
         found = format_int_user.find('d', found);
         if (found == std::string::npos)
           error->all(FLERR, "Thermo_modify int format does not contain a d conversion character");
-        format_bigint_user =
+        format_bigint_user = format_int_user.replace(found, 1, std::string(BIGINT_FORMAT).substr(1));
-            format_int_user.replace(found, 1, std::string(BIGINT_FORMAT).substr(1));
       } else if (strcmp(arg[iarg + 1], "float") == 0) {
         format_float_user = arg[iarg + 2];
       } else {
-        int i = utils::inumeric(FLERR, arg[iarg + 1], false, lmp) - 1;
+        int icol = -1;
-        if (i < 0 || i >= nfield_initial + 1) error->all(FLERR, "Illegal thermo_modify command");
+        if (utils::is_integer(arg[iarg + 1])) {
-        format_column_user[i] = arg[iarg + 2];
+          icol = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+          if (icol < 0) icol = nfield_initial + icol + 1;
+          icol--;
+        } else {
+          try {
+            icol = key2col.at(arg[iarg + 1]);
+          } catch (std::out_of_range &) {
+            icol = -1;
+          }
+        }
+        if (icol < 0 || icol >= nfield_initial + 1) error->all(FLERR, "Illegal thermo_modify command");
+        format_column_user[icol] = arg[iarg + 2];
       }
       iarg += 3;
 
@@ -675,10 +714,12 @@ void Thermo::allocate()
   keyword.resize(n);
   format.resize(n);
   format_column_user.resize(n);
+  keyword_user.resize(n);
   for (int i = 0; i < n; i++) {
     keyword[i].clear();
     format[i].clear();
     format_column_user[i].clear();
+    keyword_user[i].clear();
   }
 
   vfunc = new FnPtr[n];
@@ -702,6 +743,12 @@ void Thermo::allocate()
   nvariable = 0;
   id_variable = new char *[n];
   variables = new int[n];
+
+  int i = 0;
+  key2col.clear();
+  for (auto item : utils::split_words(line)) {
+    key2col[item] = i++;
+  }
 }
 
 /* ----------------------------------------------------------------------

src/thermo.h

@@ -15,6 +15,7 @@
 #define LMP_THERMO_H
 
 #include "pointers.h"
+#include <map>
 
 namespace LAMMPS_NS {
 
@@ -47,8 +48,9 @@ class Thermo : protected Pointers {
   int nfield, nfield_initial;
   int *vtype;
   std::string line;
-  std::vector<std::string> keyword, format, format_column_user;
+  std::vector<std::string> keyword, format, format_column_user, keyword_user;
   std::string format_line_user, format_float_user, format_int_user, format_bigint_user;
+  std::map<std::string, int> key2col;
 
   int normvalue;       // use this for normflag unless natoms = 0
   int normuserflag;    // 0 if user has not set, 1 if has

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):