Automatically set the relative atomic mass according to "type_map" #867

panxiang126 · 2022-08-12T10:14:06Z

A new function get_atomic_masses was written to get the relative atomic mass (data from: Atomic weights of the elements 2013 (IUPAC Technical Report)). So that there is no need to specify the mass_map manually in param.json.

Automatically set the relative atomic mass according to "type_map" Signed-off-by: Pan Xiang <panxiang126@gmail.com>

Signed-off-by: Pan Xiang <panxiang126@gmail.com>

njzjz · 2022-08-12T18:20:12Z

dpgen/generator/run.py

+def get_atomic_masses(chemical_symbol):
+  chemical_symbols = ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']
+
+  # doi:10.1515/pac-2015-0305


Why not use the latest data?
https://doi.org/10.1515/pac-2019-0603

I can not fully understand wanghan-iapcm's comment below. I have rewritten the get_atomic_masses function, and now it can be called by three types, i. e. element_names, chemical_symbols and atomic_number. I am not sure if this will remove his/her concern.

I mean atom name can be ANY string, not necessary element_names or chemical_symbols.
For example it is valid to write "type_map" : ["foo", "bar"].

I agree with @wanghan-iapcm. This should be documented that auto only supports the standard atoms. (For example, OW will not be supported)

I updated the documentation.

njzjz · 2022-08-12T18:21:51Z

dpgen/generator/run.py

@@ -1115,7 +1115,7 @@ def _make_model_devi_native(iter_index, jdata, mdata, conf_systems):
    model_devi_taup = 0.5
    if 'model_devi_taup' in jdata :
        model_devi_taup = jdata['model_devi_taup']
-    mass_map = jdata['mass_map']
+    mass_map = [get_atomic_masses(i) for i in jdata['type_map']]


This should not override the user config, as one may want to simulate isotopes.

updated.

Please check if jdata['mass_map'] is None is used correctly

wanghan-iapcm

The dpgen and dpdata do not restrict the atom_names to chemical symbols. This PR will break the convention.

Signed-off-by: Pan Xiang <panxiang126@gmail.com>

codecov-commenter · 2022-08-13T10:57:42Z

Codecov Report

Merging #867 (557215b) into devel (ed86867) will decrease coverage by 0.00%.
The diff coverage is 36.00%.

@@            Coverage Diff             @@
##            devel     #867      +/-   ##
==========================================
- Coverage   38.00%   37.99%   -0.01%     
==========================================
  Files          99       99              
  Lines       17754    17775      +21     
==========================================
+ Hits         6747     6754       +7     
- Misses      11007    11021      +14

Impacted Files	Coverage Δ
dpgen/generator/run.py	`62.21% <33.33%> (-0.30%)`	⬇️
dpgen/tools/relabel.py	`14.73% <33.33%> (ø)`
dpgen/generator/arginfo.py	`99.27% <100.00%> (+0.01%)`	⬆️
dpgen/simplify/arginfo.py	`96.55% <0.00%> (+0.25%)`	⬆️

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njzjz

Please update the following documentation to reflect your changes.

dpgen/dpgen/generator/arginfo.py

Line 20 in 741f4cd

doc_mass_map = 'Standard atom weights.'

njzjz · 2022-08-13T16:27:58Z

dpgen/generator/run.py

@@ -3733,6 +3734,34 @@ def run_iter (param_file, machine_file) :
                raise RuntimeError ("unknown task %d, something wrong" % jj)
            record_iter (record, ii, jj)

+def get_atomic_masses(atom):
+
+  element_names = ['Hydrogen', 'Helium', 'Lithium', 'Beryllium', 'Boron', 'Carbon', 'Nitrogen', 'Oxygen', 'Fluorine', 'Neon', 'Sodium', 'Magnesium', 'Aluminium', 'Silicon', 'Phosphorus', 'Sulfur', 'Chlorine', 'Argon', 'Potassium', 'Calcium', 'Scandium', 'Titanium', 'Vanadium', 'Chromium', 'Manganese', 'Iron', 'Cobalt', 'Nickel', 'Copper', 'Zinc', 'Gallium', 'Germanium', 'Arsenic', 'Selenium', 'Bromine', 'Krypton', 'Rubidium', 'Strontium', 'Yttrium', 'Zirconium', 'Niobium', 'Molybdenum', 'Technetium', 'Ruthenium', 'Rhodium', 'Palladium', 'Silver', 'Cadmium', 'Indium', 'Tin', 'Antimony', 'Tellurium', 'Iodine', 'Xenon', 'Caesium', 'Barium', 'Lanthanum', 'Cerium', 'Praseodymium', 'Neodymium', 'Promethium', 'Samarium', 'Europium', 'Gadolinium', 'Terbium', 'Dysprosium', 'Holmium', 'Erbium', 'Thulium', 'Ytterbium', 'Lutetium', 'Hafnium', 'Tantalum', 'Tungsten', 'Rhenium', 'Osmium', 'Iridium', 'Platinum', 'Gold', 'Mercury', 'Thallium', 'Lead', 'Bismuth', 'Polonium', 'Astatine', 'Radon', 'Francium', 'Radium', 'Actinium', 'Thorium', 'Protactinium', 'Uranium', 'Neptunium', 'Plutonium', 'Americium', 'Curium', 'Berkelium', 'Californium', 'Einsteinium', 'Fermium', 'Mendelevium', 'Nobelium', 'Lawrencium', 'Rutherfordium', 'Dubnium', 'Seaborgium', 'Bohrium', 'Hassium', 'Meitnerium', 'Darmastadtium', 'Roentgenium', 'Copernicium', 'Nihonium', 'Flerovium', 'Moscovium', 'Livermorium', 'Tennessine', 'Oganesson']


We use 4 spaces for indent.

Signed-off-by: Pan Xiang <panxiang126@gmail.com>

njzjz · 2022-08-15T06:59:36Z

dpgen/generator/arginfo.py

    doc_use_ele_temp = 'Currently only support fp_style vasp. \n\n\
 - 0: no electron temperature. \n\n\
 - 1: eletron temperature as frame parameter. \n\n\
 - 2: electron temperature as atom parameter.'

    return [
        Argument("type_map", list, optional=False, doc=doc_type_map),
-        Argument("mass_map", list, optional=False, doc=doc_mass_map),
+        Argument("mass_map", [str, list], optional=True, default="auto", doc=doc_mass_map),


Note: as the arguments are still being built, at present the default value will not be automatically applied, but only shown in the documentation.

Signed-off-by: Pan Xiang <panxiang126@gmail.com>

njzjz · 2022-08-16T19:10:36Z

@AnguseZhang you should squash merge...

wanghan-iapcm · 2022-08-17T02:28:34Z

dpgen/generator/run.py

@@ -968,7 +968,7 @@ def _make_model_devi_revmat(iter_index, jdata, mdata, conf_systems):
    sys_idx = expand_idx(cur_job['sys_idx'])
    if (len(sys_idx) != len(list(set(sys_idx)))) :
        raise RuntimeError("system index should be uniq")
-    mass_map = jdata['mass_map']
+    mass_map = [get_atomic_masses(i) for i in jdata['type_map']] if jdata['mass_map'] == "auto" else jdata['mass_map']


You may want to write a function for automatic building of mass_map rather than repeating the same line for multiple times.

wanghan-iapcm · 2022-08-17T02:29:13Z

@AnguseZhang I am against the merging of this PR.

AnguseZhang · 2022-08-17T07:12:57Z

@AnguseZhang I am against the merging of this PR.

@wanghan-iapcm Reverted in #881

For previous discussions, see [#867](#867) and [#881](#881). It is very strange that the comparison is with the version before [#881](#881). Signed-off-by: Pan Xiang <panxiang126@gmail.com>

panxiang126 added 2 commits August 12, 2022 18:06

Update run.py

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Automatically set the relative atomic mass according to "type_map" Signed-off-by: Pan Xiang <panxiang126@gmail.com>

Update relabel.py

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Automatically set the relative atomic mass according to "type_map" Signed-off-by: Pan Xiang <panxiang126@gmail.com>

panxiang126 changed the title ~~Automatically set the relative atomic mass according to "type_map"Devel~~ Automatically set the relative atomic mass according to "type_map" Aug 12, 2022

Update relabel.py

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panxiang126 added 3 commits August 13, 2022 12:37

Update run.py

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Signed-off-by: Pan Xiang <panxiang126@gmail.com>

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Update relabel.py

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panxiang126 requested review from njzjz and wanghan-iapcm August 13, 2022 10:17

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panxiang126 added 4 commits August 14, 2022 03:41

Update run.py

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Signed-off-by: Pan Xiang <panxiang126@gmail.com>

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panxiang126 requested a review from njzjz August 15, 2022 02:47

Update run.py

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AnguseZhang merged commit 544953e into deepmodeling:devel Aug 16, 2022

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AnguseZhang mentioned this pull request Aug 17, 2022

Revert changes to type_map and mass_map #881

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panxiang126 mentioned this pull request Aug 19, 2022

Patch to #867 and #881 about mass_map #893

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Automatically set the relative atomic mass according to "type_map" #867

Automatically set the relative atomic mass according to "type_map" #867

panxiang126 commented Aug 12, 2022

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Automatically set the relative atomic mass according to "type_map" #867

Automatically set the relative atomic mass according to "type_map" #867

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