Question: absolute value in queries

[eszter137]

I'd like to be able to do something like:

abcd summary -q "ABS(E_MP2_3b)>0.01"  -p "E_MP2_3b"

This would be useful when checking for the large differences between 2 calculation methods.

(It could be also solved by the OR operator but I haven't figured out how to use this yet - the following didn't work:

$ abcd summary -q "E_MP2_3b<-0.01" OR "E_MP2_3b>0.01" -p "E_MP2_3b"

$ abcd summary -q "E_MP2_3b<-0.01 OR E_MP2_3b>0.01" -p "E_MP2_3b"

)

[gabor1]

arithmetic on variables is planned, but doesn’t work yet. it’s a major undertaking ( and will always be MUCH SLOWER than the explicitly written version that doesn’t use operators). you need to put the OR inside the quotes.

This certainly worked for me: abcd summary -q 'filename~"Surf" or filename~"n500”'

I think the “or” needs to be lower case...

-- Gábor

Gábor Csányi Professor of Molecular Modelling Engineering Laboratory, University of Cambridge Pembroke College Cambridge

Pembroke College supports CARA. A Lifeline to Academics at Risk. http://www.cara.ngo/

On 16 Mar 2020, at 12:28, eszter137 notifications@github.com wrote:

I'd like to be able to do something like:

abcd summary -q "ABS(E_MP2_3b)>0.01" -p "E_MP2_3b"

This would be useful when checking for the large differences between 2 calculation methods.

(It could be also solved by the OR operator but I haven't figured out how to use this yet - the following didn't work:

$ abcd summary -q "E_MP2_3b<-0.01" OR "E_MP2_3b>0.01" -p "E_MP2_3b"

$ abcd summary -q "E_MP2_3b<-0.01 OR E_MP2_3b>0.01" -p "E_MP2_3b"

)

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[eszter137]

I think this is something similar to your example but not working:

$ abcd summary -q '"E_MP2_3b<-0.01" or "E_MP2_3b>0.01"' -p "E_MP2_3b"
Traceback (most recent call last):
  File "/home/es732/miniconda3/bin/abcd", line 8, in <module>
    sys.exit(main())
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/parser.py", line 121, in main
    callback_func(**kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/decorators.py", line 15, in wrapper
    func(*args, config=config, **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/decorators.py", line 39, in wrapper
    query_list.append(parser(q))
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/parsers/queries.py", line 136, in __call__
    return self.transformer.transform(self.parse(string))
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/parsers/queries.py", line 133, in parse
    return self.parser.parse(string)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/lark/lark.py", line 308, in parse
    return self.parser.parse(text, start=start)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/lark/parser_frontends.py", line 193, in parse
    return self._parse(text, start)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/lark/parser_frontends.py", line 54, in _parse
    return self.parser.parse(input, start, *args)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/lark/parsers/earley.py", line 292, in parse
    to_scan = self._parse(stream, columns, to_scan, start_symbol)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/lark/parsers/xearley.py", line 137, in _parse
    to_scan = scan(i, to_scan)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/lark/parsers/xearley.py", line 114, in scan
    raise UnexpectedCharacters(stream, i, text_line, text_column, {item.expect.name for item in to_scan}, set(to_scan))
lark.exceptions.UnexpectedCharacters: No terminal defined for 'o' at line 1 col 18

"E_MP2_3b<-0.01" or "E_MP2_3b>0.01"
                 ^

Expecting: {'IN'}

When changing the place of the quotes, I don't get any results:

$ abcd summary -q 'E_MP2_3b<"-0.01" or E_MP2_3b>"0.01"' -p "E_MP2_3b"

though there are definitely structures with either of the queries:

$ abcd summary -q 'E_MP2_3b<-0.01' -p "E_MP2_3b"
E_MP2_3b  count: 340 min: -2.8904e-01 med: -2.2580e-02 max: -1.0002e-02 std:  2.7190e-02 var: 7.3930e-04
                                           1 [-2.8904e-01,     -0.2611)
                                           0 [-2.6114e-01,     -0.2332)
                                           1 [-2.3323e-01,     -0.2053)
                                           1 [-2.0533e-01,     -0.1774)
                                           0 [-1.7743e-01,     -0.1495)
                                           3 [-1.4952e-01,     -0.1216)
                                           3 [-1.2162e-01,     -0.0937)
▉                                          9 [-9.3714e-02,     -0.0658)
                                           7 [-6.5810e-02,     -0.0379)
▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 315 [-3.7906e-02,     -0.0100)
$ abcd summary -q 'E_MP2_3b>0.01' -p "E_MP2_3b"
E_MP2_3b  count: 151 min:  1.0022e-02 med:  1.9160e-02 max:  4.0975e-01 std:  3.3383e-02 var: 1.1144e-03
▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 148 [ 1.0022e-02,      0.0500)
                                           1 [ 4.9995e-02,      0.0900)
                                           1 [ 8.9968e-02,      0.1299)
                                           0 [ 1.2994e-01,      0.1699)
                                           0 [ 1.6991e-01,      0.2099)
                                           0 [ 2.0989e-01,      0.2499)
                                           0 [ 2.4986e-01,      0.2898)
                                           0 [ 2.8983e-01,      0.3298)
                                           0 [ 3.2981e-01,      0.3698)
                                           1 [ 3.6978e-01,      0.4098)

[eszter137]

it seems it handles numbers within quotes as strings, this won't result in any structures again:

$ abcd summary -q 'E_MP2_3b<"-0.01"' -p "E_MP2_3b"

[eszter137]

ok, this version is working finally when removing the internal quotes:

$ abcd summary -q 'E_MP2_3b<-0.01 or E_MP2_3b>0.01' -p "E_MP2_3b"
E_MP2_3b  count: 491 min: -2.8904e-01 med: -9.7434e-03 max:  4.0975e-01 std:  3.5010e-02 var: 1.2257e-03
                                           1 [-2.8904e-01,     -0.2192)
                                           2 [-2.1916e-01,     -0.1493)
▉                                         11 [-1.4928e-01,     -0.0794)
▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 326 [-7.9404e-02,     -0.0095)
▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉                       148 [-9.5247e-03,      0.0604)
                                           2 [ 6.0355e-02,      0.1302)
                                           0 [ 1.3023e-01,      0.2001)
                                           0 [ 2.0011e-01,      0.2700)
                                           0 [ 2.6999e-01,      0.3399)
                                           1 [ 3.3987e-01,      0.4098)

[gabor1]

strings are quoted, numbers are not!! But (for strings) the quotes need to be protected from the shell by either enclosing the entire argument of the -q in ‘ (single quotes) or using backslashes on the double quotes.

-- Gábor

Gábor Csányi Professor of Molecular Modelling Engineering Laboratory, University of Cambridge Pembroke College Cambridge

Pembroke College supports CARA. A Lifeline to Academics at Risk. http://www.cara.ngo/

On 16 Mar 2020, at 16:01, eszter137 notifications@github.com wrote:

it seems it handles numbers within quotes as strings, this won't result in any structures again:

$ abcd summary -q 'E_MP2_3b<"-0.01"' -p "E_MP2_3b"

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