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qcxms / QCxMS

Quantum mechanic mass spectrometry calculation program
https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html
GNU Lesser General Public License v3.0
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conda package maybe broken? #85

Closed st1553 closed 2 months ago

st1553 commented 3 months ago

No matter what I do, the conda packaged version of this always seems to give this error when run with a coord file and qxcms.in:

-- linux-rhel9-zen3 / gcc@11.4.1 --------------------------------
py-conda-souschef@2.2.3  qcxms@5.2.1
==> 2 installed packages
Input file content (qcxms.in):
xtb
ntraj 300
tmax  10
tinit 500
ieeatm 0.6
Coordinate file content (coord):
$coord
O          3.05620       -3.62856       -0.37084
C          1.84105       -3.44086       -0.31115
N          1.25506       -2.34517       -0.90928
C          2.07206       -1.42471       -1.69967
C          2.96825       -0.61734       -0.72802
N          4.31233       -0.86051       -0.84134
O          2.55427        0.16498        0.12254
C          1.26294       -0.50658       -2.66588
C          2.21210        0.47721       -3.38791
C          0.58830       -1.37105       -3.75259
C          0.17726        0.30535       -1.93882
C          0.92150       -4.40831        0.31119
N         -0.25407       -4.09763        0.89368
N         -0.69947       -5.28629        1.40485
C         -1.87948       -5.24455        2.27729
C         -2.38327       -6.59256        2.79486
C         -3.61027       -6.55377        3.70211
C         -3.98173       -7.97964        4.10955
C          0.07434       -6.36624        1.01539
C          1.14998       -5.80882        0.32615
C          2.15367       -6.64503       -0.20620
C          2.05996       -8.02530       -0.05077
C          0.98991       -8.57447        0.63830
C         -0.00925       -7.76124        1.18350
H          2.73473       -2.04977       -2.31702
H          0.24923       -2.25331       -0.82982
H          4.86569       -0.44249       -0.10562
H          4.58539       -1.80873       -1.08901
H          2.98696       -0.05781       -3.94908
H          2.71287        1.15238       -2.68606
H          1.66283        1.10513       -4.09917
H          1.33331       -1.92309       -4.33781
H          0.01933       -0.74857       -4.45366
H         -0.10517       -2.09893       -3.31962
H          0.60809        0.99727       -1.20956
H         -0.53220       -0.34099       -1.41347
H         -0.40021        0.90823       -2.64886
H         -2.66964       -4.74284        1.70602
H         -1.60830       -4.60072        3.12339
H         -1.57703       -7.07662        3.35899
H         -2.63867       -7.22065        1.93388
H         -4.45621       -6.09361        3.18073
H         -3.40568       -5.96104        4.60004
H         -4.19587       -8.59547        3.22849
H         -4.86715       -7.98712        4.75121
H         -3.16098       -8.45698        4.65705
H          2.99158       -6.21565       -0.75001
H          2.82569       -8.66882       -0.47426
H          0.92310       -9.65304        0.75758
H         -0.81858       -8.25029        1.70941
$end
Generating ground state (GS) trajectory...
Mon Jul 22 10:12:22 PM EDT 2024

                      *********************************************
                      *                                           *
                      *            Q   C   x   M   S              *
                      *                                           *
                      *                  V5.2.1                   *
                      *        Sep 20 18:00:00 CEST 2022          *
                      *                                           *
                      *                S. Grimme                  *
                      *                J. Koopman                 *
                      * Mulliken Center for Theoretical Chemistry *
                      *             Universitaet Bonn             *
                      *                                           *
                      *********************************************

 QCxMS is free software: you can redistribute it and/or modify it under
 the terms of the GNU Lesser General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 QCxMS is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU Lesser General Public License for more details.

Cite this work as:
S.Grimme, Angew.Chem.Int.Ed. 52 (2013) 6306-6312.

for the CID module:
J. Koopman, S. Grimme, J. Am. Soc. Mass Spectrom., (2021),  DOI: 10.1021/jasms.1c00098

with respect to negative/multiple charges:
J. Koopman, S. Grimme, ChemRxiv, (2022),  DOI: 10.26434/chemrxiv-2022-w5260

for the GFN1-xTB implementation:
V. Asgeirsson, C.Bauer, S. Grimme, Chem. Sci. 8 (2017) 4879

for the GFN2-xTB implementation:
 J. Koopman, S. Grimme, ACS Omega 4 (12) (2019) 15120-15133,  DOI: 10.1021/acsomega.9b02011

 changed by input:
>xtb
>ntraj 300
>tmax  10
>tinit 500
>ieeatm 0.6
ERROR STOP  -- Unrecognized Keyword --

Error termination. Backtrace:
#0  0x5556c90fd6d5 in ???
#1  0x5556c90d36df in ???
#2  0x5556c90d3060 in ???
#3  0x7ffabe03feaf in ???
#4  0x7ffabe03ff5f in ???
#5  0x5556c90d3090 in ???
qcxms command failed during GS trajectory generation.
tobigithub commented 3 months ago

You are trying to pass on XYZ coordinats as turbomole input format. See here for correct input options https://xtb-docs.readthedocs.io/en/latest/geometry.html You can use OpenBabel to create a turbomole input file.

If you want to pass on XYZ files you need to add the number of atoms on top. Then you need to provide the input as such qcxms -i input.xyz

qcxms -i input.xyz

              ************************************************************
                       Mode:          Electron Impact (EI)         
              ************************************************************

----- Internal program parameters -----

 QC Program            : xTB
 QC Level              : GFN1-xTB
 Dispersion            : D3
 MO spectrum with      : xTB     

 M+ Ion charge(charge) :    1
 total traj.   (ntraj) :  300
 time steps    (tstep) :    0.50 fs
 sim. time / MD (tmax) :   10.00 ps
 Initial temp. (tinit) :  500.00 K

------------ EI settings -----------
 E(e-impact)   (eimp0) :   70.00 eV
 Iee/atom     (ieeatm) :    0.60 eV/atom
 relax. time  (trelax) : 2000.00 fs

--------------------------------------------
 qc path              /usr/local/bin/
--------------------------------------------
 xtbhome directory    ~/.XTBPARAM/
--------------------------------------------

 Generating uniform velocity distribution, T=     500.0
 Groundstate eTemp set to   298.14999389648438     

 initializing GFN1-xTB ...
 initialization successful!
 energy =      -74.30093
 charge =              0
 mult   =              1
 etemp  =          298.1
 M trajactory, equilibration ...        7500

             E N T E R I N G   M D   M O D U L E

step   time [fs]    Epot       Ekin       Etot    error  #F   eTemp   frag. T

input.xyz

50

O          3.05620       -3.62856       -0.37084
C          1.84105       -3.44086       -0.31115
N          1.25506       -2.34517       -0.90928
C          2.07206       -1.42471       -1.69967
C          2.96825       -0.61734       -0.72802
N          4.31233       -0.86051       -0.84134
O          2.55427        0.16498        0.12254
C          1.26294       -0.50658       -2.66588
C          2.21210        0.47721       -3.38791
C          0.58830       -1.37105       -3.75259
C          0.17726        0.30535       -1.93882
C          0.92150       -4.40831        0.31119
N         -0.25407       -4.09763        0.89368
N         -0.69947       -5.28629        1.40485
C         -1.87948       -5.24455        2.27729
C         -2.38327       -6.59256        2.79486
C         -3.61027       -6.55377        3.70211
C         -3.98173       -7.97964        4.10955
C          0.07434       -6.36624        1.01539
C          1.14998       -5.80882        0.32615
C          2.15367       -6.64503       -0.20620
C          2.05996       -8.02530       -0.05077
C          0.98991       -8.57447        0.63830
C         -0.00925       -7.76124        1.18350
H          2.73473       -2.04977       -2.31702
H          0.24923       -2.25331       -0.82982
H          4.86569       -0.44249       -0.10562
H          4.58539       -1.80873       -1.08901
H          2.98696       -0.05781       -3.94908
H          2.71287        1.15238       -2.68606
H          1.66283        1.10513       -4.09917
H          1.33331       -1.92309       -4.33781
H          0.01933       -0.74857       -4.45366
H         -0.10517       -2.09893       -3.31962
H          0.60809        0.99727       -1.20956
H         -0.53220       -0.34099       -1.41347
H         -0.40021        0.90823       -2.64886
H         -2.66964       -4.74284        1.70602
H         -1.60830       -4.60072        3.12339
H         -1.57703       -7.07662        3.35899
H         -2.63867       -7.22065        1.93388
H         -4.45621       -6.09361        3.18073
H         -3.40568       -5.96104        4.60004
H         -4.19587       -8.59547        3.22849
H         -4.86715       -7.98712        4.75121
H         -3.16098       -8.45698        4.65705
H          2.99158       -6.21565       -0.75001
H          2.82569       -8.66882       -0.47426
H          0.92310       -9.65304        0.75758
H         -0.81858       -8.25029        1.70941
tobigithub commented 2 months ago

@st1553

st1553 commented 2 months ago

Thank you so much Tobias that fixed the issue. Can close the ticket thank you

On Mon, Jul 29, 2024, 8:17 PM Tobias Kind @.***> wrote:

@st1553 https://github.com/st1553

— Reply to this email directly, view it on GitHub https://github.com/qcxms/QCxMS/issues/85#issuecomment-2257230624, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHXOD6FQBNAMBOAVXVA2FULZO3LPXAVCNFSM6AAAAABLJNIERKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJXGIZTANRSGQ . You are receiving this because you were mentioned.Message ID: @.***>