I've installed Webmo 23.0.017, with Tinker 8.10.5 and Quantum Espresso 7.2 along with gamess, mopac, nwchem, and orca on linux. I can't seem to make Tinker and Quantum Espresso work. The other packages appear to work correctly.
Quantum Espresso and Tinker get different errors. I can't tell if this is a setup problem, a version mismatch, or some other problem. The specific errors are below.
Anyone have an idea what could be causing these errors?
Quantum Espresso
Program PWSCF v.7.2 starts on 3Nov2023 at 10:12:14
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
402 MiB available memory on the printing compute node when the environment starts
Reading input from /home/webmo/webmo_data/chemlab/44/input.inp
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine card_atomic_species (1):
cannot read atomic specie from: H 1.01
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Program PHONON v.7.2 starts on 3Nov2023 at 10:12:14
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
405 MiB available memory on the printing compute node when the environment starts
Reading input from /home/webmo/webmo_data/chemlab/44/input.inp
Reading xml data from directory:
/tmp/webmo-16364/44/pwscf.save/
Message from routine qexsd_readschema :
xml data file /tmp/webmo-16364/44/pwscf.save/data-file-schema.xml not found
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine read_xml_file (1):
fatal error reading xml file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
STOP 1
STOP 1
Tinker
At line 26 of file promo.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format
^
Error termination. Backtrace:
#0 0x8eb780 in ???
#1 0x8eba29 in ???
#2 0x8ec6ff in ???
#3 0x9077e1 in ???
#4 0x907a1e in ???
#5 0x8f5ac7 in ???
#6 0x5ba6d1 in ???
#7 0x58001d in ???
#8 0x4201ba in ???
#9 0x4216af in ???
#10 0x7fe20d8fc24c in __libc_start_main
#11 0x402e19 in ???
#12 0xffffffffffffffff in ???
Webmo, Quantum Espresso, and Tinker problem
Re: Webmo, Quantum Espresso, and Tinker problem
We are aware of Tinker issues with recent version. Most notably, Tinker completely changed their "atom types" recently, which will need to get addressed in WebMO 24.
With QE, make sure that you have installed the pseudopotential library AND configured WebMO to know where to find in. (From the error, it looks like perhaps to pseudopotential has been specified for H).
See:
https://www.webmo.net/support/binaries_ ... l#espresso
Also note that QE is not widely utilized with WebMO, and so issues with new versions of QE may have arisen. Happy to help sort through things.
With QE, make sure that you have installed the pseudopotential library AND configured WebMO to know where to find in. (From the error, it looks like perhaps to pseudopotential has been specified for H).
See:
https://www.webmo.net/support/binaries_ ... l#espresso
Also note that QE is not widely utilized with WebMO, and so issues with new versions of QE may have arisen. Happy to help sort through things.
-
radzae
- Posts: 2
- Joined: Fri Nov 03, 2023 6:47 pm
- Full Name: Ed Radza
- Organization: Lane Community College
- Subdiscipline: IT
Re: Webmo, Quantum Espresso, and Tinker problem
Thanks for replying with that information. I started with WebMo 22.0.009 and have the same issue using either version of WebMO with Tinker 8.10.2. or 8.10.5. Is there an older version of Tinker that is known to work with WebMO 23.0.017?
I've downloaded the pseudo file SSSP_1.3.0_PBE_efficiency.tar.gz but I'm not sure that's the correct one. Any idea? QE gives a different error now after extracting those files into the pseduo folder.
Program PWSCF v.7.2 starts on 3Nov2023 at 12:48:30
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
149 MiB available memory on the printing compute node when the environment starts
Reading input from /home/webmo/webmo_data/chemlab/50/input.inp
Warning: card &INPUTPH ignored
Warning: card / ignored
Warning: card 0.0 0.0 0.0 ignored
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 4
Message from routine cell_base_init:
DEPRECATED: use true lattice parameter, not A to a.u. conversion factor
file C_3.98148.UPF: wavefunction(s) 3d renormalized
file O.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s) 2P renormalized
4 1
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine set_dft_from_name (3):
conflicting values for icorr
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Program PHONON v.7.2 starts on 3Nov2023 at 12:48:30
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
163 MiB available memory on the printing compute node when the environment starts
Reading input from /home/webmo/webmo_data/chemlab/50/input.inp
Reading xml data from directory:
/tmp/webmo-16364/50/pwscf.save/
Message from routine qexsd_readschema :
xml data file /tmp/webmo-16364/50/pwscf.save/data-file-schema.xml not found
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine read_xml_file (1):
fatal error reading xml file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
STOP 1
STOP 1
I've downloaded the pseudo file SSSP_1.3.0_PBE_efficiency.tar.gz but I'm not sure that's the correct one. Any idea? QE gives a different error now after extracting those files into the pseduo folder.
Program PWSCF v.7.2 starts on 3Nov2023 at 12:48:30
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
149 MiB available memory on the printing compute node when the environment starts
Reading input from /home/webmo/webmo_data/chemlab/50/input.inp
Warning: card &INPUTPH ignored
Warning: card / ignored
Warning: card 0.0 0.0 0.0 ignored
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 4
Message from routine cell_base_init:
DEPRECATED: use true lattice parameter, not A to a.u. conversion factor
file C_3.98148.UPF: wavefunction(s) 3d renormalized
file O.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s) 2P renormalized
4 1
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine set_dft_from_name (3):
conflicting values for icorr
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Program PHONON v.7.2 starts on 3Nov2023 at 12:48:30
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
163 MiB available memory on the printing compute node when the environment starts
Reading input from /home/webmo/webmo_data/chemlab/50/input.inp
Reading xml data from directory:
/tmp/webmo-16364/50/pwscf.save/
Message from routine qexsd_readschema :
xml data file /tmp/webmo-16364/50/pwscf.save/data-file-schema.xml not found
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine read_xml_file (1):
fatal error reading xml file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
STOP 1
STOP 1