From 6bc945abb0cd589d977dbd6ab67831decaa7868c Mon Sep 17 00:00:00 2001 From: anbenali Date: Wed, 14 Oct 2020 11:05:00 -0500 Subject: [PATCH] Deprecate gamessAscii from all files including nexus --- docs/lab_advanced_molecules.rst | 10 +++++----- .../GAMESS/DFT/HF/submit_convert.csh | 4 ++-- .../QMCPACK/Generic_Files/submit_convert.csh | 4 ++-- labs/misc/jobrun_vesta | 2 +- nexus/lib/qmcpack_converters.py | 2 +- nexus/tests/unit/test_qmcpack_converter_input.py | 6 +++--- nexus/tests/unit/test_qmcpack_converter_simulations.py | 2 +- tests/converter/converter_test.py | 2 +- tests/molecules/LiH_pp/gamess/c4q.in | 2 +- 9 files changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/lab_advanced_molecules.rst b/docs/lab_advanced_molecules.rst index 4c7525d8d..744ee157a 100644 --- a/docs/lab_advanced_molecules.rst +++ b/docs/lab_advanced_molecules.rst @@ -117,7 +117,7 @@ commands. jobrun_vesta rungms h2o.hf cd ../convert cp ../gms/h2o.hf.output - jobrun_vesta convert4qmc -gamessAscii h2o.hf.output -add3BodyJ + jobrun_vesta convert4qmc -gamess h2o.hf.output -add3BodyJ mv sample.Gaussian-G2.xml h2o.wfs.xml mv sample.Gaussian-G2.ptcl.xml h2o.ptcl.xml @@ -753,7 +753,7 @@ For a description of the XML files produced by the converter, see :ref:`lab-adv- :: - convert4qmc -gamessAscii single det.out + convert4qmc -gamess single det.out - single det.out is the standard output generated by GAMESS. @@ -765,7 +765,7 @@ For a description of the XML files produced by the converter, see :ref:`lab-adv- :: - convert4qmc -gamessAscii orbitals multidet.out -ci cicoeff + convert4qmc -gamess orbitals multidet.out -ci cicoeff multidet.out - orbitals_multidet.out is the standard output from the calculation @@ -778,7 +778,7 @@ For a description of the XML files produced by the converter, see :ref:`lab-adv- :: - convert4qmc -gamessAscii multi det.out -ci multi det.out + convert4qmc -gamess multi det.out -ci multi det.out -readInitialGuess Norb - multi_det.out is the standard output from the calculation that @@ -786,7 +786,7 @@ For a description of the XML files produced by the converter, see :ref:`lab-adv- Options: -- **-gamessAscii file.out**: Standard output of GAMESS calculation. +- **-gamess file.out**: Standard output of GAMESS calculation. With the exception of determinant configurations and coefficients in multideterminant calculations, everything else is read from this file including atom coordinates, basis sets, SPOs, ECPs, number of diff --git a/labs/lab3_advanced_molecules/GAMESS/DFT/HF/submit_convert.csh b/labs/lab3_advanced_molecules/GAMESS/DFT/HF/submit_convert.csh index 7dcdf748f..2856fb8ae 100755 --- a/labs/lab3_advanced_molecules/GAMESS/DFT/HF/submit_convert.csh +++ b/labs/lab3_advanced_molecules/GAMESS/DFT/HF/submit_convert.csh @@ -28,10 +28,10 @@ set thres = 0.0075 set norb = 40 # uncomment for single-determinant -runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamessAscii ${output_orbitals} -add3BodyJ +runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamess ${output_orbitals} -add3BodyJ # uncomment for multi-determinant -#runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamessAscii ${output_orbitals} -ci ${output_ci} -threshold ${thres} -readInitialGuess ${norb} -add3BodyJ +#runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamess ${output_orbitals} -ci ${output_ci} -threshold ${thres} -readInitialGuess ${norb} -add3BodyJ mv sample.Gaussian-G2.xml H2O.HF.wfs.xml mv sample.Gaussian-G2.ptcl.xml H2O.ptcl.xml diff --git a/labs/lab3_advanced_molecules/QMCPACK/Generic_Files/submit_convert.csh b/labs/lab3_advanced_molecules/QMCPACK/Generic_Files/submit_convert.csh index 5a76f1e48..4635e130e 100755 --- a/labs/lab3_advanced_molecules/QMCPACK/Generic_Files/submit_convert.csh +++ b/labs/lab3_advanced_molecules/QMCPACK/Generic_Files/submit_convert.csh @@ -28,10 +28,10 @@ set thres = 0.0075 set norb = 40 # uncomment for single-determinant -runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamessAscii ${output_orbitals} -add3BodyJ +runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamess ${output_orbitals} -add3BodyJ # uncomment for multi-determinant -#runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamessAscii ${output_orbitals} -ci ${output_ci} -threshold ${thres} -readInitialGuess ${norb} -add3BodyJ +#runjob --np ${nodes} -p ${tasks} --block $COBALT_PARTNAME --verbose=INFO --envs OMP_NUM_THREADS=$threads : $convert -gamess ${output_orbitals} -ci ${output_ci} -threshold ${thres} -readInitialGuess ${norb} -add3BodyJ mv sample.Gaussian-G2.xml H2O.wfs.xml mv sample.Gaussian-G2.ptcl.xml H2O.ptcl.xml diff --git a/labs/misc/jobrun_vesta b/labs/misc/jobrun_vesta index db224a72d..1f52103e9 100755 --- a/labs/misc/jobrun_vesta +++ b/labs/misc/jobrun_vesta @@ -30,7 +30,7 @@ jobrun_vesta ppconvert --gamess_pot O.BFD.gamess --s_ref "1s(2)2p(4)" --p_ref "1 jobrun_vesta rungms H2O.PBE -jobrun_vesta convert4qmc -gamessAscii H2O.CISD.orbs.output -ci H2O.CISD.orbs.output -threshold 0.01 -readInitialGuess 60 -add3BodyJ +jobrun_vesta convert4qmc -gamess H2O.CISD.orbs.output -ci H2O.CISD.orbs.output -threshold 0.01 -readInitialGuess 60 -add3BodyJ jobrun_vesta pw.x scf.in diff --git a/nexus/lib/qmcpack_converters.py b/nexus/lib/qmcpack_converters.py index 56f7faa27..af6fc58d2 100644 --- a/nexus/lib/qmcpack_converters.py +++ b/nexus/lib/qmcpack_converters.py @@ -428,7 +428,7 @@ class Convert4qmcInput(SimulationInput): casino = 'casino', vsvb = 'VSVB', gamess = 'gamess', - gamess_ascii = 'gamessAscii', + gamess_ascii = 'gamess', gamess_fmo = 'gamessFMO', gamess_xml = 'gamesxml', # not a typo prefix = 'prefix', diff --git a/nexus/tests/unit/test_qmcpack_converter_input.py b/nexus/tests/unit/test_qmcpack_converter_input.py index e6bec5b96..4b7881324 100644 --- a/nexus/tests/unit/test_qmcpack_converter_input.py +++ b/nexus/tests/unit/test_qmcpack_converter_input.py @@ -205,20 +205,20 @@ def test_convert4qmc_input_write(): ci = generate_convert4qmc_input( gamess_ascii = 'singledet.out', ) - assert(ci.write()=='convert4qmc -gamessAscii singledet.out') + assert(ci.write()=='convert4qmc -gamess singledet.out') ci = generate_convert4qmc_input( gamess_ascii = 'orbitals_multidet.out', ci = 'cicoeff_multidet.out', ) - assert(ci.write()=='convert4qmc -gamessAscii orbitals_multidet.out -ci cicoeff_multidet.out') + assert(ci.write()=='convert4qmc -gamess orbitals_multidet.out -ci cicoeff_multidet.out') ci = generate_convert4qmc_input( gamess_ascii = 'multidet.out', ci = 'multidet.out', read_initial_guess = 42, ) - assert(ci.write()=='convert4qmc -gamessAscii multidet.out -ci multidet.out -readInitialGuess 42') + assert(ci.write()=='convert4qmc -gamess multidet.out -ci multidet.out -readInitialGuess 42') #end def test_convert4qmc_input_write diff --git a/nexus/tests/unit/test_qmcpack_converter_simulations.py b/nexus/tests/unit/test_qmcpack_converter_simulations.py index 1d3dedc14..0704ab417 100644 --- a/nexus/tests/unit/test_qmcpack_converter_simulations.py +++ b/nexus/tests/unit/test_qmcpack_converter_simulations.py @@ -327,7 +327,7 @@ def test_convert4qmc_incorporate_result(): assert(sim.input_code=='gamess') assert(sim.input.gamess_ascii=='../rhf/rhf.out') - assert(sim.job.app_command=='convert4qmc -gamessAscii ../rhf/rhf.out') + assert(sim.job.app_command=='convert4qmc -gamess ../rhf/rhf.out') # incorporate orbitals from pyscf sim = sim_start.copy() diff --git a/tests/converter/converter_test.py b/tests/converter/converter_test.py index 7ec64f8aa..c238ff273 100755 --- a/tests/converter/converter_test.py +++ b/tests/converter/converter_test.py @@ -45,7 +45,7 @@ def run_test(test_name, c4q_exe, h5diff_exe, conv_inp, gold_file, expect_fail, e okay = True # Example invocation of converter - #convert4qmc -nojastrow -prefix gold -gamessAscii be.out + #convert4qmc -nojastrow -prefix gold -gamess be.out cmd = c4q_exe.split() if code=='generic': diff --git a/tests/molecules/LiH_pp/gamess/c4q.in b/tests/molecules/LiH_pp/gamess/c4q.in index 77a1c391e..684a127c7 100644 --- a/tests/molecules/LiH_pp/gamess/c4q.in +++ b/tests/molecules/LiH_pp/gamess/c4q.in @@ -1 +1 @@ -convert4qmc -prefix c4q -gamessAscii gms.out \ No newline at end of file +convert4qmc -prefix c4q -gamess gms.out \ No newline at end of file