Plotting in VMD

All my scripts jumbled together. Subfolders are machine-specific.

With the __init__.py, the directory is a Python module, and the functions in each Python script can be used elsewhere.

Python Requirements

Newish Python standard library modules:

argparse

External modules:

docopt
matplotlib
numpy
pandas

External quantum chemistry modules:

cclib

Personal repositories:

orcaparse

Plotting in VMD

Interactive/graphical:

# in normal terminal:
vmd_pretty_cubes.py --nsurf=1
vmd <parent XYZ filename> -e vmd.load_all_plt.vmd
# in VMD terminal:
source vmd.plot_all.vmd
# shell command, in either terminal:
./vmd.convert.bash

Text-only with no repositioning of the scene:

# in normal terminal:
vmd_pretty_cubes.py --nsurf=1
cat vmd.load_all_plt.vmd vmd.plot_all.vmd > vmd.do_all.vmd
echo "quit" >> vmd.do_all.vmd
vmd <parent XYZ filename> -e vmd.do_all.vmd -dispdev text
./vmd.convert.bash

Name		Name	Last commit message	Last commit date
Latest commit History 429 Commits
_render_scripts		_render_scripts
clusters		clusters
copper		copper
git_hooks		git_hooks
isi		isi
odysseus		odysseus
.gitignore		.gitignore
CC_SAM		CC_SAM
CXX_SAM		CXX_SAM
FC_SAM		FC_SAM
README.md		README.md
__init__.py		__init__.py
amber_extract_structure_ecoRI.bash		amber_extract_structure_ecoRI.bash
amber_prepare_pdb.bash		amber_prepare_pdb.bash
amber_prepare_pdb.py		amber_prepare_pdb.py
arch_abi.bash		arch_abi.bash
arch_find_unowned.bash		arch_find_unowned.bash
arch_fresh_install_packages.bash		arch_fresh_install_packages.bash
arch_setup_chroot.bash		arch_setup_chroot.bash
arch_vbox_notes.bash		arch_vbox_notes.bash
basename_sort.pl		basename_sort.pl
blacklight.py		blacklight.py
calculate_rmsd_all.py		calculate_rmsd_all.py
cclib_calc_com.py		cclib_calc_com.py
cclib_check_conv_geom.py		cclib_check_conv_geom.py
cclib_compare_energies.py		cclib_compare_energies.py
cclib_copper_spin_density.py		cclib_copper_spin_density.py
cclib_extract_last_geom.py		cclib_extract_last_geom.py
cclib_extract_pointcharges.py		cclib_extract_pointcharges.py
cclib_fdiff_stats.py		cclib_fdiff_stats.py
cclib_plot_geometry_convergence.py		cclib_plot_geometry_convergence.py
cfour_clean.bash		cfour_clean.bash
cfour_wrap.bash		cfour_wrap.bash
coloredpages.bash		coloredpages.bash
coloredpages2.bash		coloredpages2.bash
compress.bash		compress.bash
compressz.bash		compressz.bash
conda_export_envs.bash		conda_export_envs.bash
conv.bash		conv.bash
copy_missing_pc_inputs.py		copy_missing_pc_inputs.py
cuby_opt.bash		cuby_opt.bash
dump_bytes.py		dump_bytes.py
ert_run.sh		ert_run.sh
extract_CO2.bash		extract_CO2.bash
file_grouper.py		file_grouper.py
find_CO2_frequencies.py		find_CO2_frequencies.py
find_newest.bash		find_newest.bash
fix_molden.py		fix_molden.py
fixme_batch_divide_into_folders.py		fixme_batch_divide_into_folders.py
fixme_cclib_plot_scf_convergence.py		fixme_cclib_plot_scf_convergence.py
fixme_diff_inputs_outputs.py		fixme_diff_inputs_outputs.py
fixme_match_two_globs.py		fixme_match_two_globs.py
fixme_qchem_metadynamics.py		fixme_qchem_metadynamics.py
gamess_basis_rename.py		gamess_basis_rename.py
gamess_wrap.bash		gamess_wrap.bash
git-prune		git-prune
ipyr		ipyr
jmol_make_qcjson.bash		jmol_make_qcjson.bash
ldiff		ldiff
list_directories_and_counts.bash		list_directories_and_counts.bash
list_input_output_counts.bash		list_input_output_counts.bash
make_analytic.bash		make_analytic.bash
make_analytic2.bash		make_analytic2.bash
make_file_list_from_extension.bash		make_file_list_from_extension.bash
make_in_chroot.bash		make_in_chroot.bash
make_root_plots.py		make_root_plots.py
manipulate_rem.bash		manipulate_rem.bash
match_input_output.py		match_input_output.py
match_inputs_and_outputs.bash		match_inputs_and_outputs.bash
match_inputs_and_pbs.bash		match_inputs_and_pbs.bash
match_opt_and_freq.bash		match_opt_and_freq.bash
match_opt_and_freq.py		match_opt_and_freq.py
md5sort.bash		md5sort.bash
md5sum_dirs.bash		md5sum_dirs.bash
move_scf_failed_to_converge.bash		move_scf_failed_to_converge.bash
nwchem_clean.bash		nwchem_clean.bash
orca_basis_conv.ext.py		orca_basis_conv.ext.py
orca_basis_conv.int.py		orca_basis_conv.int.py
orca_basis_conv.int.write_file.py		orca_basis_conv.int.write_file.py
orca_generate_plot_strings.py		orca_generate_plot_strings.py
orca_make_epr_inputs.py		orca_make_epr_inputs.py
orca_make_rel_inputs.py		orca_make_rel_inputs.py
orca_move_failed_calcs.bash		orca_move_failed_calcs.bash
orca_mrci_analysis.py		orca_mrci_analysis.py
orca_print_gtot.py		orca_print_gtot.py
orca_print_localization_summary.py		orca_print_localization_summary.py
orca_significant_mos.py		orca_significant_mos.py
pdf2eps.bash		pdf2eps.bash
pdf2ps_dir.bash		pdf2ps_dir.bash
periodic_table.py		periodic_table.py
pickle2txt.py		pickle2txt.py
plot_excitation_energies.py		plot_excitation_energies.py
povray_render_vmd_inputs.py		povray_render_vmd_inputs.py
print_epr.py		print_epr.py
print_polarizabilities.py		print_polarizabilities.py
psi4_move_completed_calcs.bash		psi4_move_completed_calcs.bash
qchem_aimd_cost_analysis.py		qchem_aimd_cost_analysis.py
qchem_binread.py		qchem_binread.py
qchem_cdft_tools.py		qchem_cdft_tools.py
qchem_covp_analysis.py		qchem_covp_analysis.py

cz007297/personal_scripts

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