v20.16.0

New feature

• Add hexadecimal_indices option to print all indices as hexadecimal independently of the number of atoms or residues in PDB files.

Comits

• Changed version file to 20.16.0
• Merge pull request #86 from m3g/hexadecimal_indices
• initialize hexadecimal_indices = .false.
• print residue indices in hexadecimal and add remark
• print residue number as hex if required
• add hexadecimal_indices option
• write test messages when running
• run CI on more modern settings

v20.15.4

Bug fix

• Fix printing of connectivity when multiple connectivity lines exist per atom.

History

• Changed version file to 20.15.4
• Merge pull request #84 from m3g/fix_conect
• add test for connectivity
• write connect lines up to 4 atoms and in increasing order to follow PDB standard
• read repeated connectivity and print in the same CONECT line

v20.15.3

• Changed version file to 20.15.3
• add error message if PBCs are not set properly

v20.15.2

• Improve the progress bar printing.

v20.15.1

• Fix output status when the packing is performed for only fixed molecules. Output success instead of error.

v20.15.0

New features

• Support for Orthorhombic periodic boundary conditions. Thanks to the contributions of @yaoyi92. See: https://m3g.github.io/packmol/userguide.shtml#pbc
• New testing framework, that checks the distances in the resulting files using CellListMap.jl.

Commits

• Changed version file to 20.15.0
• support providing pbc as min and max, add test
• format code
• simplify code
• add solvprotein_pbc test
• rename is_pbc to using_pbc
• add some pbc tests
• Merge pull request #71 from yaoyi92/periodic_boundary_condition
• Merge pull request #75 from m3g/testing_with_julia
• try to install juliaup only if not installed
• uncomment the julia install line
• Merge pull request #74 from m3g/testing_with_julia
• move the pbc example to the input_files folder
• add "test OK" message.
• Update water_box_pbc.inp
• Update runtests.jl
• remove the explicit constraint in the pbc box example
• clean up comments and outputs
• for pbc we add an inside box constraint for all the atoms from -tol/2 to box+tol/2
• add comment for the example
• add water box pbc example
• output the pbc cell information in the pdb file
• set sizemax to pbc_box
• update the Makefile to include pbc
• add the new Intel ifx compiler
• implement periodic boundary condition for atom pairs and the cell linked list
• Merge pull request #72 from m3g/testing_with_julia
• add comment to script
• add solvprotein example
• add bilayer test
• add tests
• restore testing of generation of failed packing files
• tests with Julia

v20.14.4

• fix doc typo.

20.14.4

• Changed version file to 20.14.4
• update reference format and add DOI link
• Merge pull request #57 from m3g/release-20.14.3

v20.14.3

Full Changelog: v20.14.2...v20.14.3

v20.14.2

• Changed version file to 20.14.2
• improve error for wrong file types