Major Version Update: 7.00.0#1166

Merged

drroe merged 1561 commits intoAmber-MD:masterfrom

drroe:prepareforleap.remote.buildatom

Mar 6, 2026

This pull request is big! We're only showing the most recent 250 commits

Commits on Jan 24, 2026

Commits on Jan 26, 2026

Cannot finish box from Solvate with specified numbers the same way as the original since the method for determining waters out of the box is different. Just use the cell we have been using. Probabl…
drroe
committed

Commits on Jan 30, 2026

Add function to sort typenames by making the first typename < last typename
Daniel R. Roe
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Test sorting typenames and using them in std::map
Daniel R. Roe
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Have ParmHolder use std::map. Make the old class with std::vector into ParmArray; assigning nonbonds needs to be able to do addition with iterators, so std::map cannot be used in that case.
Daniel R. Roe
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Update dependencies
Daniel R. Roe
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Remove unused code
Daniel R. Roe
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Everything but dihedrals/impropers is stored alphabetical now
Daniel R. Roe
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All parameters are alphabetical now execpt dihedral/improper
Daniel R. Roe
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Commits on Feb 2, 2026

Start the version 7 changelog
drroe
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Commits on Feb 5, 2026

Merge branch 'master' into prepareforleap.remote
Daniel R. Roe
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Merge branch 'prepareforleap.remote' into prepareforleap.remote.buildatom
Daniel R. Roe
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Start LJ calculation for 1-4
Daniel R. Roe
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Add LJ 12-6-4 energy routine
Daniel R. Roe
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Add flag to turn on LJ 12-6-4 calc for 1-4
Daniel R. Roe
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Start adding LJ 12-6-4 keyword
Daniel R. Roe
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Improve feedback when LJC is active
Daniel R. Roe
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Add LJC version of nonbond calc
Daniel R. Roe
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Pass in LJ 12-6-4
Daniel R. Roe
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LJ 12-6-4 calc for standalone VDW
Daniel R. Roe
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Commits on Feb 6, 2026

Add PME calc with LJC
Daniel R. Roe
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Add LJCPME calc type
Daniel R. Roe
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Enable LJC calc
Daniel R. Roe
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Update dependencies
Daniel R. Roe
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Add files for decomposing PME with LJCPME
Daniel R. Roe
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Update dependecies
Daniel R. Roe
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Update depends
Daniel R. Roe
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Fix class name
Daniel R. Roe
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Add decomposed LJC pme
Daniel R. Roe
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Add test with/without LJC
Daniel R. Roe
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Add test save files
Daniel R. Roe
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Add 'lj1264' keyword for 'enedecomp'
Daniel R. Roe
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Add lj1264 decomp test
Daniel R. Roe
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Commits on Feb 7, 2026

Start a class for calculating CMAP energies
drroe
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Commits on Feb 9, 2026

Commits on Feb 10, 2026

Commits on Feb 11, 2026

Create separate routines for force and force+energy
Daniel R. Roe
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Make a common function to return number of possible selected atoms in mask, Natom(). Create function to check if all atoms are selected.
Daniel R. Roe
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Respect mask selection
Daniel R. Roe
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Print selected cmaps
Daniel R. Roe
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Improve code docs. Hide some debug info. Pass in force array for force calc
Daniel R. Roe
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Hide more debug info and remove old code
Daniel R. Roe
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Add a debug level
Daniel R. Roe
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Add CMAP test
Daniel R. Roe
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Do not try to calculate CMAP energy if no CMAP terms/parameters are present
Daniel R. Roe
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Have topology report whether non-contiguous mols are present
Daniel R. Roe
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Pass in just the Topology
Daniel R. Roe
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Create separate routine for fixing atom ordering
Daniel R. Roe
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If residues in molecules are not contiguous, fix the ordering by default unless nofixorder is specified.
Daniel R. Roe
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Add CMAP to new stuff. Note that fixatomorder now baked into the build command
Daniel R. Roe
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Commits on Feb 12, 2026

Fix up help
Daniel R. Roe
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Commits on Feb 13, 2026

I can't believe I got these backwards...
Daniel R. Roe
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Add TODO for renumbering after adding ions
Daniel R. Roe
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Give build the ability to just work directly on an input file
Daniel R. Roe
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Update help
Daniel R. Roe
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Commits on Feb 16, 2026

Allow the second ion to also be 0 for neutralization. This allows one to specify both positive and negative counter ions and use whatever ion is suitable for neutralization. It also allows one to a…
drroe
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Commits on Feb 17, 2026

Commits on Feb 18, 2026

Commits on Feb 19, 2026

Commits on Feb 26, 2026

Commits on Feb 27, 2026

Have make depend trigger subdirectory make depend as well
Daniel R. Roe
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Add small note about system build capability. Upgrade to lyx 2.4.
Daniel R. Roe
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Add some notes about namespaces. Update to lyx 2.4.
Daniel R. Roe
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Update the doxyfile
Daniel R. Roe
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Add subdirectories
Daniel R. Roe
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Add some namespace documentation
Daniel R. Roe
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Script to extract current version number no matter where you are
Daniel R. Roe
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Script for automatically updating the version string in the Doxyfile
Daniel R. Roe
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Automatically update doxygen version number when doing make docs
Daniel R. Roe
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Have make docs call GeneratePDFs.sh
Daniel R. Roe
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Cpptraj needs to be modified if unhandled radii set
Daniel R. Roe
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Add help for the source command
Daniel R. Roe
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Update PDFs. Start adding section to manual for building systems, containing the build, sequence, and source commands.
Daniel R. Roe
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Add note about improved sequence command
Daniel R. Roe
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The sequence command is now located in the system build part of the manual.
Daniel R. Roe
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Commits on Mar 1, 2026

Commits on Mar 2, 2026

Fix up help text
Daniel R. Roe
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Add documentation for some datafile options
Daniel R. Roe
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Commits on Mar 3, 2026

Commits on Mar 4, 2026

Add warning about missing residues to build
Daniel R. Roe
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Start code for allowing redirection of all problem details to a file.
Daniel R. Roe
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Add reportfile keyword
Daniel R. Roe
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Add manual entry for reportfile keyword
Daniel R. Roe
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Add sections for build help
Daniel R. Roe
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Simplify the build example
Daniel R. Roe
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Hide check setup timing behind TIMER ifdef
Daniel R. Roe
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Hide detailed template/parm load behind ifdef
Daniel R. Roe
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Hide the leap prompt as debug info when loading leaprc files
Daniel R. Roe
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Update Cluster build files
Daniel R. Roe
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Fix ParameterSet location
Daniel R. Roe
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Fix reporting overwritten addatomtypes entries, and report duplicate entries by default - it's useful info
Daniel R. Roe
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Do not recommend addmissingres command yet because it is so not ready for prime time
Daniel R. Roe
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Move hint about fixatomorder from Topology to ParmFile since we really should only need it after a topology is loaded
Daniel R. Roe
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Add StructureCheck report mode without leading frame arg
Daniel R. Roe
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Hide some build timers behind ifdef TIMER
Daniel R. Roe
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Add file output timer
Daniel R. Roe
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Add missing leaprc
Daniel R. Roe
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Previously, specifying '-shared' would silently disable libsander support in cpptraj. Create a new category of linked libraries that is cpptraj-only that will not be linked to libcpptraj so that li…
Daniel R. Roe
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Add warning about leaps value of PI
Daniel R. Roe
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Just report split off groups
Daniel R. Roe
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Warn about ignoring set default cmap on/off
Daniel R. Roe
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Make sure the box isnt too small when doing nsolvent to prevent clashes across unit cell boundaries. Disable truncoct for now
Daniel R. Roe
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Add note about clipX being 0 if truncoct is ever enabled for nsolvent
Daniel R. Roe
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Add note about nsolvent not working for truncoct yet
Daniel R. Roe
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Add note about nsolvent functionality being experimental
Daniel R. Roe
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Commits on Mar 5, 2026

Start modxna info class
Daniel R. Roe
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Add to build
Daniel R. Roe
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Get modxna info from mol2 file
Daniel R. Roe
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Cant be in the Cpptraj namespace because if included in Topology will clash with the Cpptraj class.
Daniel R. Roe
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Move out of the Structure namespace
Daniel R. Roe
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Remove references to ModXNA_Info
Daniel R. Roe
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Save ModXNA info in Topology
Daniel R. Roe
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V7.00.0 - MAJOR VERSION BUMP! Addition of system build/parameterization code, among other improvements. Lots of changes under the hood as far as topology/parameter handling goes.
Daniel R. Roe
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Hide debug info
Daniel R. Roe
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Update year
Daniel R. Roe
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Start adding a short libsander test
Daniel R. Roe
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Finish short libsander test
Daniel R. Roe
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Combine into the existing test dir
Daniel R. Roe
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Add missing inits
Daniel R. Roe
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Add missing init of sander var
Daniel R. Roe
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Update manual pdf
Daniel R. Roe
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Expand the build section of the manual
Daniel R. Roe
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Fix checkstructure in parallel
Daniel R. Roe
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Commits on Mar 6, 2026

Add a bunch of missing variables in printf statements
drroe
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12-6-4 tests need PME
drroe
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Support more default options
Daniel R. Roe
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Make unhandled set or set default options in leaprc files an error. Read more set default options
Daniel R. Roe
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Read set default flexiblewater and deleteextrapointangles
Daniel R. Roe
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Replace option vars in AssignParams with DataSet_LeapOpts
Daniel R. Roe
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Revert; not all leap options pertain to parameter assignment
Daniel R. Roe
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Put the defaults in variables
Daniel R. Roe
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Allow default scee and scnb to be overwritten by set default sceescalefactor etc. Trap IPOL, not yet supported
Daniel R. Roe
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Check for bad leap options when building directly from leaprc
Daniel R. Roe
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Allow existing aliases to be overwritten
Daniel R. Roe
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Allow flexible water option to be turned on
Daniel R. Roe
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Handle flexible water option. Try to choose a better default top name
Daniel R. Roe
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Add help/manual for flexiblewater
Daniel R. Roe
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Note IPOL > 0 not yet supported in changelog
Daniel R. Roe
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FFTW is recommended
Daniel R. Roe
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