DRR - Cpptraj: Fix reading mdout from pmemd TI #54
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drroe
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Aug 25, 2015
DRR - Cpptraj: Fix reading mdout from pmemd TI
drroe
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Mar 25, 2021
drroe
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Apr 4, 2021
* Start adding a new class, GIST_PME, that will inherit from Ewald_ParticleMesh and implement GIST-related PME stuff * Add recip and self6 calcs * Add long range correction for gist * Add direct space sum routine. * Bring HelPME up to PR #54 * Expose sumq and vdw_recip_term via functions * Add some per-atom vdw stuff needed for PME_GIST * Expose more of Ewald to inheriting classes * Expose more of Ewald_ParticleMesh for inherting classes. Add implementation of ErfcFxn * Add direct space calcs * Make switch function available to inheriting classes * Fix exclusion array type * GIST with LJPME not ready for primetime * Add PmeOptions class. * Add help keywords. Ensure all variables are initialized. * Add functions to return private vars * Add Init for Ewald_ParticleMesh with PmeOptions * Start adding PME to GIST. Initialize some uninitialized vars * Create non-inlined version of adjust for GIST_PME * Make LJ PME keywords a separate function for things that do not support it * Start adding PME GIST data sets * LJ PME not yet allowed for GIST * Ensure energy calc is done for any occupied voxel (occupancy > 0 instead of > 1). * Update tip4p and tip5p tests for occupancy threshold change * Finish PME init * Add debug level. Do PME init and setup. * Add solute/water id and solute index arrays * Start adding actual PME calc. Need to save whether atom is solvent or solute separate from atom_voxel since we now might care about whether solute is on or off the grid. * atom_voxel_ and atomIsSolute_ arrays will be accessed by atom # * Add PME solute grid assignment * Un-comment the pme calc function * Do the order calc for CUDA as well - not sure why that was behind the ifdef * Enable pme calc * Add avg voxel energy calc for pme data * Print out sums - they seem to be only for debug * Start adding separate avg routine for non pme energy * Use new averaging routine * Add nopme keywords * Add orthogonal pme test * Fix default lj pme assignment * Add non-orthogonal test * Add info comparisons * Move DEBYE_EA to Constants * Add separate PME printout for testing * Add headers for PME output * Dipole calc should be done whether or not we skip energy * Remove duplicated code * Add code docs * Print options when using pme * Add regular ewald options. * Rename ; will use for all Ewald * Change to EwaldOptions * Use EwaldOptions in PME * Use Ewald_Regular * Use EwaldOptions * ewcoefflj keyword can turn on LJ pme * Have GIST PME use EwaldOptions. Update depends * Fix up help for energy. Pass LJ switch width for regular ewald * Remove old code * Fix printout of LJ options; now all in EwaldOptions * Reenable some timers * Move var closer to where it is set * Start fixing openmp * Add more internal arrays * Internal arrays are per atom, not voxel... * Add doc * Ensure direct arrays are zeroed out. * Ensure contributions from other threads are summed into 0 arrays * atom_voxel was unused * Add access to internal arrays * Add function to return energy on a specified atom * Use reworked GIST_PME. Make numthreads a class variable * Comment out some unused stuff. * Remove old code. Add Ewald timing to output * The PME GIST grid arrays do not need to be threaded * Hide some debug info. Fix citation in output * Minor version bump for GIST nw_total > 0 fix and addition of PME * doeij does not work with PME, trap it. Also make doeij with cuda an error. * Fix spacing * Make function const * Was accidentally doing the order calculation twice. * Do not run the PME tests for cuda. Slightly increase the test tolerance for GPU. * Try to fix CUDA compile. Need a better way to determine arch flags... * Add list of cuda flags. * Try a better way to set up the shader model flags * Add shader model cuda version check * Remove old configure logic * Consolidate direct space energy calc into one function. Add adjust energy kernel. Use adjust energy kernel. Make PME GIST output file v3 because of additional PME columns * Compare PME GIST output if present. Not uploading it because its too big for GitHub * Make GIST PME off the default for now until the output stabilizes. * Fix help option * Fix GIST and energy command entries * Protect when no LIBPME * Add tolerance to the info comparisons. * Break up giant apt-get install command into separate ones to make it easier to debug * These are better described as to-do * Try to DL and build our own netcdf * Try to make sure netcdf binaries are in the PATH. Try to fix cmake variable names. * Make var point to actual library * Cmake build seems to have problems with the static netcdf compile. Try using .so instead.
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