Latest
Accepted version
Accepted version
Final version
Accepted version
Latest changes for review 2
Almost done
Draft of response to reviewer
Spelling checked, bib entry fixed
Added Ewald
Added Ewald
Latest versions
adjusted temp in screeing
added ewald to screeing factor
Latest edits
modified screeningFactor_Dipole.pdf
"modified screening plots"
"corrected polarizability plots"
Kathie's fixes
Added one new reference
Latest changes to supplemental, some typos in main ms.
Latest version of supplemental
Latest changes
Latest edits
Latest
Latest version
Latest stuff
updated polarizabilityQuad
new figures and tables
added ewald in polarizabilityFigureQuad
corrected supplemental materials
New figures, some edits
Added some scripts to produce field line figures for the schematic
added schematic for dielectric method
Latest edits
added ScreeningFactor_Dipole.agr file
modified plots
Latest updates
Latest version
latest version
Added missing figures
Madan's Latest edits
edits
Latest changes
Final revisions
added result for dipole and quadrupole
Latest edits
Don't need these in svn
Edits
added Methodology
Updates
combining tables
ref add for UA Properties table
Edits
Latest edits
Edits
Edits
Edits
added molecule
Edits
updat sup_info
edits
Supporting infoZ
Supplemental Info
changed name
Edits
bare particle density
removed xmgrace formating
NP25 density plot
source files for density plot
source files for density overlap plot.
Edits
figures
figure
Edits
-m "added methodoloy"
Updated figures, with graph titles as text objects.
Updated figures. Titles for graphs changed to text objects and aligned.
Edits
edits
Prepping for publication to J. Chem. Phys.
Update source files for the figures.
Adding figures for ligand/solvent ordering, corrugation of the particle, and interfacial thermal conductance.
Last version
added quadrupole.pdf image
Added new tex file for dielectric.
Added Q notebook
Latest stab at a dielectric paper
Hopefully final version.
Added Pt_33_root3 to the supporting information figures directory
last edits
NN solid to dash dotted lines
Nearest neigbhor with 10 nn
A supportinginfo image with the additional nn data has been created...
PdEnergy_CO has been added
PtEnergy_CO has been added
initial thoughts on responses and a quick and dirty graph to talk through with you with regards to the nearest neighbor comment
Best so far
C(4x2)
Nearing the end
A number of smaller edits
bleah
Some small changes to the draft.tex
Read through and made some small changes to the supporting info
I think this is better, but still not a great figure (haven't added it to the supporting information yet
Some supporting info updates, as well as a figure update
Added a cover letter
Added an abstract and made some minor changes for language
Nearing the finish line
Couple small changes in draft.bib and .tex
TOC template
Citation has been resolved and a few \ce have been added
Almost there.
Completely redone/expanded intro
Fair number of edits to draft.tex
Forgot one new figure from previous commit
Updated for version 2.3
Supporting info has been created and partially filled in. Additionally a graph was noticed to be missing a chunk of data and was remade (domainSize_Pd_SI...)
Nearest neighbor with small symbols and error bars are complete
New nearest-neighbor graphs with error bars, still figuring out best way to display them
Recent edits
557 figure, more colorgrid, and \ce and (###) checks
Colored grid
Updates
Added one more domain sizes graph
New system figures (pink/gray) along with a number of images for the supporting information
edits
Finally done with figures?
Upgraded bib file and draft
Edits
Configurations are on the side of the figure now
Pd Energy and Pt Energy Figures created
edits
Symmetric movement
New Figure with 5 configurations
Couple paragraphs and Pd_Energy figure
PdEnergy.pdf file
Pd energy and configuration files
Updated diffusion data and added/modified a paragraph about the diffusion
Resolved some bib file conflicts
Edits
Added a couple lines about c(4x2)
All CO, Pt, and Pd should be in \ce now
new
Recent edits
first attempts at describing CO Pd
Color palette changed and new images generated
Color changes for all graphs
Edits
Fractional population NearestNeighbor graph
Decluttered domainSize images
Edits
First attempt at dosing information
New images and most values in the binding energy table
Redone nearest neighbor image
Couple edits and replacement of domain figures
Adding agr as well in case we need to change things
Redone domain graphs
fda
Edits
Pt_error...
Some more recent edits
Some recent edits
Most recent edits before weekend
A few more edits
another round of edits
Added to introduction, inserting edits
Discussion is 'done'. Need to write/re-write introduction and start inserting citations while finding all of my 'todo' areas and getting those numbers/values, etc.
Adding more to discussion
Added a couple of sections to the discussion
JCP version now that PNAS said no
Current set of figures are all present in the figures subdirectory and present in the tex document (admittedly placed willy-nilly
Added 'publication' ready graphs into figures/domainAreas
Adding various folders and files and the many many changes I have made to the tex document. I will be more proactive about commiting as I think I am getting a decent rough draft put together
Bibtex update
Added RNEMD viscosity calculation references
Corrected SP-orient.agr
Latest version
missed bComicStrip, added.
Added plots and Supplemental_Information.tex
New table
Latest
Added new z-profiles of Basal and Prismatic systems.
Added the SPC/E Eta(225K) shear rates.
Latest
Updated d_dynamic data.
Updated contact angle data.
Added error bars for the orientational interfacial widths for each of the four facets.
Latest
Added the Contact angle plot for the 4 crystal facets, and an idea for a graph representation in WCA_Plot_inlay.pdf
Added prismatic_shear_3.png.
Latest + figure
Fixed changes from today, still need to work on SPC/E justification.
New stuff
Added mW citation, more info about Furukawa QLL exp. technique, and fixed Gernandez -> Fernandez
Latest changes
Missing refs
adding PNAS template
Big file
Adding .xyz files for meeting with Dan.
Revised - Conclusion.
Revised - Results/Discussion Dynamic water contact angle.
Revised - Intro.
Revised Methodology - Droplet Simulations.
Revised Methodology - System Construction
Revised Methodology - Water Model paragraph.
iceWater3.tex is the PNAS templated manuscript, edit this document not iceWater2.tex from now on. Not sure how to delete or remove iceWater2.tex from the svn repository.
added images of systems and more paper revisions
Rought draft to intro done
adding revisions made a while ago
I meant to only add the directory PtPd, not both directories, hence the removal of COonPtAu
Joseph: Starting my paper on Pd and Pt 557 surfaces
Revised paper, made minor changes
Wrote an Abstract
revised Results/Discussion C. Coefficient of Friction and wrote the rest of the Conclusion
stuff
stuff
FInal Version, I think.
These are generated files - they don't belong in the repository
added kappa table and other changes to iceWater2.tex
Changes
Changes
adding all the files
updating
Closing in on final status
Spelling errors
Spell check
Nearing final
Newest version
Latest
Edits
latest
Diffusion and Time correlation function has been tabulated.
Ewald point is modified to line
Edits
Added average potential energy for both 9A and 12A.
Edits addressing reviewer comments. Updated plots with new data.
Fixed Zahn reference
Final edits for resubmission
Latest version
added plots for dipolar and Quadrupolar crystal for three different cutoff alpha
Latest changes
Most recent version including dielectric stuff
wrote the interfacial width results section
added more images and xmgr files
adding the images, .tex, and .bib files
Final versions of figures in eps format.
edits for submission
Ready for submission
Fix
Better references
latest
more edits
Changes
Last round, I hope.
Added schematics
Edits
Nearing the end
Latest fixes from Madan & Kathie
energy drift for rc =12 A
Changed equation table
attempting to commit pptx files
Latest edits
Latest changes
Adding figures back for paper 1
New figures
New figure
Added some references
Didn't need this file
Latest version
Edits
initial import
Final edits and submission zip
Added source files for data and figures
Latest edits
Edits
updated grant
Updates
Some changes
moving to trunk
Moving to trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
Doesn't belong in trunk
autogenerated file removal
Initial import
Initial import
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Didn't belong in trunk
Shouldn't have been in trunk
Done!
Last
Forgot to remove a couple of files from version control.
Archived old corr data into "OldCorr." Added all of the reran corr data and worked it up into "RerunCorr.agr." Added new data to stacked plot and renamed it Rerun_Stacked.agr."
Added response data with Cho frequency maps included
Fixed equation numbering.
Fixed Cho to Choi and the tick marks of the field map graph.
Added updated figures for proof
Edits
latest edits
More edits
Edits for version 2.2
Changes for force field files
Final Edits and response
--This line, and those below, will be ignore-- A force_combined_slope_correlation_modified.agr A energy_combined_slope_correlation_modified.agr M force_combined_slope_correlation.agr A torque_combined_slope_correlation_modified.agr
Colormap changes, some text edits
Final version maybe
Spelling and sentence structure
Many changes in advance of publication
Updates
SOme modified / new figure files
Figures updated and include full sets of data with averages.
Don't need these
DataforFigure7
StackedUpdated
FullQuantumData
Fig 3 Graph
Data
Data
Cleaning up excel spreadsheet
Some minor edits
Final edits! Fixed references and a couple things in the text
Added .eps versions of all figures
Nearly done
Edits
Fixes, new language, new figure
edits
Reorganized
edits
Significant edits
This is also autogenerated
Removing autogenerated files
Some edits
10thBondCorr
citation1 fixed
XXX citation fixied
edits
Figure 3 update
Edits
Modified figures
Figures 4/6
Figure 6
Edits
deleted some aux files
Averaged and normalized classical
Figure
Data
Edits
edits
Corr data add
New fig
New stuff
Contour plot
Figure 4
Edits
Figure work
ChemDraw
edits
Added Fig 1 to the paper.
More raw data
Images and raw data
Edits
Edits
Edits
Working
text
Text
Stuff
essage=text
eth
text
Text
Added Convolved spectra.
3 Elip side-by-side and some text added.
Spectra x-axis fixed
added the other images, first add was correct as well.
Add cigar images, maybe?
Images into figures.
added some figures
Added more to methods like fields used and Gaussian params
nitrile paper
New Paper on Nitriles
Migrated plots to main directory
Edits
most recent edits
Updates
Modified a figure and inserted it.
Migrated much to Supplemental, nearing completion on manuscript 1.
Edits + data
more edits
More edits for brevity
More work on the methodology section
Latest edits
Added a bunch of stuff from the NSF proposal to the MS, still missing the refs.
Added response letter
Latest version
changed interface_width_by_shear_rate plot to match those in the manuscript. Added explanation to lines on tau_comic_strip plots
revised manuscript, added fit equation for d(basal) and d(prismatic). Edited text changing values for these displacements, and changed comparison text in conclusion to match the new arguement.
Latest version
Latest version
added interface_width_by_shear_rate , an answer to a reviewers comments
Added cover letter
latest version
Nearly final version.
revised bComicStrip and pComicStrip. Copied pComicStrip.2 to pComicStrip and added it to the svn
Nearly final
Nearing the end
added the .jpg of the basal and prismatic systems
Edits of the conlcusion
Fixed a few refs
making sure revisions sent
Edits
Updates
Added PDFs and edited up through page 13.
Some editing
revised again, handing this copy to Dan at group meeting
orientational section done, need to revise coefficient of friction section/conclusion/intro/abstract
added (a),(b),(c) to basal and prismatic .eps images
basal_Tau_comic_strip.eps and prismatic_Tau_comic_strip.eps now are formatted correctly (epsi trick)
added basal_Tau_comic_strip and prismatic_Tau_comic_strip. These are the images showing the three different Tau's of the fitted orientational TCF. Also svn del a few older files that were no longer needed
added basal_control_1000_frames.llcorZ
added the .lcorrz-OLD with snapshots at 1000fs instead of 10fs as in .lcorrz-NEW for comparison
making sure new .lcorrZ is added, copied to a new name and added again.
added latest .lcorrZ
Initial Import
Initial Import
Added Tao.dat, .lcorrZ, the reduced_data of .lcorrZ (pruning data so no negative values in the correlation function)
fixed calculation of coeff. fric. for interface, should have been 1/slope, not just slope.
Added CoeffFric.3, CoeffFric .arg file that has the mass weighted velocities plotted against the applied momentum flux.
fixed q_z equations
fixed q_z equations
revised intro
intro
Added an RNEMD section, updated bib file
deleted .png files
added .agr files, i hope
more edits
Made some edits
Fixed a 2
Edits for factor of 1/2 in reciprocal space portion.
Some minor edits
Updated text, fixed a sign error
Revised .tex again, wrote a conclusion
Added an explanation on the self term and start of a bibliography file
added SystemImage.png
first import
working on .tex file
working on iceWater.tex
Added bComicStrip.eps , pComicStrip.eps , CoeffFric.eps all after ps2epsi was used to make them look correct
Added the .arg files for the images revised the pComicStrip.2 and bComicStip images revised the CoeffFric.2 image
added CoeffFric.png and IntWidth.png Need to still add the control data points to the IntWidth.png
added the ComicStrip images
changes
New Paper
Final edits
Just making sure it is most recent -JRM
Added details about slightly different bonding lengths on single and double layer platinum
most recent data, affine scale, 1.8 eV in table
Minor changes
Edits
new table
adding in force field validation
Final
Final version
Changed color scheme around
Added color to step separation graph
Figures updated based on earlier discussion
Added a figure
new version
Lots of eps and pdf files
Captions, a final read through, and some image and reference work still to go
I think the discussion is in a pretty good place right now
Still needs a bit more work in discussion, but most of the changes Dan and I talked about this morning have been implemented
Most recent pdf->bib->pdf->pdf
Few new images/graphs added
Updated to Achemso
added a table of energies
New figure, restructured results...
Starting to restructure results section
Ever closer, the horizon looms. Most recent as of Friday afternoon before I left for happy hour.
Many of the suggestions Dan made have been incorporated
Most recent
Ever marching onwards to completion
added an abstract, started cleaning other things up
svn added some images
Discussion partially done, seems to be really coming together
Results section has undergone a major overhaul, finally starting to shape up.
Cover letter, new ps versions of some figures (converted to EPS for submission).
Added Hase papers, fixed a few grammatical issues
Done!
Almost done
edits
Edits
Last commit before I shut down prudence
added some images, new graph for diffusion with x error bars, and a couple small things in the tex file
Major edits.
edits
A few changes
formatting
Adding references, force fields, ordering
Some edits
Fleshing out results section wrt diffusion
Diffusion figure added
Table 4, diffusion constants updated
Done for the day
Simulation Methods still needs work certainly, but it is finally beginning to reach a presentable state
Working on simulation methodology, specifically cross interactions and the simulation protocol
CO parameters section, dipole moment, quadrupole moment, and experimental values obtained
FIrst round of edits
not much changed, but most recent version
about to massively rewrite simulation methodology so wanted a back up with my tiny changes over the past day
Patrick and Joe read through it a bit and changes some small things and talked about areas that needed the most work
adding some proposal stuff
Latex file, two bib files, and a couple images
.tex, .bib, figures
initial import
initial import
mistake
New import
mistake
New import
Added bibliography style file, and did formatting.
first complete version of RNEMD docs. additional refs and cartoon with it. plus some other edits.
RNEMD edits
updated Langevin Hull section
final version
final edits?
Made changes from reviews.
modified isothermal compressibility plot, removed outdated compressibility plots
added xmgrace file for pAngle figure
added error bars to SPC/E compressibility plot
edits
added documentation for Langevin Hull
M stacked.pdf M stacked.ag
new RhoR figs
cover letter
edits
updated a figure
M langevinHull.tex
M langevinHull.tex
M RhoR.pdf M RhoR.ag
M langevinHull.tex
M langevinHull.tex
A RhoR.ag
AM RhoR.pdf
M langevinHull.tex
M langevinHull.tex
M langevinHull.tex
M langevinHull.bib
M langevinHull.bib
M langevinHull.tex M langevinHull.bib
edits
new figures
fixed
figure
figures
raw stuff for images
EOR file.
PDB for 4GPa spce water.
VRML file for langevin hull.
Added files for flyaway
missing figure
added stuff
M stacked.ag
M pAngle.pdf
M pAngle.pdf
M pAngle.pdf
M pAngle.pdf
M stacked.ag
added coordinate sketch
A stacked.ag
a few edits
modified the parallel figure
edits, bibliography
working on parallel
more edits
Added stacked plot combining pressure and temperature.
more edits
edits
AM flytest2.pdf M flytest2.png
edits
modified figure slightly
D new_isothermal.pdf
A new_isothermalN
AM flytest2.png
M langevinHull.tex
forgot a figure
edits
editing the methodology & intro sections
fixed a few references
AM new_isothermal.pdf
M langevinHull.bib M langevinHull.tex
final version!
answer the question why nivs is better than swapping for inhomogeneous system.
minor change.
some changes according to reviewers' comments.
M langevinHull.tex
M langevinHull.bib
pdf doesn't belong in svn
started some edits
new import of Langevin Hull paper
new directory for langevinHull paper
mistake
acident
accident
Import of working copy of Langevin Hull paper
adding coverletter stuff
final edits
more edits
nearing the end
calculated J^* in distribution plot.
final edits (we hope)
change the plot again.
change to another plot.
change a plot.
lots of changes
acknowledgment
deleted spce plot.
drop a plot, add more swapping details, and some other small changes.
more edits
final push for publication
changes in two LJ plots. and other small changes.
edit two plots for LJ thermal.
new data added, and other minor changes.
a few edits
changes to shear's legends. new results added. and other minor changes.
some legend changes and other minor changes.
add polynomial references. other minor changes.
edits
edits
edits
active edits
Merging Shenyu's version
new version of docs for new program
minor format changes.
added more gold thermal data and corresponding change in discussion.
minor changes
edited gold thermal part.
edited gold thermal table.
edited LJ result tables.
more changes
minor edit to gold thermal.
combined Au result tables. deleted excessive plots.
edit interface plot.
remove more old plots.
remove old plots
fixed some stuff in the bibliography
minor edit to some captions.
add more citations.
add more citations for NEMD and EMD background info.
combine shear plots into one. and other minor change.
combine two distribution histograms into one. and some minor edit.
more citations.
more citations.
Updated figure
add more citations.
missing bst file
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edited one citation.
added abstract. modified conclusion and interface part.
add eamGrad plot and result table. modified gold thermal conductivity part.
modified spce thermal conductivity discussions
modify LJ thermal discussions.
modify results of LJ thermal.
modify simulation details part. rearrange results part.
a few changes in intro and method part.
draw a demo for RNEMD. finish a rough version.
rearrange some parts
add interfaceGrad plot and result table
add interfaceDensity plot, modify tables.
add more plots and tables.
Added a figure
add histSwap and histScale plots.
add thermalGrad plot.
add shearTempScale plot
add shearGrad plot, fix some eqn.'s
recent edits
added new references.
Fixed bug is Sutton-Chen force calculation in parallel.
Removed remaining MPI from metallic potentials. Bug in MPI calculation of energies in Sutton-Chen.
adding interface
removing MPI responsibilities from the lowest level force routines. This is in preparation for migrating these routines (LJ, electrostatic, eam, suttonchen, gay-berne, sticky) to C++
missing shtool for build
converted some dynamically allocated arrays to std::vectors
pythonification of affineScale, translate in md2md, removed spurious cutoffGroups in waterBoxer. Perhaps we need a python md-file parsing library?
Removing CGAL
Removing CGAL from all code
Removing CGAL dependence
Removing CGAL, cleaning up ac-tools directory
fixed mapping bug
fixed a bug confusing id with localID, stopped adding NULLS to triangles also.
fixed a iproc bug
Re-write of convex hull.
Re-write of ConvexHull.
fixing busted mpi configure
fixing mpi configure
More MPI convex hull bug fixes. noffset corresponds to the correct array indexs. Still mismatch in forces between serial and parallel versions.
fixes for surface atoms that expose multiple hydrogens, updated python set syntax
RNEMD temperature and exchange reporting
added RNEMD scaling
added options for RNEMD
update data
added results. modified simulation details.
more checks for parallel molIndex stuff
worked on the paper
Stupid parallel bug fixes. Why was this ever working?
continue simulation details
Bug fixes in the SelectionEvaluator and SelectionCompiler Added print option in Restraints
continue computation details
continue methdology
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correct a typo
add one reference from Maginn. correct a few equations and some typo.
Added a bib file, started fixing references
Added JCP bibliographic style file
initial import
Adding alternate water models to Amber parameters. The approved model for Amber is still TIP3P, but if you want reasonable water dynamics, you need SPC/E. OOPSE/OpenMD will now give you the choice.
Fixed bug in Polynomial
Added missing restraint file
Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
Relaxed structure at low T to be not so high up on the PE wall.
Adding hybrid analytic / companion matrix polynomial root solver adapted from David Eberly's Wild Magic code
New hotness
units for thermalConductivity, spelling error fixed
Latest version of SMIPD with gamma set to thermal conductivity
Adding restraint keywords to Globals
Adding one RNEMD sample
fixed one more bug for charge - non-charge interactions
Single / Double for C++ MPI bindings
Parallel version of RNEMD
Modifications to support RMSD calculations, removing classes we aren't using.
making way for jama versions of these routines
Removing unused tnt classes
Fixing a parallel bug in the self-self interaction.
Hopefully a fix for the skipped charge in parallel
Adding boundary element hydrodynamics to SMIPD.
only create RNEMD object if we need it.
Adding Madelung energy sample directory with explanatory notes
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
Fixed odd bug in electrostatic for self-term forces with neutral molecules
bug fix in DLM, added temperature profiles and uniform bins to RNEMD
Added a getStatus routine to check the temperatures
fixed a bug in self interactions
Final Version
adding jama and tnt libraries for various linear algebra routines
Beginning import of SVD and RMSD code to handle orientational restraints of flexible molecules. Work in progress, doesn't compile yet.
Bug fix
Debugging, but still unstable
fixed some bugs, added some logic to sort stuntdoubles
Adding options to RNEMD for selecting particular StuntDoubles
Added handlers to Integrator to call RNEMD at the right times. Added initialization to RNEMD to make sure values from the MD file are available.
Adding RNEMD
adding support for RNEMD
Added keywords for RNEMD
Adding samples for SMIPD.
Chuck's dissertation for PhD Jan 2009
Different method again for Langevin Dynamics.
Cleaning up some cruft.
Code clean-up. Removed old langevin code.
use the viscoConvert in OOPSEConstant
added viscoConvert
Stupid getRandomNumber return 4;
missing energyConvert in kinetic energy
Fixed bug in variance.
Added global variable.
More attempts to get SMIPD to themostat properly
doing zeolite sample
fixed a few bugs in the options, added base atom types
General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
Fixed segfault in because of directional atom in SMIPD.
Fixed a QHULL autoconf bug
Fixed a bug in QHULL autoconf logic
many changes to keep track of particle potentials for both bonded and non-bonded interactions
Fixed Memory Leak in ConvexHull.
More changes to SMIPD. Attempting to find memory leak.
Returned old LD forces to SMIPDForceManager.
A few simple mods to remove gcc compile warnings
Fixed nanovol so it now builds.
Fixes for Inversions for use with Amber
Work continues on constant pressure langevin dynamics.
Fixed makefile.
fixed using autoconf 2.6.2
integrators/Makefile.in needs to be created
integrators/Makefile needs to be created
Only build SMIPDynamics and register it if we have qhull
Fixed MPI bug in opening elements.txt.
Case typo for Hull.hpp.
Adding back more missing files.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
fixed thermo bug
Added some logic to print out a special pair distance as a column in the stat file. To use this feature, use taggedAtomPair = "0, 10" and printTaggedPairDistance = "true" in the md file. Then, the distance between integrableObjects 0 and 10 will be computed and printed in the stat file on each statWrite.
turned off db
Inversion fixes and amber mostly working
server migration
Fixes for Torsions and Inversions, Amber is mostly working now.
Exclude is gone. Replaced by a generic PairList to handle 1-2, 1-3, and 1-4 interactions as well as the exclude list
more changes for 1-2, 1-3, 1-4 interactions plus some initialization-ordering fixes to make gcc -Wall happier.
Added support for scaled 1-2, 1-3 and 1-4 interactions.
fixed a missing F[\rho] error for calculating particle potentials in the many body force fields
fixed a strange compiler structure alignment problem with the intel Mac compiler (structs that cross between C and fortran appear to need 8-byte boundary alignment on this compiler).
fixed a spurious visitor deletion
Many fixes
Just reconfigure and it works!
All your base are belong to us!
All Your Base are belong to us!
fixed some incorrect types
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Changed parameters for S-S interactions on gold surface.
Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
Cleaning up oopseformat and adding inversion terms
Changes to thiol model.
Hopefully md-solvator is done.
Adding the Amber_FF files to OOPSE distribution
Adding infrastructure for Amber force field
Adding infrastructure for Amber force field.
More md-solvator work.
Fixed a number of bugs in slab_density calculation
Md solvator writes out md files now. Index problem.
More progress...
More changes to md-solvator. Still don't know if it works.
More work on python version of md-solvator. Pretty sure mol loop is busted.
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Added files to module section of Makefile.
Added files to Module section.
Added TraPPE torsions for thiols.
Adding Trappe torsion types and fixing Opls types
Code work on thiols and TraPPE torsions.
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Changes.
Removed accidental print lines.
Added model for thiols.
Fixed typo in LJinteraction types. LJ-metal appears to work now.
Added minimizer sample for metal.
Added parameters for Lennard-Jones Thiol potential.
Fixed a bug in BlockSnapshotManager.
Edits on Hydro and Langevin Dynamics
working on langevin.
Added back correct form, still not updating frames.
More changes, still broken.
add langevin and hydro in.
Files for Hefland moment.
Checking in changes for Hefland moment calculations
OOPSE docs for version 4
Committing changes made to AtomVisitor to render xyz2pov scenes
Added repeat box options to make larger systems
Changes....
Nearing the end
adding refs.
Changes about metals
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
fixed compile flags on Mac
fixed compile flags for mac
Changing functional form
Adding iterative looping to get better estimates of friction forces from full-step velocities
formatting check
Added surfaces for Ni and Pd.
Added more surfaces.
Fixed sign error in MnM based on atid's.
Added new samples directory for metal surfaces.
Added samples for metal slabs.
Ready for review.
writing.
writing.
writing.
WRITING.
writing.
writing.
writing.
add figures for ld
add more citation.
Ready for submission
MnM interaction now works.
writing.
Changed some logic in Polynomial, PolynomialTorsionType, and CharmmTorsionType to allow for polynomials to be set via the = operator.
writing the dissertation.
writing up the dissertation.
writing the dissertation.
writing up the dissertation.
writing the chapter md.
writing the chapter md.
add the figures in chapter md
Changes to MAW. New form of the potential and cleanup.
add the figures.
writing up the dissertation.
delete the old frustration.pdf
newest version
final version?
Adding submitted version
new figures
add a figure.
writing the dissertation.
Changes to simparalell to remove MPI stuff.
Adding new md2md utility program
add a reference.
fixing configure process
updating configure process
*** empty log message ***
edits
change more notations
change some notations
Editing
Imported Dissertation
Fixed for MPI.
removed old roughShell figure
Adding two missing figures
fixing a configure script error
Correcting a few typos
Adding GofZ.cpp
Adding GofZ.hpp
new visitors for some odd molecules
fixed bug in physmem for 64 bit machines
Nothing important
Fixed Langevin Dynamics and DLM
fixed printing of memory available
added stat2visco
fixed a few correlation functions
Added a few visitors
A few formatting changes to prettify the code
Removed older version of openbabel from our code. We now have a configure check to see if openbabel is installed and then we link to the stuff we need. Conversion to OOPSE's md format is handled by only one application (atom2md), so most of the work went on there. ElementsTable still needs some work to function in parallel.
Build fixes for include files.
add one ref
Editing introduction
added a figure
Updated figure
load all the data
add the numbers in
Changes to do hydrodynamics modeling and to explain a diff file
in progress
add table
updates
add graph.agr
rerun NVE for sphere and composite model.
getting closer
Adding sketch
change the sketch.pdf
Updating paper
Fixes for building.
add sketch files in
working on model systems section
Add the text about langevin simulation on different shaped molecules.
Changes to optimization flags.
Removing Qhull from cvs.
does ifdef check for computational geometry packages
Fixed nesting bug in USE_CGAL and USE_QHULL.
Initial code for AlphaShape.
Define USE_QHULL.
New configure
Check CGAL and qhull defines
Added CGAL and qhull defines
Added CGAL test
*** empty log message ***
Many fixes for Charmm-type torsions.
Added more chamges to nanovol.
Fixed Makefile.in for cgal.
Added new config.h to deal with cgal.
Added configure for CGAL.
final version
Cooling rates added and refs.
Adding information about Tg
Temperature-volume plot.
*** empty log message ***
*** empty log message ***
Added volume calculation for hull.
Changes to Build system.
Added m4 file for qhull
fix p2 for tails
add some ref
fix citation.
edits
edits
a little fix.
fix a problem.
add translational diffusion coefficients into the table.
Added table
EPS files for stupid JPC-C.
add relaxation table.
Fixes to figures and equations.
Added abbreviations for journals.
editing still!
Added cooling rate reference.
Added references.
More changes.
new references
More changes.
Things keep on changing.
made changes
added an image
Fixed some bugs in LDForceManager.cpp
Fixed some temperature and conversion constant bugs in Sphere and Ellipsoid
Added pretty pictures.
new stuff
modified plot
Changes to nano.bib
adding conclusion
Added density stacked plot.
Edits
More changes.
Added new diagram.
Added PDFs of some figures, prettified for publication.
Added w6 as a function of R
Added stacked bytype plot.
Fixed data issues.
Added: Action Correlation function (for viscosity), Directional RCorr (for non-spherical bodies) Modified: LCorr (for multiple axes)
All data there.
Edits
Fraction of atoms with icos order.
Added stacked plots for W_6 and Q_6.
Edits
Added file for stochastic boundary conditions.
More stuff added.
More on Bond Order parameters.
More writing.
Case typo in Vector.hpp
Testing files for NPT Langevin dynamics convex hull calculation.
Added code to compute bond angle distributions.
More writing on paper.
more writing
Added more references.
working
added stuff from orp.
big changes underway
removing derived files
Adding cross section image
Added bibliography file.
Added analysis section.
Added plots
Added cooling plot figure.
Added cooling plot.
Updated docs to version 4
nanoglass paper
added a check for non-initialized MnM_map
Bug fixes for non-declared objects
initial edits
submitted version
Nearing completion
nearing completion
add a bit discussion
friday edits
Edits
add the parameter table
add more ref
more edits
editing in progress
Changes to MetalnonMetal derivatives.
missing figure
Adding a few more figures
forgotten figure
add the 2lipid model fig
change tex file a bit
change the phaseDiagram fig
Added a giant phase cartoon figure
added some figures, modified the tex file a bit
changing figures around
More bug fixes to Metalnonmetal.
draw domains on the plot.
add the phaseDiagram.agr
add the original image file for lipid molecular structure.
change the sP2.* and tP2.* images
added renders for dppc molecule
revise lipidMM.eps
adding MetalNonMetal interactions
Added more Morse and Lennard-Jones part of metal-nonmetal.
Formatting to prettify the code
adding the image files and write the introduction section in tex file
Just some formatting fixes
removed MWM as an atom type property
removed a stray is_MWM
One more to add.
Install process is incomplete
Install process should add some basic text documents
Install process should install the manual
Adding more missing files from metal-nonmetal interaction.
Added c-fortran interaction map.
More changes to MnM.
more changes to MnM.
More Changes to MnM.
Added metal-non-metal section
Makedepend is regenerated each build. Don't need it in repository
Broken files on install
Bug fix to types.
Changes for Non-Bonded interactions.
Added MnM forcefield.
Changes for MnM forcefield.
Added metal-nonmetal forcefield.
Changes to allow for non-bonded interactions.
Non-bonded interactions added.
Adding support for non-bonded interactions to OOPSE.
Structural change to how spohr atoms will be parsed. Will be more like bonds.
Addition of section parser for Spohr water-metal potential.
This file is no longer used
create mdRipple
Fixed Makefile problems with the samples and added several missing makefiles.
Starting NPT Langevin. Added new force manager files.
Removed nanorodBuilder.
Pos copied into a malloc array now.
Build change.
Fixed more bugs and removed more CGAL.
Removed CGAL from makefile.
Removed nanorod builder from OOPSE.
Addded QuickHull to cvs.
Removed CGAL from OOPSE and replaced it with qhull.
Removed debug message from simcreator.
Removed debug message from simParallel.
Changes to sutton-chen force.
Fixed pot in parallel.
forgot the if (do_stress) condition on the previous commit
fixed a bug where the pressure tensor wouldn't update for atoms in the switching region when # of atoms in a group = 1
Added md file for half of a icosahedron.
SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
Added Bond Order Parameter as a function of radius.
more changes for atomic virials and Lennard-Jones force switching
Massive update to do virials (both atomic and cutoff-group) correctly. The rigid body constraint contributions had been missing and this was masked by the use of cutoff groups...
Adding a starter file for the secondary prism {1,1,-2,0} face.
adding new ice surface files
forgot a tolerance for simple cubic lattice magic number determination
Fixed conversion bug in self_self, when adding self energy to mypot, energy needs to be converted by pre11.
Fixed a bug in NeighborListNeighbors.
new stuff
Imported sources
Spherical boundary conditions.
fixed a bug in waterBoxer
Support for printPosOnly in Dump2XYZ.
Added printPosOnly to Dump2XYZ as a userbase(BETH) request.
adding md-solvator
Added the ability of waterBoxer to deal with non-cubical boxes.
Added thetacorr functions to dynamic props.
Added more error reporting to simParallel.
Changes to add thetacorr to dynamic props and fixes to radial rcorr.
Remove snapshotcentroid from makefile.
Removeing snapshot centroid and adding support for COM calculaton from snapshot.
More changes to mdsplit.
Breaking more mdsplit stuff....
Changed how mdsplit gets file names. Full path is now removed from name.
Fixing an implementation problem
BSM has to talk to reader about center of mass properties
Adding the ability to compute Center of Mass properties on reading in a dump file. DumpReader must be told if it needs to do this, however.
Final edits for resubmission
Added function to calculate volume based on ellipsoid definded by radius of gyration.
Add more reference about elastic Ising model.
Getting ready for publication
starting rewrite of paper to satisfy the reviewers
added a reference
older versions of the h2(q) fits. Newer version uses log-log plot
reorganizing for new version of paper
added a rawData directory with descriptive filenames
added log version of the h^2(q) fits to satisfy reviewer
Making changes to satisfy the reviewers
Added a few frustrating references
new ideal structures
Added a bunch of bond order parameter test cases.
bug fixing Wigner 3-j import to C++
fixed a configuration error
edits
Code to run radial rcorr.
Added preliminary support for CGAL and computation of convex hull.
added figs and response start
Adding support for radial rcorr.
Added interface to change number of neighbors in calculating neighbor list.
fixes for BOP
Fix to makefile.
Histogram bin change.
Added support for nanoparticle density profile.
Import from sources
possible fix for unnormalized BO
final version after Steve's edits
user selected dampingAlpha now gets set
self-term sign clarification
returned to half self-term values
corrections added
THe one day paper editing session.
more changes
working on the paper
fixed the bib file and some references
Imported sources
Support for OOPSE RealType.
fixes for CGAL
Changes to nanorod builder for new dump format. Changes to configure to test for new version of cgal.
fixes for open babel
more openbabel updates, also changing velocitizer to thermalizer to avoid a filename collision on case-insensitve file systems
Updating OpenBabel to version 2.0.2. These files aren't used anymore
updated OpenBabel to version 2.0.2
Slight changes to oopseformat to allow importing of openbabel's perceived atom types into OOPSE md files
Added velocitizer utility program, added samples of its use to the builder samples.
fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
bug fixes for vacancies
Adding samples for builders
bug fixes
bugfixing shapedLattice to have crystal origin at one of the occupied lattice sites
More typos...
Typo in mdSplit.
Fixed printing of OOPSE version at header and trailer.
fixed a few bugs
fixin figures and tables of contents
Changed nanoparticle builder for new dump syntax.
now the -n command works
Ridding the world of widowed and orphaned lines and abstracts greater than 350 words
fixing missing lattice arguments, adding a builder sample
adding builder samples
nearly complete rewrite of randomBuilder
oops with the affineScale
who needs .in files for perl? using env
fixing bugs in randomBuilder
Fixing the builders to prepare for OOPSE-4 release
Added utility to split dump file frames into md files.
forgot to adjust the makefile
added solvator and adjusted waterBoxer
improvements to waterBoxer
fixed a bug in waterBoxer for invalid water names
Proofed appendix. Final form unless there are later catches.
down to proofing the appendix...
Starting cleanup for 4.0 release
Cleaned up the code for BondOrderParameter and added a bunch of comments. Fixed a memory leak or ten.
Lots of proofing corrections. More to come...
Some efficiency fixes (now computes Wigner 3-j coefficients only once in the constructor).
Refinements. Just a little proof checking left...
Mostly done with BondOrderParameter. Only a few performance tweaks remain
fixing bond order parameter code
refined the reaction field dielectric passing
more changes and an abstract included
bug fixes (still broken, however)
Following Rein ten Wolde article
done accept for the abstract and SHAMS section
more bug fixes
more changes to BOP and SH
fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics
Fixed a bug in Wl code in BondOrderParameter
Bugfixes in BondOrderParameter and SphericalHarmonic
added SphericalHarmonics, fixed a few problems with BondOrderParameter
fixed bugs (mostly in BondOrderParameter)
Adding BondOrderParameter to StaticProps
Working on BondOrderParameter
latest version
Latest Version
updated plot and text on newer results
fixed a DumpReader bug, took out extra printing statements in residentMem and BlockSnapshotManager
And a couple extra figures
Thar be changes in these documents
Converting to pdflatex, changing eps figures to pdf, adding Makefile and applescript previewer
new draft of the Langevin paper
changing configure script to process the new utilities
added some features to waterBoxer
added the waterBoxer script
added comment info
adding NgammaT integrator
modified affineScale to work with the new OOPSE files
fixed TI MPI bug
fixes to zang writing
converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
adding in some figures
now builds properly
Imported sources
I may have messed some stuff up...
removed extra file in Hydro.cpp
Changing utility programs to use the new file format
fixed some bugs in DumpWriter, eliminated some extra printing of debugging information
Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
adding lots of tred stuff
added some tred stuff
more changes
fixing up some chapters
lots of additions and figures
change the globals.cpp to make sure we can set targetPressure and surfaceTension to be negative.
adding the figures to cvs
Extra textra
Chapter separation...
fixed an ordering issue in quadrupole-charge interactions
added text and figures in the tip5p-e application section
starting change of file formats
Changing atom2mdin into atom2md to reflect new unified file format
some text adjustments
fixed a pvf bug
fixed dumpConverter problems
added dumpConverter
removed shapes sample
fixed a spelling bug
added perl interpreter to affineScale script
added perl substitution for affineScale script
added install target for scripts
Adding a directory for scripts Adding affineScale script
fixed a getSigma bug
bunch of changes
Added fork() and wait() so we can loop through multiple jobs.
Added tred to sample water.md files
Added TRED water visitor for Dump2XYZ visualization
Added TRED parameters to forcefield
adding final version of dissertation
Added a few more changes.
more format correction to avoid widow lines
format corrections
fix an undef reference
fix some strange behavior of CVS
change the size of roughShell.eps
fix legends on some figures.
adding definition of bundles.
It's sort of working now.
minor correction.
references corrections
fixed d / sigma0 confusion
minor corrections.
corrections from steve
testing commit logger
fixed a bug
removed printing of GBN and GBM from previous debugging
added handler for log database
Fixed more buggies
Fixed a bug in the fftw part of the configure script.
Interface for getfile.
More runParallel goodness
First commit of code to run multiple amber jobs in parallel
visitorScheme --> visitorList in the source code of Visitor Pattern
Incorporated supporting info into pairwise chapter
removed icc from C++ search lines, did some formatting work on GB module, mucked around with a GB example
Adding more changes to orientational bond order parameter.
minor correction
update the plots of auto-correlation functions
Resistance tensor
Added utility function to winger3jm from slatac.
It builds now. Added individual system analysis sections for pairwise methods
Added the multipole interaction routine. It doesn't work yet, so it's not included in the build.
Fennell Dissertation
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
more corrections.
fixed forces and torques for GB
more minor corrections.
Version 0.95
more corrections.
version 1.0.0
more corrections
more corrections
more corrections
more corrections
fix some widow table problem
more corrections.
more corrections
more efficient file reading for thermodynamic integration, and fixed some formatting
Beginnings of a order parameter.
Adding code for bond orientational parameters.
more corections
adding periods at the end of equations
more corrections
finish conclusion of Liquid Crystal
finish conclusion of Liquid Crystal
minor corrections.
rename r22_220.eps to s22_220.eps
move the legend
adding r22_220
adding more images
more corrections
Change the case caption of tables
more corrections
adding auto-correlation functions
more corrections
more corrections
finish abstract
more corrections
format change
more corrections
finish conclusion; some format checking correction
MPI thermodynamic integration works now.
finish abstract
finish abstract
minor fixes
fixed a build problem... GB_12b_ratio no longer exists (replaced with BG_l).
minor fixes
correction to Langevin
correction to Chapter one
adding order parameters and pair correlation function into method setion
adding order parameters and pair correlation function into method setion
Added support for Winger3jm coefficients.
fixes for mpi thermodynamic integration, close to fully working...
finishing temperature control of Langevin
output the principle axis of GB
finishing temperature control of Langevin
finishing temperature control of Langevin
finishing temperature control of Langevin
added mpi compilers, demoted pg compilers after pathscale
adding roughShell model
minor change
adding a picture of two banana molecule in pentane
adding some images
adding some images
minor fixes
minor fixes
minor fixes
seperate Langevin chapter
fix format error
seperate Langevin chapter
move friction tensor section to chapter2
minor fix
minor fix
minor fix
fix broken reference
minor fix
fix figures of Lipid chapter
reformulated some of the electrostatics
more reference fixes
more reference fixes
more reference fixes
more reference fixes
minor format change
minor format change
minor format change
minor format change
format change
minor format change
minor format change
minor format change
Minor format change
minor format change
minor format change
minor format change
minor format change
minor format change
adding visitor UML structure
minor fixes
adding pattern
adding pattern
damping now works for charge-quadrupole and dipole-dipole
corrections
adding processing of dynamicProps
adding processing of dynamicProps
adding processing of dynamicProps
adding architecture and 3-stage processing of staticProps
Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in
adding architecture
adding architecture
more reference fixes
change the size of the long table
more reference fixes
adding definition.eps
more reference fixes
change the size of figure
adding appendix;
add langevin paper into chapter 2
fixed some typos
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
more reference fixes
minor fixes
minor fix
minor fixes
minor fixes
minor fixes
fix typo of \ldots
minor fixes
minor fixes
minor fixes
minor fixes
minor fixes
fix reference problem
Added methods to access GB_mu and GB_nu from the force field options
Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
fix reference problem
Adding more figures
Adding model section into Chapter Liquid Crystal
Add the RippleOP to calculate the orderparameter of the ripples.
Finish Introduction in Chapter Liquid Crystal
begin Liquid Crystal Chapter
adding more images
minor change
minor change
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Adding Lipid Chapter
adding images
Fix a type promotion problem
replace double with RealType
What?
more changes
more changes for MPICH with profiling libraries required
MPI stuff
fixes for Hydrodynamics
fix a bug in parsing HydroProp file
Fixed a bug when spherical boundary conditions were off.
fixed an initialization bug of Hxy.cpp.
wrapping back to PBC by molecule instead of by individual atom
fixed the bugs of Hxy.cpp.
Last bug showed up in 2 places, fixed the other one.
Fix a bug of printing empty line in DumpWriter
change the order of include path and library path
Adding single precision capabilities to c++ side
Adding single precision capabilities to the fortran side
adding --enable-single to configure script
Getting fortran side prepped for single precision...
electrostatic refinement
zlib fixes
Autoconf fixes for FFTW. Multiple FFTW version support.
*** empty log message ***
Changes to calculate undulation spectrum
adding support for Gay-Berne atom
adding a gay-berne switch to Dump2XYZ
Adding qpole
finding ifort arguments that won't die under two different versions of the intel fortran compiler
initial draft
missing makefile was hanging up 'make clean'
final changes for publication
plugging EPAPS citation into .bbl
formatting adjustments
Now in preprint style
Addressing some review comments
adding NPAT and NPrT
Added random builder to cvs.
Change in siminfo used in nanoparticleBuilder.
Added random builder
Added a random builder to oopse.
Using OpenBabel element table to pick vdw radii for hydrodynamics if the LJ sigma can't be found.
Adding spherical boundary conditions to LD integrator
Added EAM atom types to Hydro models
important something from candidacy exam
minor fix
Important extended system methods from OOPSE papaer
put spline subroutines in the EAM module
Removed sqrt splines and shape stuff (doesn't work, so why was it in there?). Changed some of the water samples to use shifted_force. Probably should set the defaults to use the damped version now that we sped it up.
some minor fixes
Finish Production section
Electrosplines added...
splined up sticky
Complete rewrite of spline code and everything that uses it.
Finish Structure Properties of Analysis Section
Finish Initialization of Molecular Dynamics Section
Finish Generalized Langevin Dynamics
Finish Hydrodynamics
Many performance improvements
Adding Hydrodynamics
added a cubic spline to switcheroo
Since status.F90 is used by interpolation.F90, the former needs to be listed above the later in the Makefile.
Finish Rigid Body Dynamics
changed the interface a bit
added some logical flags
Wiped the spline with derivatives and corrected a boundary comparision error by eliminating the check. This algorithm REQUIRES known first derivatives at the endpoints.
bug fixes for interpolation module
Heavily modified interpolation module, also moved to "utils"
adding constrained hamiltonian for rigidbody
adding constrained hamiltonian for rigidbody
adding introduction for rigid body dynamics and first integral for geometric properties
Added interpolation module.
minor fix
adding (1)Example of Splitting Method; (2)Error Analysis and Higher Order Methods;
*** empty log message ***
adding Liouville's theorem section and Phase Space and Ensemble section
adding splitting method
adding Geometric Properties
adding introduction to geometric integrators
adding Generalized Langevin Dynamics and Symplectic Manifold.
adding Ergodic Hypothesis
adding newtonian mechanics
minor fix
adding Lagrangian Mechanics and Hamiltonian Mechanics
adding more references
minor fix
fix a spelling error
adding design pattern
added tengDissertation
Imported using TkCVS
added gb-bilayer
Imported using TkCVS
Added status module to simParallel for error reporting.
NPrT might work now
Fixed memory leak bug where SCList capacity was not reset to zero on destruction.
More testing of nanoparticleBuilder.
Added check to make sure md file exists.
Fixed latticeOrt in shapedlatice and latticebuilder.
Fix the normalization problem in calculating correlation functions
(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only
Makefile for nanoparticle builder.
Added nanoparticle builder to makefile
Debugging changes to nanoparticle builder.
back to previous DynamicProps
some changes
fixed a caption
Adding position correlation function. The command line option for DynamicProps is now changed. --rcorr is for position correlation and --rmsd is for mean square displacement.
Figure adjusted and Steve's recommendations incorporated
initial proof of supporting info.
update writeBeads method
remove a unknown method
just messing with some figures
The off diagnal is not set
Throw exception if the file can not be opened for preprocessing
updated plot and supporting information
added some files and updated a figure
readying for pubs
Added shaped lattice.
nearing completion
data fixes
more with the supporting
results
more supporting stuff
commenting out some stuff
fix a bug in calculating hydrodynamics tensor when the radius of beads are not the same
recip. space convergence citations
alternative image
updated ewald figure
Fix a bug in friction calculation for ellipsoid
changes
Verify the correctness of Ellipsoid's hydrodynamics properties
intro
still padding SI
padding the supporting info.
Spell checking
All sections filled
Added a figure and some more text
padded the ewald summation section
ewald is a changin'
New version of Hydro is working now.
refactor Hydrodynamics module.
Generic Shaped Lattice for oopse. Can overload to get spherical or nanorod.
LagevinDynamics is working?
fixed a const problem
more citations and some spell checking
group and rf sections added, adjusted the preview script
unit conversion for diffusion tensor is wrong
change the epsilon of numeric_limit
correcting the unit in HydrodynamicsModel
using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.
paper
Adding RoughShell and BeadModel
adding hydrodynamics module into build system
makefile should reload the preview window now (added an applescript)
changing equations and adding text
Updated some plots and captions. Added a Makefile.
adding Cholesky Decomposition
we're writing a paper. What more do you want?
minor caption adjustments
fixed a caption
better graphics
Modified some figures
modifed introduction and figures
LangevinDynamics in progress
added a new figure and modified the methods and results & discussion
organizational changes
organizational changes are starting
adjusted figures
added a figure
Abstract and conclusion added
some more introductory work...
Fixed a double/int bug. Surprised no one ever noticed before...
More introduction stuff...
many additions, fleshing out the introduction...
Bug fix - KSH
Separated supporting information.
fix bugs in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out product of Rij
Bead Model is working
Adding Hydrodynamics Module
considerable additions - rough draft on Results and Discussions finished, plus the addition of a bunch of tables and some updated figures
Additional content and several figures added.
fixed a spelling error
fixed a problem with cutoff radii being set larger than 1/2 the length of the shortest box dimension. added a few fortran utility routines
Changed Names of class files.
added some plots and text
*** empty log message ***
fix a bug in converting integer to double
added an eps of the pdf
started writing
added DPD molecule type parameters
Fixing a bug which reads the wrong frame of trajectory file during analysis
adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly.
fixed a bug in rigid bodies that contain directional atoms
Adding visitor for GBlipid atom type
added CXXFLAGS to the LinkOptions to allow compilation with icc9 (skipping the gcc-4 std c++ libraries).
Missing brace caused the last commit not to build
Changes to cutoff radius setting to a more logical procedure - still may change...
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X
Adding :LegendrePolynomial
starting paper
Changes to nanoparticle builder
Added Makefile for nanoparticle builder.
Cleaning up for 3.0.1 release
Prepping 3.0.1 release
new version number
Updated Documentation
Getting ready for release!
Testing commit
Removed MixingRule from Globals. Handled by forceField now.
Added NPAT to Globals integrators.
*** empty log message ***
testing to make sure GNU make is the make that was used to build OOPSE
changed compiler search order
Changes in Sutton-Chen units
fixed some version info and the copyright date
added some missing checks for header files (particularly zlib.h), used autoheader to help generate config.h.in
added some missing checks for header files (particularly zlib.h)
fixed a dependency problem for the Executable builds
Missing Makefile in this sample directory
Old makefile.in no longer required
All of the OpenBabel stuff needs to be installed
Changed formating.
unifying function name in electrostatics
fix make install problem for metals samples
remove samples/metals from install list.
filepp can not handle multiple line macro, just convert multiple line macro into single line macro.
Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles
autoconf modernization and cruft removal
autoconf modernization and cruft-removal
fix some error messages
instead of printing to std::cout, throwing an exception when error is found.
Fixed a spelling error
Changed conversion factor.
Sutton and Chen should be working now.
Fixed SC bug with SIM_uses_SC
fixing RhoZ
Added energy scaling to section parsers.
replace isType<int> with isInteger
remove extra forceFieldOptions from SC_FF
Add force file.
Sutton-Chen no longer segfaults or produces 0 potential, but rather produces Inf for the potential. Progress....
More Sutton-Chen bug fixes.
Long range potential return from fortran is already accumulated, it should not be accumulated again; nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;
In order to compile MPI version, we need to cast const char* to void* for stringstream.str(); Previous Makefile use bjects of single version to make the MPI library;
Sutton-Chen bug fixes. Almost there...
Changes in forcefield.
added files for sutton-chen
More cvs changing.
More moving...
More changes to directory structure.
More Directory changes...
More changing of directory structure
Fixed issue with symbol naming and added call to set force options in SimCreator.
More changes to forcefield options.
Force options passed to fortran.
Force option changes.
changed __FUNCTION__ to __func__ to match C99 standard, and then added an autoconf test to check for __func__ usability. Changed some default compile flags for the Sun architecture
added the STL check
make minor change to build oopse under solaris
the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro to handle it. Adding exception handling to SimCreator.
Removed one parasitic argon atom which was living inside the GB particle. No alien-like ripping out of the stomach was required.
replace grammar for numerical parsing
fixed a cutoff bug
Removing compiler dependencies and replacing them with real autoconf checks
Adding checks for various features used by ANTLR
fix a nasty negative integer parsing problem by refining the grammar
made some minor changes to allow compilation with the portland group compilers
fixed compilation problem for icc7
added missing include
added some checks for pathscale compiler
added copyright
added info printout
added pathscale
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
This should really break things.... Started adding support for ForceOptions to section parsers.
*** empty log message ***
Added forceOptions to section parser
Removed geometric distance mixing from individual modules and now use force options to detemine what the deal is.
Further fixes for compiler issues.
Fixed ifc public-private issue.
Added support for fortran force options.
Fixed a bug in checkTorsion
Changes to SC.
Changes to build twinned crystal
Overloaded interface for dumpwriter.
remove deprecated keywords from samples
Fix parsing error in OptionSectionParser
Adding handler for CLAY force field
Fixed build bug in openbabel.
reformat error message
Adding .frc file for CLAYFF
adding more checking for topology
Spurious semicolon removal
We've made big changes. This isn't 2.0 anymore.
removing deprecated nAtoms and nComponents lines
adding SelectionToken.cpp
Adding FragmentStamp
Errors are no longer thrown with consts (fixes compilation bug on the Mac).
Got rid of spurious printing out of timestep
Got rid of spurious printing out of junk
Change build process for libOOPSE.a so that the libraries aren't unpacked. libOOPSE.a is now made directly from the object files
added check for egrep (grep -E) needed for new build of libOOPSE.a
adding DataHolder
Added Gay-Berne / Argon test case for the cutoff policies
update Makefile
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
Code to calculate rho(Z) to calculate density profiles for water slabs.
added checks for some functions to configure script
Changed file names that conflict w/ oopse file name object files.
compilation bug
parsing by filepp
Cutoff Mixing fixes
compilation issue
Cutoff mixing fixes have been made.
Adding ParamConstraint.cpp
adding openbabel data files
adding support for soft linking
Adding support for soft linking
Adding linking stuff
rename mdinConverter to atom2mdin
fixed a bug
Adding some config checks for OpenBabel codes we are using
Adding some checks for OpenBabel code
Unifying config.h stuff from OOPSE and OpenBabel
Unifying config.h stuff and making sure the OpenBabel codes can find our default (and environment variable) Force Field directories.
adding ForceFieldOptions
OptionSectionParser get compiled
ForceField optional parameters....
adding mdinConverter
adding more readers/writers
adding openbabel
register openbabel readers/writers
included shifted potential self term
just some parameters
adding openbabel
removed unnecessary commented code
cleaned up the charge-charge interactions a bit...
just playing
fixed a bug in the shifted_potential case
just playing around - we need to refresh all the samples sometime soon...
Made preforce calc public in suttonchen.
Sutton-Chen added to SimInfo
Added Sutton-Chen to force loop...
Added sutton-chen to makefile.
Build Fixes for sutton-chen.
Missed makefile for sutton-chen.
Sutton-chen stuff
Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
Forgot to add some files
added in a 5th order polynomial switching function option
added in a 5th order polynomial switching function
playing with switching functions again
playing with switching functions
Added force files for Sutton-Chen and Quantum Sutton-Chen
Added a keyword and ability to output forces and torques
Added a keyword for output of forces and torques
Working on shifted_force...
Just testing...
removed a poorly commented section
improvements in shifted-force
mmm... damped shifted force...
More work on SC.
More work on suttonchen.
removed some test code
forgot to add the screening method header
changing how we deal with summation and screening methods
again, changing how we deal with summation and screening methods
debug stuff for rf removed
Added suppport to atypes for MEAM and sutton-chen
removed some testing code...
fixed a capitalization problem with NPT integrator initialization
nothing
still fixing up wolf...
In process of adding sutton-chen forcefield.
changed the default switching radius to 85% of rcut
reaction field looks to be working now - for charges and dipoles alike
reaction field looks to be working now
added a test molecule
added a test atom type
added charge-dipole reaction field - don't know if it works...
streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF
minor changes when testing reaction field
reaction field now works for charges
Fix the other branch of force calculation in Torision.cpp
Still had some globals toUpper problems - these changes should fix those...
nothing
fixed an MPI compilation bug in GayBerne
fix an index mismathcing between c and fortran
added samples for the cutoff methods that Yang Zheng has been working on
fixed gb/lj and gb/gb torques and a rotation matrix bug
added a few GB test cases
Fixing GB parameters
Changed the parameters for the Gay-Berne type
merged reaction field with electrostatics.F90
Customized StatWriter is working
using notation from Cleaver paper
bugtracking gb
Another bug fix
fix some namespace issues in Globals
changing GB architecture
Adding samples for gb tests
fix a seg fault when try copy a string to event's err_msg, there are still tons of memory leaking problem in Globals
Change error message in Globals
Constraints for parameters are working now
Adding .md files for GB/LJ tests
Adding some Gay Berne tests
Adding some cutoff tests
Add parts for the GayBerne LJ
Adding Parameter Constraint class
added default restraint spring constants into Globals
rewrite Globals
Fix to forceManager to pass potential array to fortran.
Don't remember what we did
simplifying long range potential array
Testing new cutoff methods
Messing with 2-point water models
Breaky, Breaky: c-fortran interface now expects an array for pot.
More Change goodness for calculation of potential.
More changes to MPI potential calculations.
Breaky Breaky: Add Support for seperating potential contributions.
Free some variables that weren't freed before.
Design change for nanoRod builder --twinned.
Added code for nanoparticle builder to cvs.
Bug fix, undeclared local variable in MPI.
Fixed MPI bug with Row and Column indexing of groupToGtype. We now have two seperate maps groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer that is set to groupToGtypeRow in the single processor version.
fixing up the samples
There is still something wrong with inertia tensor projection
erase output of inertia tensor. There is still something wrong with current implementation.
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fixed an annoying mass ratio bug that results in simulation failure with massless particles
maybe some work on wolf
just some random changes when testing
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame (previous commit is wrong)
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame
working on wolf
fixed some samples
updated
using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation
Rotation matrix multiplication order error
tracking down quaternion bug
Added DIP atom types for 2-point water model
fix a bug in convert rotation matrix to quaternion
Added define for ifc 7 so derfc is external. Other compilers should treat erfc as intrinsic.
Changed erfc to derfc and declared it to be external to fix issure with ifc7. Hopefully this will not cause a problem with other compilers where derfc is an intrinsic function.
MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer.
Added support for skinThickness keyword to Globals.
fix a typo in DumpReader
fixing up some samples
slowdown fixed - now roughly the same speed as the old version when using dipoles energies are now exactly the same between the old version of OOPSE and this version
turned rf on
Fixed "dum-dum" where we ignore the skin thickness and hardcode listSkin to be 1.0. We now get listskin from skin. This will get fixed to where we can manually set skin thickness.
added error function
Removed print statement for angular momentum and inertia tensor from velocitizer.
Removed print statements for remove angular momentum.
Bug fix: If we are not using LJ (say we are using EAM), we probably shouldn't rebuild the LJ mixing map.
DumpReader using pure c++ io
Fixed a defaultCutoff bug (HEMES!)
libz additions
added check for zlib in configure
adding zlib support for DumpWriter
adding testcase for zipstream
adding zipstream.hpp
fixed up some sample md files
Fixed bugs in reaction field, now it appears as though it really is working...
reaction field seems to work now, still need to do some testing...
Added keywords for compressed dump files.
xlf found a bug that ifc missed...
fixing some summation method issues
fixed a capitalization error
moved a header file around
it builds now, but there are known issues - particularly with reaction field...
some fixes but even more breaking (cutting out the old way to do reaction field)
Working on adding WOLF
Fix a bug in DumpReader in case readFrame is called without calling getNFrames
forgot to add a header
Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.
changes to include the coulombicCorrection selector
added in the undamped wolf, in the process of doing the damped wolf
some changes to activate the coulombicCorrection selector
just some testing
Equilibrated the sample
re-added Cl- and Na+
EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes.
fix to put back calculation of r in do_prepair
fixed a bug in the createMixingMap routine. It should now set doShift correctly
Added nGroupsInRow for mpi build.
Added access to mpi logical variables
bugfix on the grouptype finding algorithm
adding c-side interface to change cutoff Policy
Some bug hunting
Just a longer test
Added allocation for gtypeCutoffmap etc..
initialized atomTypeMaxCutoff(i) to zero
wrote createGtypeCutoffMap
made some changes for implementing the wolf potential
updated getEAMCut
added some probably nonfunctional get*cut routines
Added eamType map to atid map.
fixing some of the problems in the interactionHash and gtypeCutoff routines
added fCutoffPolicy.h
breakage in progress
putting spaceballs back where they belong
Complete rewrite of Lennard Jones module
Breaky Breaky BREAKY breaky breaky
In process of re-write for group based cutoff....
fixes in progress
fix a bug which does not update me_i and me_j correctly
Changed cutoffs... Segfaults nicely now...
fixed ACX_MPI to ignore some text error messages from pathscale compiler
std::bind2nd is in <functional>
replace c++ style comment in c files
Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.
*** empty log message ***
More breaking and destruction of force code. Does not build at this point...
Breaky breaky!
fixed a bug and ran a simulation
working version of DensityPlot
Changes to remove angular momentum.
changed the abstract of the paper and redraw the phase diagram
changed the abstract of the paper
Fixed bug in typo in nanorodBuilder.
Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
Removed balance from the Darkside (files)
Removed balance from doForces
Updated tap sample
Included a tap dimer for testing purposes
Re-entered the TIP4P-Ew water model. It was apparently wiped earlier this month...
ran make cvslog
adding AtomNameVisitor
dding resetIntegrator
adding resetIntegrator
adding DensityPlot into StaticProps
adding SCDOrderParameter into StaticProps
adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps
Fix to print pressure tensor.
adding keyword printPressureTensor
NPrT in progress
NPrT in progress
NPAT is working
fix bug in NPAT and NPrT
adding NPAT and NPrT integrators
just some tap changes
Modifications to temper the dipolar strength in the first solvation shell for tap
added a tap example for testing purposes
Modifications to tap. Also correcting changes to the previous merge that were not caught
Fixed merge issues between Kyle and Chris so OOPSE will actually build.
help
added gb
Better tap
Couple of changes for TAP water. Need to parametrize.
Fixed build issues under ifc7.
More geometry builder changes.
Changed SHED to TAP
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
Adding support for generic geometry to nanorodbuilder.
More changes to nanoRodBuilder....
*** empty log message ***
Added TIP4P-Ew
Fixed issues with nanoRodBuilder....
Got rid of write statements and am closer to a working shapes
Fixed gcc4 bug...
adding CharClassificationFunctor to fix the locale problem of c++
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
axed because file causes havoc on Mac (capitalization confusion of filenames)
Working on the shapes parser...
gmake in case people forget
fixed the spacing on the banner. Vanity.
Version string in banner (and version numbers in config.h)
Documentation changes
xemacs has been drafted to perform our indentation services
Jedi mind-trick warning messages have been added to make users ignore CGAL.
fix make install
add Makefile of samples
some samples are not installed correctly
configure now searches for perl to use with filepp
Fixed a bug in RigidBodyStamp section of MoLocator
*** empty log message ***
nanorodbuilder now exit's when libCGAL is not present.
fix one more warning message in make_nodes
Changed interface name for SGI Compiler
oops... bad sample
Change typo in CGAL.
fix some warning messages
added CGAL checks
Added destroy methods for Fortran modules.
Added destroy method to clean up memory
more memory leak are fixed
File not needed for nanoRodBuilder.
fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice)
refactory lattice
refactory LatticeFactory and LatticeCreator
refactory LatticeFactory and LatticeCreator
refactory LatticeFactory and LatticeCreator
cleaned up vector_class memory leak fix by deallocating in reverse order of how we allocated. Also migrated MoLocator into utils directory
added lattice directory
added lattice directory, so all of these files are now redundant
cleaned up memory leak fix
added lattice subdirectory
no real changes here, maybe added a space by accident
added quadrupole sample
updating samples
destory atom type in fortran side
Further changes to vector_class destroy function.
Fixed pointer memory leak in vector_class.
Updates to deallocate object in fortran.
minor change to TI output
Changes to delete atypes...
Added code to delete vector.
avoid multiple inherit in basic_ifstrstream
Importing nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....)))
forget to delete prepareVisitor in Dump2XYZ
fixing of the quadrupoles. look! it's divide by 3 like stone says!
fixing of the quadrupoles
change the parameter name in constructors
One more bug fix for GNU make versions < 3.80
Fixed the uc and lc functions for GNU make versions < 3.80
added some stuff to clean out module files during "make clean"
quadrupole interactions should be working with a remaining question of interaction magnitude
messing with samples
oops... messed up a sample
Altered signs to fix charge-dipole interactions
changes during debug of charge-dipole
added Cl- and Na+
reinitialize buffer_stack_ptr in BASS parser
Building nanorod builder.
Initial import of nanorod builder.
support '+' and '-' in atom type name;clean the code a little bit
fix a bug in converting rotation matrix to quaternion
fixed the wrapping
LipidTranVisitor should do the wrapping
First round of formatting changes
Added a Makefile and changed reference.bib to ripple.bib to make the Makefile work correctly
Cleaning up an extra mac metadata file
cleaning up some extra mac metadata files
Initial import of ripplePaper
added Documents
fixed the cutoff eps
fix a bug in getting the dimension of histogram
added a reference
melting temp change
Fixed ssdrf free energies and transition temperatures
avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps
Corrected changes to the forcefield files
Make sure electrostatic_module provides data for reaction_field
Chris debugging stuff. HE WILL CHANGE THIS BACK, RIGHT?
constant back to correct value
fixed an install-related bug. $(InstallCommand) had been set to $(InstallData)
VelocityVerletIntegrator already deletes and Nullifies restWriter, so Integrator shouldn't do it.
fixed three typos
first run at charge-quadrupole interactions
forgot a couple of makefiles
added some samples
fix a typo in MultipoleAtomTypesSectionParser
pairs inside cutoff group should not be excluded
settled on a unit for quadrupoles
quadrupoles for SSD models
clean up SimInfo; modify the images of SelectionExpression.html
fixed a bug in MPI restraints
adding exclude pairs for rigidbody and cutoff group
fixed a doxygen problem
messing with the split dipole test cases
updated some documentation
LinkedList removal project starts now
using map to replace link list
adding test case of split dipole
Oops... MPI now builds...
adding test case for split dipole
added fortran-side support for split dipoles
fixes to restraints
fixing restraints
minor change
First commit of the new restraints code
adding IndexFinder
fix compilation issue
fix a bug in SectionParser (lineNo is not updated)
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
change the format of DUFF2
new electrostatic module
added splitDipole and fixed quadrupole stuff
removed #include lines for outdated charge and dipole interfaces
addded a few fun charge-dipole test cases
fixing a strange icc8 bug (we think).
OOPSE_itoa!
Electrostatic Unification Project
Dunno
Using OOPSE_itoa and checking a NULL left over from the LinkedList days
electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map
electrostatic unification project
making some cool test cases
Added a charge for Chlorine
Fixing a bug in BitSet.cpp
SPRNG eradication project
Cleaning up config.h.in by adding comments
avoid using const char*(hope can fixed the missing atom type problem)
adding base class of Random Number generator
info_ in Velocitizer is not initialized which causes a seg fault
remove default parameter from MersenneTwister.hpp which causes all kinds of trouble. Refactory random number generator
Adding unit test for random number generator
fixed a file inclusion problem
fixed compilation problem
replace SPRNG by MTRand
Change the name of test case
adding testcase for random number generator
fix compilation problem for g++ 3.4
adding OOPSERandNumGen
Fixed the damned build problem with the libraries not being removed in make clean and make distclean (at least we think it is fixed).
Making small modifications to allow for use on MPI machines
adding MersenneTwister random number generator
Adding a modified version of MersenneTwister.hpp
selection expression
adding soft potential to LJ Module
adding documentation for selection expression
adding basic_teebuf which can operate on multiple stream simutaneously.
Added ssdrf sample
reactionfield get fixed
Fix a bug in GofRAngle
Fix for compilation on the Sun
fix for compilation on the Sun
fix problem in sun
adding LipidTransVisitor, GofXyz is working now
Corrected filename collision for EAM on Mac OS X
Updated copyright information
corrected filename collision for EAM on operating systems which are not case sensitive (aka Mac OS X)
more bug get fixed
fix a bug in GofXyz
make processHistogram non-abstrct function
*** empty log message ***
finish GofXyz
change the output format of 2D radial distribution function
forget the const correctness for BitSet
The change of interface of BitSet cause a bug in SelectionEvaluation
return residentMem in byte
fix a bug in writing out the value of cosang
using PhysMem - RSSMem to estimate avaliable memory
change the default bin number
change the suffix of output files;fix the problem of counting in staticProps
fix a bug in BlockSnapshotManager
BlockSnapshotManager is using reference counting now
replace std::make_pair by VariablesType::value_type to make Sun Compiler happy
adding typedef to TokenMap, using TokenMapType::value_type instead of std::make_pair to make Sun compiler happy
bug fix in StaticProps
(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
cast of NULL to satisfy xlc++
*** empty log message ***
bug fix for null termination
bugfixing residentMem
bugfixes for residentMem on LINUX
added residentMem
modifications to estimate memory in use by other processes autoconf fixes ps syntax checking config.h file cleaning
ps niceness
ps strangeness
fix a bug in BlockSnapshotManager.hpp
default length for staticProps is 1/2 smallest length of first frame
fix a bug in VelocityVerletIntegrator : last frame is written twice
begin bug fix
refactory CorrelationFunction
bug fix and start of switch for type of correlation function
fix a bug in calculating bytes per stuntdouble
more fix
fixed a bug in CorrelationFunction
fixed a bug in SimInfo::getCutoff()
adding staticProps and dynamicProps into Makefile.in
maximum length defaults to the cutoff radius
adding Algorithm.hpp
dynamicProps get built
dynamicProps in progress
more work in dynamicProps
adding dynamicProps
adding command line option to DynamicProps
adding command line option for DynamicProps
adding dynamicProps
adding SelectionManager.cpp
adding one more constructor to Snapshot to create customized DataStorage
adding beginSelected, nextSelected method to SelectionManager
adding support for physmem
adding supprot for physmem
adding physmem
more work in StaticProps
change the filenames
adding GofRAngle
remove some useless files
staticProps in progress
adding GofR
add getRigidBodyAt function into Molecule class
update help info
support select internal index selection, for example, select DMPC.3
update help info for Dump2XYZ
selection librarys added
adding Makefile
issue commented out in wildcards
forget to reset the pc which cause reevaluate return NULL
fix a bug in determing the global index for rigidbodies
minor change in Bitset
selection library is working
remove SelectionVisitor
IgnoreVisitor and XYZVisitor now use selection library
adding SelectionManager into SimInfo
dump2Xyz now take advantage of selection library
minor change in BitSet
adding missing implementation
half of the selection utility is working need to debug within keyword and atomproperty keyword
selection library get built
fix BitSet
remove some useless files
adding wildcard class; NameFinder is finished
more work in selection library
selection in progress
selection library in progress, except SelectionEvaluator, other files are compiled
adding boost::any
add SelectionCompiler.cpp
Selection in progress
adding selection library
forget to add eorWriter
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe
fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
forget to set dipole for lipid head group
fix a bug in loading initial extended system parameters
forget to set maxIterNum_ in NVT
remove WATER.cpp
sync Makefile
moved Package variable into subdirectory makefiles to speed up the building process
Fixed publication details in banner
added dummy subroutine to avoid empty unit, synchronized this dummy routine between C and fortran
separating modules and C/Fortran interface subroutines
more fixes for gnugetopt
fixing for gnugetopt
using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2)
no message
fix a bug in global index
remove include Integrator.hpp in Minimizer
compile getopt and getopt1 if we need to
template flags
formatting
fixed a MakeDir / MkDir problem added BinDir target
port to SGI platform
change the order of linking (object file comes first and then follow by user built library)
remove useless debug info
minor fix
missing tab
missing tab
LinearVisitor get fixed
merging new_design branch into OOPSE-2.0
remove some useless force fields
adding new format of EAM force field
rename newDUFF.frc to DUFF2.frc
fixes
minor word change
touch up changes
merged the paper
Fixed Makefile test bug under OSX and possibly other BSD's, replaced test -f *.mod with ls function since BSD test apparently doesn't support wildcards.
revisions
adding new EAM force field files
fixed grammer and typos
fix another bug in WATER.cpp
improvements
fix a bug in WATER.cpp when initializing the new Charge AtomType
adjustments and inclusion of supplemental
*** empty log message ***
merge WATER force field into DUFF
change the force constant of bonds
CVS was messed up. Now it's fixed and updated.
minor fix in DUFF
minor fix in force field file
the short version
minor fix
new ForceField format
further updated phase diagrams
updated phase diagrams
updated plots and some minor wording changes
new title and text adjustments
replace misuse of using namespace std in header files
fixed a sample
spell check
minor text changes
text and figure adjustments
new plot and some text alterations
add PolynomialTestCase
Addint StringTokenizerTestCase
change Makefile
improved restraints - mpi should work fine
improved restraints
oops...
Back to normal... Oh... Restraints should work in parallel now
Improvements to restraints
just some testing changes, I'll return to the original on next commit
new DUFF forcefield
adding new format DUFF force field
Fixed a mixing list bug that slowed down the force loop
working sample
working towards parallel restraints
Commented out some write statements
Got rid of some write statements
Fun with ice
Added the linear visitor
current status of the debugging process
included visitors and minimizer
new changes
time to break SimSetup
added new classes in progress
isLinear and linearAxis are virtual in StuntDouble, but are implemented by DirectionalAtom and RigidBody In StuntDouble, they should return false and "-1" but there should be logic to figure them out in the other two classes
Don't remember what I did
Breaky Breaky
fixed useXXX in the entry_plug so that it only is set if the atoms really are in the simulation
testing force fields
testing shapes
mess up ......
Shapes looks like it's working
these core classes get compiled
more work on Molecule class
still debugging
shapes rcut calculator added
shorter run
rewrite Molecule class.
Remove some deprecated files
More painful reconstruction is coming !!!
More work on StuntDouble, Atom, DirectionalAtom and RigidBody
remove old Vector3d.hpp from application/simpleBuilder
Minor change in next_combination
Done with combination
change documentation of next_combination.hpp
ReplaceWildCard is working
adding replace wildcard function
Minor change
STL next_permutation like next_combination is working
fix of setDipoles
forgot to advance lines in the shapeFile
forgot the orientation line
fixed duplicate declaration foo
uncommented .in line
next_combination in progress
adding next_combination test case
STL Compatible combination sequence generator
bug fixed in GenerateCombination.hpp
a STL next_permutaion like next_combination function.
no message
ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way
ReplaceWildCard in progress
Adding Test Case for ReplaceWildCard
adding ReplaceWildCard.hpp, need test
Adding Generic TupleMatcher, wild char matching is on the way
Adding Generic Tuple3 and Tuple4
bug fix
subclass foo
more char* -> string conversion
char* -> string
Making ShapeType into a ShapeAtomType, fixing some isXXX
define name collision
forcefield refactoring for shapes
adding sample shape directory
DataStorage passes unit test
Changes to help advance shapes
Changes to Shapes force field reader
Snaphot and SnapshotTestCase in progress
add getArray function to RectMatrix and Vector classes
adding GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc.
more classes get reconstructed
GenericFactory pass unit test
Refactoring in progress
more work in Snapshot
Dear god! It runs and conserves energy!
strDUP not strCOPY
fixey fixey the breakey breakey
compiler flags
fixey fixey
Added un-busticated fortran files and c/Fortran interfaces
More on AtomType and DirectionalAtomType
Adding AtomType
Snapshot and SnapshotManager in progress
adding test case for Snapshot and snapshotManager.
Breaky Breaky. Fixey Fixey.
remove some junk files
remove backup of GenericData.hpp
replace old GebericData with new GenericData
Added newLJtype to lj module.
Added interface for fortran lj module.
GenericData and PropertyMap pass unit test.
fixed a fortran name problem
adding generic data test case
Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo!
Fortran/C++ interface de-obfuscation project continues
Fortran/C++ interface de-obfuscation project (It is a very long story)
Math library pass the unit test
Snapshot and SnapshotManager in design phase
namespace problem prevented linking
fixed include
more fortran name mangling
yet more fortran renaming
Fortran name cleanup continues
fixing some broken fortran stuff
name sanity on the fortran side
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except diagonalize(), all of functions in math library pass the test
Added correct prototypes for C-fortran interface functions.
Added correct prototypes for C-fortran interface functions.
more bugs get fixed at math library
Added new files for fortran interface.
regressing
working on shapes for portability
working on shapes
changed around findBegin
more bugs are fixed in Vector class
fix some bugs in RectMatrixTestCase
implement more test cases
more tests on math library
adding more testing units
fix some bugs in Quaternion class
Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi)
Working on getting Shapes into OOPSE
Added ShapeType
adding vector test case
adding generic factory and vector test case
math library in progress
add quaternion class
adding test file
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
forget to use namespace oopse
Changed optimization flags for XLF and XLC.
adding ifstrstream test case
fix include
fix incompatible declaration in jacobi
adding Makefile
adding test case for ifstrstream
add ifstrstreamTestCase
add checkFilename Option
add SquareMatrixTestCase class
adding basic_ifstrstream
math library in progress
FileReader in progress
Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons
adding PropertyMap class
adding testing unit
adding RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
adding c++ coding style
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
fix a bug in filepp
using filepp to generate dependencies instead of compilers
filepp can be used to generate dependencies for c/c++ now
Minor additional rephrasing
remove -module from F90Options
adding rules to move fortran 90 module to target directory
fixed makefile.in
remove "use bytes" which causes problem in sgi machine
add Makefile
fix Makefile under water directory
remove argon.dump and argon.eor from Makefile
Remove some Makefile.in
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fix make install
adding make install
add Makefile to sample directory
fixed some numbers and changed some wording
moved the getopt stuff
more build fixes
adding doxygen configuration file
filepp can handle different fortran module case and suffix
Chris doesn't know about the OOPSE-2.0 directory structure yet
Yeah yeah, we'lll get around to it later
cleaning up build process
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
Made the file reading more intelligent in Restraints. No longer gives uninformative seg faults.
cleaning up
Cleaning up a bit
fix make statistics
adding GNU make functions to combine all of the static libraries to a big library
preparing for better cutoff plots
adding shared library flag
move mpiSimulation_module to DarkSide
building MPI version;using static library instead of shared library
pass __FORTRAN90 instead of __F90 to filepp
add make cvslog
more work on the parallel build
changes to backport declare flags
Started work merging shapes
remove sfmakedepend from cvs tree
add oopse_ as library prefix
fix a space trimming bug in filepp
A few minor build changes
adding fortran90 make dependency tool
make clean is smart enough to only remove object files belong to current package. turn off silent mode
define DEV_ROOT as relative path
get the relative path by shell script
eliminate DEV_ROOT by relative path
add PackageLibs; fix dependency rule
updates
Working on make stuff
If makefile does not exist, print error message
fix dependencies rule
still working on build process
add print statment to rules
change Makefile to relative path
remove StringUtils.c which cause headache in bulding libutils
change directory structure of application. Every executable file is replaced in seperate directory
Keep that lib around, please.
starting a configure version
move fortran files around to solve dependency problem
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fix fortran dependency problem
add yacc and lex rules
adding include path to F90Options
change suffix from .cc to .cpp
change the #include in source files
Import of OOPSE v. 2.0
fixed some table wonkiness
ran ispell
fixed grammer in abstract
better gofr and sofq
updated image and a little text change
quick wording change
Fixed a char italic issue
Included rhombahedral distortion comments
another fig update
update figures
changes to last bit
new sofk plots
changes for packet
bib changes
changes
minor changes
fixes in error values
Added reference
Considerable changes to content and references
figure updates and whatnot
changes
added a plot
Added gofrs and refs
changes
changes
minor changes
some changes
Added references
Minor corrections
Added figures
Added an introduction
Added a figure and started in on the conclusions
More results and discussion
Added figures and expanded results and discussion section
updated bib file
started methods section
Thus starts the free energy ice i paper...
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Restraint loop is now more versatile
Fixed an algorithm error for thermodynamic integration with charges
minor fix
Initial import of OOPSE sources into cvs tree
removed antique code and fixed linking problem
removing old copies of sysBuild
refine Vector3d.hpp
remove anonymous struct from Vector3d.hpp
change butane.md
First documentation in OOPSE!
added zcons directory
Post-submission clean-up
add Makefile.in into zcons
add zconstraint samples
simpleBuilder version 1.0
working version of simpleBuilder
Added Water.frc discussion, improved the integrator section, added references
Added two new figures
simpleBuilder is built but Makefile is broken
add function isAtomInRigidBody into MoleculeStamp
add getForcefiled into simSetup
simpleBuilder in progress
new updates
SimpleBuilder in progress
Added utility functions to grab the mass from the force field.
edits done
add simpleBuilder
refactorize Lattice class
Forgot to add them
change parameter of calling sprintf
BASS eradication project (part 4)
BASS eradication project (part 3)
BASS eradication project (part 2)
BASS eradication project (part 1)
better error messages
Fixing required keyword annoyances
Fixing ifdef lines
fixed an ifdef problem
Install procedure modifications
warning message for nProcessors > nMolecules
modify 5x5.bass
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add init files
add init file
rename NVT.bass to argonNVT.bass
add 5x5.in
add butane.in
changed minimizer keywords
fixed typo
fixed sample makefile
minimizer sample changes
removed beadLipid
remove beadLipid
Added core-shell nanoparticle files.
remove TP4init.in
change init file name for tip4p and tip3p_ice
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change init file name for ssd
remove SPCEInit.in
change names for init file
remove eor file from cvs tree at minimizer/water directory
change init file name in lipid directory
remove beadLipid
remove init_argon.eor
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remove eor file
change names for argon
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add init file for ssde
Fixed bug in calc_eam with mixtures and cutoffs associated with mixture.
support SSD_E SSD_RF SSD1
SSDVisitor support SSD_RF, SSD_E, SSD1 now
remove ^M from ZConsReader.cpp
remove unsupport keyword
Made init files more OOPSE like.
Changed init files to be more OOPSE like...
added sample directory
fixed icc7 incompatibility in linking
Added tip3p_ice to Makefile
Added more metal sample to OOPSE for bulk simulations.
Added sample files for bulk metals and a bass file for both voter and FBD formulations of EAM.
Checked a bug where eor file wasn't being written at the end of the run
Fixed a bug where eor file wasn't being written at the end of the run
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cleaning up for export
removing staticProps from cvs tree
removing staticProps from cvs tree
removing static props from OOPSE-1.0 tree
using gengetopts --unamed-opts="SHAPEFILE [OUTPUTFILE]"
Changes for CGI and for gengetopts --unamed-opt="PDBFILE"
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fixing getopt_long
change protected method writeCorrs to public
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minor fix of format string in quicklate.c
remove zsub from cvs tree
remove some comment lines
remove an extra semicolon from OOPSEMinimizer.hpp
Shouldn't have been in CVS
Fix for thermodynamic integration of rigid bodies
These can be generated via lex and yacc at compile time
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changes for gnu getopt and fixed SPRNG configure script
fixing for machines that don't have lex and yacc
Makefiles don't belong in cvs repository
Makefiles don't belong in repository
Makefiles don't belong in repository
Updated configure for new samples
tip4p makefile.in added
ssde makefile.in added
ssd files sorted added
spce makefile.in added
dimer files added
Cleaned up this file considerably
Initial import of OOPSE-1.0 source tree
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New web address
Minor changes
Expanded the water.mdl file
Added the SPC water model
quick change in tp4.bass
Added TIP4P water sample
Added SPCE water sample
Good ssde simulation sample added
Fixes for MacOS X with xlc++ and xlf
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Added a bunch of stuff
Added C70 sample
fixed a bug in Mat3x3d.cpp
added SHAPE force routine
fixes
Got rid of the _RB_0 in the shape name
Added a range parameter to the visualizer
started functions
Tolerance input is accepted with the -t flag (default 0.01)
Setting up shaper to accept a tolerance
Recentering of the visualized potentials, adding tolerance option
Added 2 new samples
Coefficients are now multiplied by the normalization factor - no longer do we need normalization in the visualizer
Fixed the phi grid range for the final time (hopefully)
atan2, not atan!
Really fixed the phi range problem. Apparently s2Kit10 has a data in ordering problem
Changed gridbuilder phi range to run from pi/2 to 2pi+pi/2
Fixed the pdb files
New cholesterol.pdb
Added cholesterol
More samples added
Fixes for visualizer for amira
work on visualizer
Shape file output format adjusted
Added a few samples
got rid of sample PDB files. Others will be added later in samples directory
renamed forcer, modified factorial, fixed makefile
Removed some unnecessary C functions from the SHT code
Added more friendly progress comments
Spherical harmonic tranformations are fully integrated and working
Added evaluation stuff
Adding visualization parts
Fixed linking specification issues
touch up changes
Major progress towards inclusion of spherical harmonic transform capability - still having some build issues...
Now prints out a .xyz file of the reference configuration
Fixes to gridbuilder. Now gives proper sigma, s, and epsilon values
roll in progress
a few bug fixes
Fixed the grid builder rotation problems
Now calculates energies and builds the grid files. There are still bugs, but it compiles and runs...
Fixed XCode auto-indent to match XEmacs
Built principle axis determination and molecule rotation into calcRefCoords in RigidBody.cpp
GridBuilder updates grid vectors
Added GridBuilder.cpp and .hpp. Doesn't calculate energies yet...
Cleaned up unused variables. Added findMaxExtent to RigidBody.cpp
Added a bandwidth command-line option
bug fix on vdw files
fixed a subdirs bug
configure isn't really necessary
Major changes for rigidbodies
nicer error message formatting
Fixed dependency bug (we hope)
roll in progress
Sample now does variant
General fixes for formatting
Converted D's to E's in the funcfl files so that C can read them.
changing file extensions to be more in line with what's actually in the file
Added a bunch of files for EAM variants
Modified EAM to use forceFieldVariant, show sample in Au.bass
Modified EAM to use forceFieldVariant
Added forceFieldVariant global
reorg of EAM force fields to have variants
Fixed a thermodynamic integration issue. Force and torque scaling loops over atoms, not stuntdoubles
Removed debugging printf statements
Fixed indexing bug in stamps
Roll in progress
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3) these classes use anonymous union and struct to support double[3], double[3][3] and double[4] 2. adding roll constraint algorithm
Fixed a bug in NPTf (vScale was declared in the cpp file in addition to the declaration in Integrator.hpp file)
Fixes from gcc -Wall
Dan cleaned up the pressure calculation a bit... Got rid of some unnecessary lines of code in Thermo.cpp
small bugfixes
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constraint algorithm for minimization is working
Fixes
Moved to SHAPES
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Migrated vdw files from OOPSE
fixing for a separate existence
forcer was a binary
Initial import of SHAPES code
More work on Fortran side of error handler
fixed a typo in autoconf script
Unifying the error handlers
Not used anymore
forgot to add these
new rattle algorithm is working
Config changes for fortran access to SimError
new implementation of constraint
fixed a bug which only writes out the first atom of a molecule
SHAPES go somewhere else
Fixed groupOffset bug
Working on MPI scripting for autoconf
Shouldn't have been in CVS
keep the compilation directories around
Why is this in CVS?
formatting error messages, dependency fixes
starting fortran-usable version of simError
Probably shouldn't be in CVS
Formatting Changes, removed writeRaw
Formatting Changes
Bug in Makefile.in
severity levels in simError
Bug fix (fixes of skipList and neighbor list under MPI)
Bug fix (memory leak)
Testing
Cutoff Groups for MPI
Fixed bug in useLiquidThermInt routine in ForceFields.cpp
Implemented a separate solid and liquid thermodynamic integration routines
cutoff group in progress
Added useLiquidThermInt keyword and changed useThermInt to useSolidThermInt
Paving the way for separate solid and liquid thermodynamic integration routines
bugfix starting
Fixed a bug in Integrator.cpp where it called writeRaw() when useThermInt = false...
Bug fix for SkipList
Makefile doesn't belong in CVS
bugfix in simsetup?
Cutoff group changes under MPI
Fixes for xlc++
groupList new bases on global index of atoms
Modified the nifty banner
Fixed off-by-one error in groupStartRow and groupStartCol
in the progress of fixing MPI version of cutoff group
Compacted all of the 8 copies of the force loop into one.
std::cerr missing
pressure tensor fixes
Removed unnecessary variables and changed error messages in Restraints.cpp
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Fixes for stress / pressure tensor by cutoff group
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Fixed an error in Restraints.cpp... Too many arguements in a function call.
Added Bass keyword useThermInt.
Fixed Thermodynamic integration code.
this is the ripple codes
Got PDB reading working, and matching atom types too!
Major changes to skipThisPair for efficiency
Changes for SHAPES potential
Hopefully this commit included the bass keywords
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
more revisions
fixes for skip list
add some keywords
add minimizer sample
fixes for MacOS X compilation
Fixes for compilation under Mac OS X with IBM's xl compilers
Added a nifty neato banner
Removed an extraneous write
Starting to change the error model
const char* fix
MPI fixes and removal of extraneous write statements
added more revisions to the paper
get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
efficiency fixes in CutoffGroup
Added the cutoff Groups to the default water.mdl file
fixed a bug in CutoffGroup::getCOM()
bug fixes for cutoffGroups
adding generic Vector3 class
adding instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
Fortran-side changes for group-based cutoffs
adding CutoffGroup.hpp
fix two bugs in siminfo which cause infinite loop; fix anoter one in CutoffGroup which causes seg fault
adding cutoffGroup into OOPSE
bugfix for cutoffGroup
starting to rearrange the prose after the intro.
Fixes to libmdtools to use the simplified cutoff stuff in the BASS library
BASS changes for adding CutoffGroups to molecules. Also restructured the plethora of cutoff radii into one cutoffRadius and one switchingRadius. Also removed the useMolecularCutoffs keyword
optimize DumpWriter
New module for fortran group-based switching function
Many changes to get group-based cutoffs to work
added more tables.
added more tables
added in all of the general global keywords. Still need to add the zConstraint and minimizer keywords.
adding to the table
adding a separate file to work on the bass keywords.
C++ pass groupList to fortran
fixed two bugs in calc_charge_charge when using molecular cutoff
fix an unmatched c/fortran interface
keep the previous position of cantilever in SMD
fix a bug in Molecule.cpp which initialize massRatio before creat the array. fix two bugs in ZconsVisitor
Adding molecular cutoffs
work on molecular cutoffs
useMolecularCutoffs added to Globals
add center of mass of the molecule and massRation into atom class
modified the defaults for the system init time and system init state.
finished removing the trajectory analysis. took out the rattle derivation. added a section concerning the creation of init files. currently working on a table of key words for the package.
Fixed a bug in calc_charge_charge.F90
add reaction field correction to charge-charge interaction
change the calculation of pressure tensor
fixed another bug in InitFromFile. MPI verion of OOPSE is working again
fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
remove some useless files
fixed getCOMVel and velocitize at thermo
DUMP2XYZ 0.99 version
Fixed a charge bug
forgot to add this
fixed the makefile, and fixed some visuals on the schemes
finished cleaning up the old tex files
Just copied over the changes from the dissertation. Also converted the figures to pdf. All revisions now take place on the oopsePaper.tex file
fixed a bug in CompositeVisitor which cause the double counting problem
Dump2XYZ is almost working except atoms in rigidbody are double counted
new implement of quickLate using visitor and composite pattern
final final copy. really really sent to the printers this time.
fix a bug in setting exclude list
final copies sent to the printer
updated all equations, and finished all requested revisions
fix whole bunch of bugs :-)
some more updates.
revised the diffusion numbers.
Added the WATER.frc force field
fixed for get_potential
Change DumpWriter and InitFromFile
some more minor fixes
returned the referencess to the thesis layout, and fixed the equation grammer in the Introduction
started on some revisions
Now molecules can keep track of their own IntegrableObjects (and RigidBodies). Also a bug-fix so that SimInfo can keep track of RigidBodies (which was done incorrectly before).
Added Integrable (will back out momentarily)
Oops. Those were old.
Forgot to add IntegrableObjects
Adding RigidBody code
Changes for RigidBody dynamics
Slightly longer test run
Changes for RigidBody dynamics (Somewhat extensive)
added a makefile
more gcc friendly configure script who knows
more gcc friendly configure script
incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint
added lst styles, and some preliminary fixes to the intro.
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
final draft submitted to the readers.
final draft submitted to the readers.
added revisions to the Preamble and to the Introduction
semi-final draft
added support for files larger than 2 Gb
who knows?, but it works for the most part
making progress on the results section
added several figures to the lipid paper, changed the ndthesis class around a little. some small fixes in oopse.
NPTf complete, NPTxyz complete
NPTi complete
added gofz code
NPT work in progress
add LARGEFILE_SOURCE64 macro to support large file
More DLM changes
more changes for integrators
Fix a couple of bugs in zsub
Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE
finished the rmsd coding. hasn't been debugged
started work on rmsd
added citations to the bib, and started on a honking huge section of RATTLE in the oopse chapter.
switched params for tcR systems
Work on integrators
halfway through revisions in OOPSE
worked out the diagonalization bugs in head and whole
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remove the old implement of minimizer from cvs tree
Using inherit instead of compose to implement Minimizer both versions are working
added discussion of multiple image periodic boundry conditions, and added a figure to match the discussion
debugging the director code
cleaned up the references and the tables in the lipid section. also spell checked the thing.
added scd correlations, and director and order parameters for the head groups
made a makefile
finished up the rough draft of tcProps with Scd corr
adding function shakeF in order to remove the constraint force along bond direction
lmost finished with the readWrite routines
finished most of the actual dump scane.
started some cleanup on oopse. added a conclusion, finished the foreword, and found all the undefined citations
added a little bit more to readWrite.c
started on som io
added an introduction to oopse, and started smoothing out the wrinkles.
little changes in the twoChain figure
started work on some parameters and initialization
This commit was generated by cvs2svn to compensate for changes in r1047, which included commits to RCS files with non-trunk default branches.
single version of energy minimization is working.
added a lipid figure. started converting oopse.tex
added some OOPSE sections
started a bug fix on the massive memory overusage by OOPSE
added some revisions to the intro
Stripped out the hardwired LJ_rcut
Fixed some typos
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added a degeneracy figure
added a new euler fig, and fixed some things in the degeneractyy section
final version
Single version of energy minimization for argon is working, need to add constraint
Figure added
I hate revtex
Add one more file into Makefile.in
Add some lines into global.cpp to make it work with energy minimization
Now enthalpies of formation
Changes in response to JCP reviewer
Added black and white version's of figures
More corrections and fixing of experimental numbers
typed up the lipid section
Fixed a reference
Ran iSpell
Fix a bunch of bugs :-) Single version of conjugate gradient with golden search linesearch pass a couple of functions test. Brent's algorithm is still broken
More discussion of the orientational results as well as a description of the experimental tau_2 calculation.
started work on the complete project. Made a makefile, and added preambles
little changes, added the start of the conclusion.
Further improvements. Discussion of the results in the table was added.
fixed .bib file problems
Adjustments made based on reviewer recommendations. These include an expansion of diffusion data as well as inclusion of a table containing heat capacity, coordination number, and orientational relaxation information.
added in the RSA paper to the dissertation
NLModel0, NLModel1 pass uit test
little fixes
added the new figure into the Introduction
finished putting equations in Introduction added an euler rotation scheme picture
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to avoid cyclic depency, refactory constraint class
added some equations
ran spellcheck
Functor.hpp pass unit test
added a shifted potential figure
begin unit test of minimizer
updated the two figures in the introduction
added some figures to the Intro. Also lots of equations
Adding GoldenSection and Brent LineSearch Method
finished typing in the intro, and started on the lipid chapter
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser. This involved changes to WATER.cpp and ForceFields amoung other files. One important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on the next commit...
member list fixes for rigid bodies
Adding MinimizerParameterSet class.
Revision of NLModel0 and NLModel1
revision of NLModel
Added point-charge models to water.mdl file, updated ssd.bass to use new SSD name
Fix to new RigidBody stuff
Longer run time to test SSD water in MPI
Longer run time to test gold in MPI
Longer run time to test argon
More BASS changes to do new rigidBody scheme a copy of WATER.cpp from this morning
More BASS changes to do new rigidBody scheme
revision of constraint for Nonlinear Optimization Model
Changes to BASS reader to use Euler angles for orientation instead of unit vectors required changes in MoLocator
Changed orientation lines from unit vectors to euler angles
Convert Eulers in degrees into radians
Changed default orientation in BASS to use Euler angles in the following order: phi, theta, psi Removed the ability to set orientation using a unit vector
Changed default orientation in BASS to use Euler angles in the following order: phi, theta, psi Removed the ability to set orientation using a unit vector
Fix broken atom assignment for rigid bodies
added in the last bit about symplectic integrators and the liouville formulation
a few corrections to the introduction
added changes to the introduction
started adding in equations to the introduction
Corrected spelling in several directories, and stated WATER.cpp
constraint class in energy minimization
added periodic boundry conditions citation
minor corrections to the previous commit
added changes into the Empirical Energy section
started work on the lipid chapter
Adding energy minimization
Energy Minimizer
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Corrected .bib file entries
ran spell check, and fixed some little typos
Made some error messages more user-friendly
worked listing schemes into the document
Updated the default water to SSD/E
Adding warning if sample time, status time, thermal time and reset time are not divisible by dt
Adjusted the SSD part of the paper...
Added a bunch of dummy targets so make won't complain
Fixed old bass file
BASS changes to add RigidBodies required a change in how the MoleculeStamps are used by divideLabor in mpiSimulation.cpp
BASS changes to add RigidBodies and LJrcut
added in changes to the Monte carlo andMolecular dynamics section
adding the monte carlo section to the intro
forgt to add these earlier
did some work, started on the introduction chapter
fix a bug in creating eor file
fixed a bug where only MPI jobs could write eor files
fixed an struct mismatch error in the mpi initialization of the AtomStruct
Fixes for Dumps
Changes for altivec
Documented the Spud Toss
changes for charge charge interactions
More work for adding charges
autoconf fixes
fixed a periodic box bug
autoconf compatibility changes for icc8
Changes for adding direct charge-charge interactions (with switching function)
Some changes for new MPI organization and direct charge-charge interactions
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Energy Minimization method
fixed some things in the periodic image part
open and close the eor file whenever it is used instead of rewinding it
Made changes to the rigid body stuff...
change the interface of writeFrame
more changes to eam section.
More typo fixes.
Changed section on eam.
added new revisions
Merge the code of writeFinal and writeDump; Adding sortingIndex into DumpWriter; Fix a bug of writing last frame twice in integrator
revision
fix a bug in copying string
Dumpwriter only write out the atoms on master nodes
Updated the rigid body and ssd sections
added the cover letters
removed extra files
remove extra files
Edits for publication
tagub is not a bug. Just roll it back fix a bug of copying string to a pointer Still have Seg fault, it looks like a random MPI seg fault in totalview
Fix a bug of declaration of tagub
rotated the lipid figure added eam to the Emperical Energy
Added daw entry.
New DumpWriter (Attempt #4)
added a lennard jones section to the Emperical Energy section
added some work on the Introduction chapter
A work in progress...
null terminate some strings just in case
refixed the NVT readin XS state bug.
added strncpy to DumpWriter
fixed the restart from NVT exstended state bug
Added rigid body discussion and added to .bib file...
First Stab at fixing DumpWriter
added support for the ignore XS state info flag
Fixed a bug of sending message from master node to itself in DumpWriter.cpp and InitializeFromFile.cpp
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Periodic Boundary Conditions
started adding some changes from before break
performance fixes in the dipole dipole and reaction field code
Making do_Forces a little more sane
reworked the directory structure to reflect the Outline of the paper. All major sections now have their own tex file
Attempting to increase performance by reducing spurious function calls
mangling forces even further
mpich mucking
mangled do_forces...
Added bitmask to do_forces property lookup
Added third-party directory for code not written by us. Also added Mersenne Twister random number generator code. This will eventually replace sprng as the random number generator used by OOPSE.
Fixes to profile code.
More profiling fixes.
Another change for MPI in timing.
Small update to timing in MPI
the profiling commands work now. Will start adding PROFILE ifdefs into the code
added some profiling routines
working on adding GofRtheta and GofRomega additional work on randomBilayer
working on adding GofRtheta and GofRomega
added some profile functionality
Added functions for simple profiling in fortran.
Fixed bug in parallel EAM. rho_row and rho_col were scattered into the same array. Unfortunately, MPI zeros the array between scatters so half of the sum was being lost. Fixed by added a temp array for column scatter, then sum loop over nlocal.
Adding missing figures....
test commit...
finished gofRtheta and added gofRomega. both need to be debugged and tested.
Changes for gradients (to do minimizations)
removed the randombilayer header
edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from bilayerSys to randomBilayer
backed up the old DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and TB3 in DUFF.frc
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
begun work on add ing in the GofR,CosTheta
Fixed a bug in SimInfo ordering of radii
D'oh, more color plots...
Again, more color plots...
Added color denseSSD plot
Fixes for rotation
Learned to use cvs add and cvs remove...
Really added color figures.
Made color figures!
Added Vectors
Changed ice 0 to ice i.
Considerable corrections to both text and figures from the previous commit. Now in the true pre-print form. This is the updated first draft.
Massive changes to content. Declared as first draft.
added a routine to SimInfo.cpp to inline a min function.
reordered the rcut/ecr/boxSize initialization removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
Added support for compiling fortran without use of mpich modules. We use mpif.h instead.:
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
Fixed plots by including SSD1 data. Made several images more condensed and easier to read. Begun altering text to match the new focus.
added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
fixed the includes in the Make.dep
did a merge by hand from the new-templateless branch to the main trunk.
bug Fixes include:
* fixed the switching function from ortho to non-ortho box.
!!!!! THis was responsible for all of the sudden deaths we saw.
* some formating in the string when we write out the extended system state.
* added NPT.cpp to the makefile.in
some work on trying to find the compression bug
added template stuff to the Maikefile template little changes to some printf format statements
added template stuff to the Maikefile template
bug fixes for rList problems
Fixed bug that size(q0) was being queried before q0 was allocated.
fixed a stdlib.h include error in bass.l fixed a little bug in the first time step, regarding the setting of ecr and est in fortran
fixed a stdlib.h include error
som efixes to the way rcut is setup, as well as additional debugging comments.
C++ compatibility for templates
Refixed broken makefile
compatibility fixes
add chi and eta to the comment line of dump file.
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
Portability fixes
Compatibility fixes
started trying to understand extern "C" stuff for pointers
fixes for compatibility
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes Some fortran changes will need to be reversed.
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes
mod file fixes and portability stuff
Stuff for MOD support in other compilers
added routines for the sysbuilder to work with simSetup remved the QuickBass routines, and had all parsing go through SimSetup. LatticeBilayer is in complete working order now.
added routines for the sysbuilder to work with simSetup
fixes for configure, sysBuild
put QuickBass, MoLocator, and latticeBuilder into a Builder Library overhauled latticeBilayer into its own program. Removed sysBuild from the Makefile
Started work on integrator stuff
New File
Formatting changes to get out of RevTex nonsense
work on bilayer builder
fixed a merge problem
added eam ForceField files to the init fixed an eam mpi parmeter setup bug added the init file to the makefile
added eam ForceField files to the init fixed an eam mpi parmeter setup bug
added eam ForceField files to the init
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
added useInitTime to the BASS syntax. * useInitTime = false: sets the origin time to 0.0 regardless of the time stamp in the .init file * default=> useInitTime = true;
added the staticProps directory to the build list for both configure and configure.in fixed a number of bugs in the staticProps code. gofr is now working.
added the staticProps directory to the build list for both configure and configure.in
added the staticProps directory to the build list
Fixed a plot (fullContours.eps had bad labels).
dded my handwritten pages from 10-16-03
changed format to preprint article
Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
removed the props directory, and moved everything over to staticProps
Contiuned work on staticProps. should be in a position where it will compile and run first runs.
Fixed bug in calc_eam.
added Au init file for eam.
removed entahlpy from the statwriter and thermo.
changed the formating ogf the error statements in simError added a function to get the maxCutoff near completion of the staticProps code. still needs the pair loop, and the loop to allocate and read each frame.
changed the formating ogf the error statements in simError added a function to get the maxCutoff
changed the formating ogf the error statements in simError
finishing up the constructs needed to get this program up and running
changed f90Flags so they are no longer overwritten by the compiler.
added mpif90 mod check back same for conifig.in fixed wrappers to extern "C"
added mpif90 mod check back same for conifig.in
added mpif90 mod check back
fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7
light change in syntax. no signifigant change.
fixed some additional remarks from icc -w3 (extra verbose output)
cleaned things with gcc -Wall and g++ -Wall
fixed a bug in configure
fixes for configure
moved readyCheck in the integrator so that it is called before the first Statistics are written.
Added a bunch of Make.dep files to CVS
Removed NPTfm from Integrator.hpp. Some small syntax cleaning in NPTfm and SimSetup
fix bug in calculating maxCutoff
Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
Added zcons.tex
added NPT base class. NPTi is up to date. NPTf is not.
I must have changed something, but for the life of me I can't recall it...
Just added to the make file...
Added the integrator.tex file with figure. This is the same as the ssdePaper, so it needs to be adjusted for the OOPSE paper. Also updated the oopse.bib file.
removed mpi++ from the makefile
goofing off to test NPTf and NPTi
fixed bugs in NPTf, found (nearly) conserved quantities for both NPTi and NPTf
fixed a typo in the makefile.
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fixed NPTi to now work with constraints.
fixed ecr grow in SimInfo fixed conserved quantity in NPT (Still some small bug) NPTi appears very stable.
made additions to lipidIntro
SSD portion of paper added (ssd.tex).
added an intro to the lipid part
add conserved quantity to statWriter fix bug of vector wrapping at NPTi
added AllCorr. It eill still need some work
Added integrators to Makefile.in
Entered changes for configure into ChangeLog
Adjustments to the introduction. Minor additions to the methods section. Chris
added more work on getting gofR working.
First CVS commit. Minor changes in the introduction. More changes to follow... Chris
added the beginings of the GofR pair correlation. added identification of identI in matchI.
updated the ChangeLog added two new NPT integrators, they still need work.
updated the ChangeLog
a rough draft of the intial simulations
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Added parallel section of paper.
dependency on config.h
fixed sprng problem
New Makefile for metals sample
Changes to autoconf / configure method of configuring OOPSE
added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
added resetTime to the Global namespace.
Removed big file
This is the paper that got scooped
added zConstraint types to the AtomTypes file. added two rendering scripts to to aid in rendering. Note:renderRange does not work.
added zConstraint types to the AtomTypes file.
added a charmm citation to the bib file. finished adding all of the equations into DUFF.
added my J. Peter Grace fellowship.
fix a bug at MPI version of PolicyByMass
added some text to DUFF, changed the preamble from two column to preprint format.
Added: check uniqueness of molIndex
added the first functional parts of the PairCorrType Abstract classes.
put in some writing on initialSimulations
fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we turn on the optimization flag, it causes a seg fault
added the disertaion bibliography got the directory setup to build standalone texts.
added the disertaion bibliography
More fixes for stress tensor parallel bug.
This commit was generated by cvs2svn to compensate for changes in r728, which included commits to RCS files with non-trunk default branches.
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 molMembershipList use global index instead of local index
set default force substraction policy to PolicyByMass
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added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. commented out some print statements in Zconstraint hard coding some system init into bilayer.sys
added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. commented out some print statements in Zconstraint
Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits
changed the Makefiel a litle. Fixed a bug in MPI_DUFF. The atom block type was not being properly constucted in MPI. (The MPI struct had 6 doubles declared versus the actual 11)
changed the Makefiel a litle.
More FreeBSD fixes
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did some more work on DUFF.
added the lipid figure, and did some work on DUFF.
little changes to finish the port from make current to currMake
overhauled the makefile to build oopse.tex from the infiles rather than mess with includes. Also renamed header and footer to preamble and bibEnd respectively. make current has been replaced with currMake to tke a look at a single tex section.
added some work to DUFF
added a currMake script to replace the make current
small bug fix on frequency of output dumps.
played a little with the headers in DUFF
made some changes.
user can setup seed in bass file now, if he does not specify any value for seed, oopse will take the value of seconds of system time as seed
updated the Changelog. added some bug fixes for setting the random number generator seed value. fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
updated the Changelog. added some bug fixes for setting the random number generator seed value.
updated the Changelog.
bug fixed in ghost bend class
quick makefile fix, in make links. added -f to ln -s.
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reformmating ZConstraint and fixe bug of error msg printing
Fixed sysBuild -bilayer works. Nanobuilder still broke.
Tested MPI version of Z-Constraint Method
started working on DUFF
finished a rough draft of the dynamicProps section. added calculation sheme to the staticProps
Stable ZConstraint with average force substraction strategy
added text to the analysis code.
Added some profiling code -DPROFILE.
harmonic potential & z-contraint method
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trying to debug eqn references
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
debugging globals
formatting fixes and new atypes in LJFF
fixed a few references to older stuff...
Added comment line for getgetopt.
Missed del of files before.
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commit makefile
added harmonical potential to z-constraint method
changed how the comment line is handled to allow greater flexibility.
Changed makefile to only build quicklate.
added utils/sysbuilder to be built.
Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new atom allocation in libmdtools.
added method of moving zconstraint molecules to specified positions
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Added zConstraint into the BASS language syntax.
changed the number of degrees of freedom to account for zConstreints
EAM works...... Neighbor list also works.....
moved frameCount's functionality into DumpReader. also split props into staticProps and dynamicProps. (currently only have staticProps)
fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint.
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
Bug fixes for eam...
added the main equations to the analysis section
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edited the header to be a revtex style two column layout.
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added a current.tex to allow for looking at your current work, just change the include to the current tex file also seperated all header info into header.tex so that oopse.tex and current.tex will behave the same.
This commit was generated by cvs2svn to compensate for changes in r662, which included commits to RCS files with non-trunk default branches.
stable version of Z-Constraint
add index range checking into ZConstraint
added z-constraint parameters to the globals
Added Z constraint.
More bug fixes for eam.
working on the props code
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Added bass models for metals
Added eam to simSetup and added changecutoffeam.
Changed configure to look for both upper and lower cass .mod files
rewrote the makefiles a little to install two scripts for rendering
module use fixes for eam and do_forces.
added a '-' to the formating of the pov output file. also removed pov2anim from the project. It will be replaced with shell scripts
Finished most code for eam....
added the scan function to the DumpReader. It should now save the start of each frame in a vector.
making some changes to read dump files
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Fixed a current time initialization bug in InitFromFile.
some initial changes to Dumpwriter and friends to accomadate random file access
Initialized currentTime to 0, in case no one sets it.
fixed Initializefrom file to start the simulation from the time specified in the init file.
reoved some binary files
added DUFF lipid models to the AtomTypes file
fixed the AtomType file not found bug.
Started work on a DumpReader
Fixes for SSD/E
Changes for SSD/E
commented out an eam line
fixed spelling issue
added info module
Added massive changes for eam....
final fixes
Fixed a the centering on the Periodic Box. Also corrected the y and z switch in the box vectors
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More up to date version of EAM_FF
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
Started work on Hmat stuff to replace box Lengths
Made quickLate aware of Hmat. quickLate is now somewhat more intelligent about periodic boundaries and wrapping.
Fixed bug in updating mixing lists
added a quick wipe-and-update script for quick rebuilds on BoB
more fixes for box changes
removed some debugging print statements.
fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.
working on fixing ssd bug
Fixes for the NPT ensembles
cleaned up simSetup
added KMol
fixed some bugs, Changed entry_plug to info where appropriate
added more command line arguments
Fixing force field line
Fixing pressure tensor
more archaic code fixes
removed old outdated code
fixes to get rid of get_vx and set_vx
removing get_vx
Added NPTfm
Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
Broken SysBuilder
Fixes for samples
Removed some debugging write statements
Fixes for get and set routines in Atom and DirectionalAtom
added get and set routines to Atom and DirectionalAtom
added a nanoSysBuilder that takes different cmd line arguments.
found a bug. Unit vectors were not being updated
Working on NPTim
Switched the bond in the force field back to constrained, to preserve energy
working on som integrator bugs
Starting to worry about all the strtok() calls in our code
Fixed Hmat and some namespace strangeness
Fixed hmat in DumpWriter (MPI) and eor.
fixed some bugs
Added nanoBuilder and a general Lattice builder.
Bunch of 1-d array -> 2-d array stuff
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Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
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starting some work for xlate
adding in dan's NPT stuff
This is the dp and read file
Fixes and merging NPTf
Removed Qmass
Fixes for both NPTf and NPTi
Fixes in NPTi migrated into NPTf
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fixed box scaling
NPTi
cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Fortran flexi-BOX
Fixes for flexi-BOX
working on adding the box matrix to everything.
Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic boxes. wrapVector needs to be finished.
Changed over the bonds to Harmonic bonds in the DUFF frc file fixed constraints.
Changed over the bonds to Harmonic bonds in the DUFF frc file
Fixes to NVT. Check them!
added Harmonic bod into the DUFF forcefield and BondExtensions.cpp
Doing some work to debug the constraint code.
NPT fix
Most of the integrator and NVT seem to be working now.
NVT additions
slowly converting to new integrator and forcefield names.
finished the basics of the integrator and SimSetup.cpp
doing some work on SimSetup to clean it up / get it to work with the new Integrator.
minor changes in an attempt to fix output times.
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex some work on the integrator. ( incomplete)
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex
mostly final version
First completed rough draft (spell checked even).
fixed the left alignment bug. Bugger if I know what was causing it.
about halfway there.
nothing major just some little changes here and there.
added constrainA and constrainB to the Symplectic integrator
updated the logo a little as well as some of the colors
starting to add in the stuff for the poster.
This commit was generated by cvs2svn to compensate for changes in r544, which included commits to RCS files with non-trunk default branches.
currently modifiying Symplectic to become the basic integrator. bilayerSys.cpp altered for building tb3.
currently modifiying Symplectic to become the basic integrator.
added some member variables for position, velocity, etc.
changed how NVT is now derived from Integrator
fixed an a mismatched Ghostbend bug.
all seems to be working
still working on the bilayer code
doing some work to overhaul sysbuild.
optimized the ssd calc loop
Added bead lipid model to the sample directory
finished adding the Tail beads into the Trappe extended force field
added the TailBead atom types to the TraPPe_Ex forceField
fixed up the TraPPE_Ex force field. there were some duplicate entries added a two chain lipid to the lipid.mdl in sample
fixed up the TraPPE_Ex force field. there were some duplicate entries
added the utils subdirectory to the configure script added the CH branching group to the TraPPE_Ex fource field
added the utils subdirectory to the configure script
I added the calcPi.c
calculation of the pi
added optimization to the compile
We update the Makefile.
we have succesfully debugged the program. it is ready for use in any application we want.
fleshed out all of the ideas we wanted to see in this interface. it is still not yet debugged.
started some initial rewrite for the template.
Added binary extensions
changed the name of madProps.c to commandLine.c
This commit was generated by cvs2svn to compensate for changes in r516, which included commits to RCS files with non-trunk default branches.
updated xyz2pov to put out better pov scripts. I'm begining to think pov2anim isn't as useful. not sure if I should up date it, or just leave the rendering steps to shell scripts.
Added a quick readme, and Identified myself as the author
this should be the last of the random crap to toss out.
killing some files
killing misc . crap that shouldn't be inb the source tree. cleanning up the makefiles
killing misc . crap that shouldn't be inb the source tree.
Rearranged the source tree to be easier to distribute. Added autoconf and automatic dependency generation
added some stuff, and forgot to update. who knows whats different now.
added all the files
i quick fix to th distance in the random bilayer builder
added a new test for constraint failure
fixed up sysBuild to where it should now build our systems
almost finished.
bilayerSys and sysBuild both will build now. woot!
finished bilayerSys.cpp sysBuild still need to write the bass file. MoLocator.cpp is currently empty
Added eam force files...
More eam work.
working on the system builder
Fixed ordering on NVT calculation in integrators.
working on a system builder
added Ghost bends to the TraPPE_Ex forceField added sysBuild to the utils Makefile
added Ghost bends to the TraPPE_Ex forceField
Added first mangling of EAM.
fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.
Bug fix in progress for NPT
added a globalIndex counter to Molecule
Working on ConstantStress
fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.
fixed a bug in symplectic, where presure was only being calculated the first time through.
added pentane to the alkane model file
Added volume and enthalpy to status file
fixes for NPT and NVT
It works (kinda)...
Fixes for NPT / NVT
Moved expand neighborlist to init_FF.
fixes for NVT
fixes for nvt / npt
dt/2 fix in nvt
Fixes for affine transform
Changes to integrate the NVT and NPT ensembles
Fixes for NPT and NVT
fixed a sign error in the radial portion of SSD.
doing some testing in sticky through Symplectic.
Working on NVT
Fixed transpose bug in mpi reduce for tau and virial.
bug fixes
Many fixes to add extended system
Fixed a bug caused by my experimentation
Added ExtendedSystem infrastructure for NPT and NVT calculations
Added targetPressure to BASS
final mods to try a fortran compiler
Bug fixes for simulation module rewrites
bug fixes for compilation
bug fixes to fortran wrappers
Breaking c and fortran, c gets smarter, fortran gets dumber...
fixed a memory read bug in neighborlist
Changes for Extended System
Fixes for ExtendedSystem
Added the SGI award in 2003, also edited papers and presentations to separate the two.
Added extended system header
changes for extended system code
renamed nvt to extendedsystem
added some little fixes here and there.
fixed a possible call before initialize bug.
just little things like deleteing unused variables and such.
a few fixes to simError.h also some fixes to Molecule.hpp
a few fixes to simError.h
fixed some small things with simError.h
Starting work on NPT
Added NVT file (very broken for now)
Changed Readme, added some files
dipoles mostly work, but there is a memory leak somewhere.
Fixed a bug where MPI was not getting the proper atomIdents.
more bug fixes....
Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI
Fixed bug with pot_local not zeroed.
Fixes in MPI force calc and in Trappe_Ex parsing.
bug fix in DumpWriter.cpp
Bug fixes in read-write routines.
fixed a bug where the Excludes were not being created properly
mpi fixes and debugging mpi read write from file.
fixed long range interactions in Trappe
MPI buggy, fixed mpiRefresh issue.
fixed a bug where excludes were not being initialized
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Fixed a single processor segfault bug.
fixed the compile time bugs, Source builds and links
fixed a few more bugs.
added the Molecule.cpp file
fixed the makefile
fixing some compile time bugs
I have implemeted Molecules everywhere I could remember to. will now attempt to compile.
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
finished conversion of TraPPE_ExFF to use Molecule
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
fixes for local->global atom numbering in MPI
little bug fixes here and there.
Fixes to fileio for MPI
bug fixes many bug fixes
Making DumpWriter less dependent on sequence of atoms on the other processors. Node 0 now fires potatoes at other processors to get them to send french fries back.
the skeleton for making the molecules is in place. ForceField needs to be updated next.
fixed a couple of the "static" bugs in Atom and Exclude
still working on the SimSetup routine. also fixed some things in Exclude.hpp
Added Atom.cpp and Exclude.cpp
Fixes in Atom and Exclude list
Make Atom.cpp able to add and delete ranges of atoms
added an Exclude class with static arrays similar to the Atom class
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
Finished globalIndex.
MPI stuff for passing out molecules
working on load balancing
Fixes for Parallel thermalization
fixed an mpi include bug in THermo.cpp
Fixed bugs with calculation of potential energy and temperature.
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added dummy files to keep the build deirectories from being pruned.
moving tests to samples
moved tests to samples
Tests are becoming samples
Added makefiles in tests directories
electrostatic changes for dipole / RF separation
little bug fixes here and there
added an argon test simulation
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added some test bass files for experimenting with
fixed bug where short range interactions were not being calculated. removed some debug print statements
various write statements for debugging
added links to the makefile in forceFields
Fixed F_MACH_DEP bug
Makefile fixes, directory re-org, autoconf fixes
Added license file
Fixed makefile
Makefile for forceFields
Readme changes
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Makefile fixes for depends
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.
Bug fixes in TraPPE. calc_LJ_FF.F90: Removed print lines. TraPPE_ExFF.cpp: Fixed so idents are being set.
more bug fixes...
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fixed a bug in the torsions.
Working on the Makefile
Fixed bugs in atype_module.F90 atype_module.F90:new_atype: status was reused for force field checks, created new variable FFcheckStatus to be result of FF checks.
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fixed some bugs. LJ argon works. Error calling new atype for SSD in TraPPE_Ex.
Fixed bugs. Single version now runs w/o segfault. Still a conservation of energy bug. do_Forces.F90: Fixed pot not being passed to do_pair. neighborLists.F90: Fixed bugs in checkNeighborLists atype_module.F90: Fixed bug with allocating atypes on each new_atype call.Now checks to see if atypes is null, then calles initialize(16). vector_class.F90: Fixed some bugs with how MatchList was being allocated.
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compiles and links. And promptly segfaults.
some initial bug fixes
added GB
last little changes before compiling and debuging
shed implementation of the Fortran interfaces.
getNlocal no longer in force_globals
brought force_globals back from the dead to fix circular references
adding more to the interface
bug fixes for new fForceField.h
working on the fortran init ForceField interface.
fortran-side fixes to play nice with C
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merged stable-0_5 into the main trunk
blah!
mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)
Updated the Makefile to contain all of the new fortran
vector class tests correctly.
deprecated the ssd forcefield in C++
Bug fixes in vector_class.
fixed some bugs in BendStamp from when Ghost Bend was implemented.
last minute changes
Minor alterations to the layout
changed the font
spellchecked it.
A near final product
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Setting up my CV.
made som e revisions to the application.
fixes for the exclude lists
just working on some changes to the application.
initialization routines, bug fixes, exclude lists
Fixed some more compile bugs in do_Forces.F90.
forceGlobals is gone (part3)
Stick a fork in it. It's rare.
bye bye atypeGlobals (part2)
bye bye forceGlobals (part 1)
fixes for major rewrite
Massive rewrite
MPI bug fix
bunch of fixes
Massive sticky rewrite
added the force parameter files into the distribution
Fixed mixing list to work with new atypes using vector class.
rearranging source files
Added allocation of module arrays.
Bug fixes
Fixed bugs, added logical routines
Changes to vector_class and removed all traces of linked list.
Fixed a bug
Did a bunch of match/find routines
Bunch o' stuff, particularly the vector_class.F90 module
finished adding the ghostBend into the TraPPE_Ex force Field
Changed generic lists so they work correctly
Massive rewrite underway. This way be dragons.
Added ghostBend into SimSetup. only need to add awareness to TraPPE_Ex
Changed names of calculation modules for do_Forces.
More changes to code. Hopefully these will commit smoothly.
some cleanup
Removed extra copy of dipole dipole
added the ghost bend bend type.
Added stuff for Dipole/Dipole and ReactionField
GhostBend addition
added fortranWrappers and Forcefield.cpp to the makefile
implemented the new fortran force interface
More code clean-up.
Dan Goes Crazy
dded more static arrays to the Atom class;
Split force loop into subroutines. Moved wrap out of simulation module.
finished conversion of all function wrapping into fortranWrappers.cpp and .hpp respectively
cleaning up all of the function wrapping
Changed code to use one generic force loop. Only one super atype that has all information is now used.
overhauled TraPPE_Ex forcfield in C++
Made changes to lj_FF.cpp to pass stress tensor.
added randomSPRNG.hpp to the package (oops, should have beenthere to begin with.) added ssdFF++.cpp to the makefile
Changed lj_FF to use new neighbor list module.
fixed some changes to the Globals in libBASS Added some files to the Makefile and added ssdFF++.cpp to the C++ side of things
fixed some changes to the Globals in libBASS
OOPSE has been braought up to date with the mdtools devfelopment tree. mdtools should no longer be used. All development should take place in the OOPSE tree.
Added neighbor list module that auto expands...
Added simulation struct...
Changes...
Changes they are a comming....
added changelog and NEws info
incremented the version to 0.6
oose and oopse build and distribute!
oopse compiles and links!
oose builds and links oopse builds but can't find mpich++
libmdCode builds.
added mpi for libmdCode (still working out the kinks)
added some checks for libmpich and got single processor to build in libmdCode
dded some stuff
working on getting this distribution working
added libmdCode and a couple help scripts
libBASS and libmpiBASS are completely self encapsulated.
added mpiBASS.c and .h for the mpi libraries
Successfully added all the source for libBASS
Added SSD atypes.
Initial commit of ssd force module.
Fixed bug with pot energy.
Changed to single version. No change.
Changed to single version.
We have working code today... MPI bug fixes to DumpWriter.
Fixed some bugs, made some more.
MPI is Brooooooken...
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MPI is Broooooken. Saving poor state so I know where to begin with.
fixed a bug in the final eor file.
Changes in mpiBass.
Bug fixes for mpi version of code
Added a generic util code directory and moved Linux_ifc_machdep to it. MPI changes to compile MPI modules.
Force loops seems to work, velocitize never being called....
Add print lines to simBASS and fixed Makefile to link w/ icc.
More bug fixes... Forgot to build sprng
For some unknown reason the Single processor builds. Has not been tested!
final version before the single processor build
added generic atypes
lj_FF.F90 and simulation_module now compile. Logical bug still exists in lj_FF.F90 lj_atypes_list.
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added the fortran function wrapping to the mpiSim class
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added wrapping of fortran to a private function of SimInfo
modified the box vairable on setSimulation to be a length 3 array
Added init function to c++ force module.
More changes to lj_ff. Force loop almost ready.
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added some stuf to implement thefortran interface in LJ_FF
this completes the addition of fvortran function wrapping into the LJ_FF class.
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started some additions to wrap LJ down to fortran. INCOMPLETE!
tarted some additions to wrap LJ down to fortran. INCOMPLETE!
A few more changes to force loop.
starting down the crooked path of the fornographer.
More changes to lj_FF.
just some initial fiddling
removed a ps file that should not be backed up
This commit was generated by cvs2svn to compensate for changes in r226, which included commits to RCS files with non-trunk default branches.
fixed up LJ_FF
fixed up the LJ_FF implementation. It is now the standard for building a force routine.
Finished thermo and randomSPRNG classes.
More codeing on fortran force backend.
Thermo now can use SPRNG or rand48 (if not MPI). Finished up work on randomSPRNG. Still need to fix access to MPISimulation.
Added more code to randomSPRNG classes.
Added classes to handle random number generation.
Changed thermo getKinetic and getPotential for MPI. Added header for SPRNG random number generator class.
Added SPRNG header file.
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+ added lennard-jones force module and corresponding class. + created forceFactory directory.
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finishing work on making DumpWriter parrallel
Added mpi to InitializeFromFile read in.
Added replan of gather-scatter routines for future load balancing.
Finished updating mpiSimulation to work with c++.
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added the pareDumpLine routine to the Initialize from File class
Changed name of mpi_force_module to mpiSimulation to match with C++ code.
Initial mpi io conversion.
finished adding in the code to divide and set up the atoms and such across all of the processors.
fixed typo with #ifdef.
Added mpiComponentPlan.h a dual fortran c header file defining mpi simulation parameters for both c and fortran.
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made some shanges to streamline the setup in SimSetup
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cleaned up the divideLabour interface to use the information about Moleculestamps in the entryPlug.
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added the extraction routines so that the moleculeStamps corresponding to the actual components used in the simulation are now persistent throughout, and accessable through the SimInfo object.
Working on the clean removal of key Molecule stamps from the Hash table. stamps will be moved into a persitient linked list.
Added divideLabor.
First addition of mpiDivideLabor to split mpi simulation among processors.
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added files to divide the molecules among the processes.
Addition of c wrapper header for for fortran module proceedures.
some quick optimizations to the indexing in the storage arrays
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made some finishing changes before begining to work on the io
This will run the single processor version of libmdtools
if the libMPImdtools is working this should be the code to run it.
Initial commit of wrappers for fortran module proceedures.
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The simulation can run successfully on parrallel computers!! Now all that is need is the parrallel io routines, and parrallel forces
initial modifications
added simError.h to the makefile
This commit was generated by cvs2svn to compensate for changes in r179, which included commits to RCS files with non-trunk default branches.
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overhauled the makefiles to be more elegant with regard to builds.
ie. now the name of the library will change when you select single or mpi
build in the Makefile.inc compilers and flags will also be updated
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Fixed the whole lot to be simError safe, ands compiles. Not yet tested however
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Bass shopuld be simError safe
the BASS event loop has finished converiosn to simError. However, it as yet untested.
continuing to refine the error checking in the BASS processing
MPI Force rewrite in progress...
Initial commit of mpi routines for force decomposition.
First commit of mpi force code.
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working on the conversion of the BASS inititialization to be parrallel safe
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adding simError into the mpiBASS Event loop
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finished updates on the easy simError change overs.
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still working on conversion over to simError
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adding in simError
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finished work on the error handling struct and functions
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started work on a global error handling scheme
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making further modifications to make FOrceField objects mpi aware
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more tinkering with the forcefield event loop
minor revisions
more minor changes to the mpi structs
finished adding in the extra structures needed to pass info through mpi. Still need to add the implementation.
finished adding the static storage arrays to the atom class
Changing internal storage of positions, torqes, forces, velocities, etc. not sure here, still working
Changing internal storage of positions, torqes, forces, velocities, etc.
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adding ForceField mpi awareness adding mpi FOrceField awareness
adding ForceField mpi awareness
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changed mpiInterface.c and .h -> mpiBASS.c and .h for clarity of purpose
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Added lhs of assignments..
Fixed double inclusion of mpiBASSEventType with define in header file.
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Clean up with icc debug flags...
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Include makefile
quick bug fix to bassDiag
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added stamp and template diagnostic features
Added make include.
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changed dirs...
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Initial mpi support
Addition of mpiInterface to code base.
First stab at passing base events to mpi....
begin the pain that is MPI. abandon all hope ye who check out this branch.. P.S. we've added consistent BASS error checking
fixed allot of warnings, and adde the molecule
starting work on the molecule class starting to add in the molecule class adding in the molecule class
starting work on the molecule class starting to add in the molecule class
starting work on the molecule class
the final copy went out this morning. YAYYYYYYYYY!!!!!!!!!!!!!!!
made some final revisions, and started to add some figures
added a bunch of igures
text is finished YAY!!!
finished the revisions of the first draft now only lacks a complete results section, and a future Directions section
revisions to the first draft halfway complete. completed the introduction.
added command line arguments, and a time smoother
fixed a little seen output bug. (Tarega is not always default)
fixed a cosCorr and GofR flag bug, as well as the GofR scaling bug.
running into some problemsd with the figures.
made some changes to the Makefile, and added the sections I think I should write
did a little more typing
additions to the lipid model
got the water SSD model section "done"
added the ssd figure
added some equations and other misc stuff. needs lots of work.
just writing, not much editing yet
This commit was generated by cvs2svn to compensate for changes in r93, which included commits to RCS files with non-trunk default branches.
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VS: ---------------------------------------------------------------------- added more figures, and fixed the slides. GFave a practice talk 6-16-02 with this.
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fixed somebugs with start frame
added a utility to output what time of each frame
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added the capability to specify a start and end frame for cosCorr and GofR
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spell checked
I think I have most of it the way I like it, just need to change the correlation functions, and the final pictures
fixed some figures almost done with slides
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added figures fixed more of the graphs
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changed some of the figures, and put some more polish on the intro
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flexible atom selection
made a new figure. trying to add it to the slide
fixed the citations. continueing to clean up the slides.
switched in Chuck's magic slide enviroment
added a crapload of crap that may or may norbe neccassary. Time will tell. Also, got footnote references working.
This commit was generated by cvs2svn to compensate for changes in r60, which included commits to RCS files with non-trunk default branches.
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This commit was generated by cvs2svn to compensate for changes in r56, which included commits to RCS files with non-trunk default branches.
fixed the Makefile
added all of the pictures. And gave a practice talk based on this version. Now begins the process of cleanup and additions of citations.
getting there. Most everything but the motivation slide has been filled out. Lacks only pictures and Diagrams.
Skeletons of most every slide
made some changes
This commit was generated by cvs2svn to compensate for changes in r49, which included commits to RCS files with non-trunk default branches.
This commit was generated by cvs2svn to compensate for changes in r47, which included commits to RCS files with non-trunk default branches.
added the cos correlation function
got the GofR code working, and slimmed down the memory usage.
finished working on the command line options, and started working on the GofR added the GofR header, and moved the strructure definitions to the madProps.h
finished working on the command line options, and started working on the GofR
made a header directory, and fixed the Makefile to work with it the new header dir
made a header directory, and fixed the Makefile to work with it
took out a reference file
This commit was generated by cvs2svn to compensate for changes in r38, which included commits to RCS files with non-trunk default branches.
fixed the ordering on the end of file test
moved the actual routine into a seperate source from the main. This allows the routine to be used in other applications.
This commit was generated by cvs2svn to compensate for changes in r34, which included commits to RCS files with non-trunk default branches.
cleaned up the output a little
fixed makeRandom to set up a correct simulation
fixed a bug in getA( double the_A[3][3] );
added the getA( double the_A[3][3] ) routine to the Directional Atom Class, to facilitate easier RotMat aquisition
adding the routines to the proogram `
adding a program to make a lipid configuration with random dispersion of lipids.
fixed some bugs in the Makefile
removed xLate.cpp which was part of a seperate project
fixed a precision error in the calculation of the temperature. Also fixed the order that dump file are written.
removed a misc file
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This commit was generated by cvs2svn to compensate for changes in r16, which included commits to RCS files with non-trunk default branches.
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nose hoover chains added
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Import Root
initial checkin
initial checkin
Standard project directories initialized by cvs2svn.