changelog

一个很好的分子动力学程序

Version 2.5.32
Oct 18, 2002
(1) Added bug fix from Luming Shen (thanks) in cdpairf.c, PAIR_Parse()

      else if (Deriv==0) 
		   Value = F1(tc,x);

    is replaced by

      else if (Deriv==1)
		   Value = F1(tc,x);

Version 2.5.31
June 1, 2002
(1) Added bug fix from Qikai Li (thanks) in cdfunc.c, InterpolateTable()
      F->ExteriorValue = a[6*F->NumCoeff];  ===>
      F->ExteriorValue = a[  F->NumCoeff];

Version 2.5.30
Jan 20, 2002
(1) Corrected auxillary pair potential in module cdcsi.c.
(2) Re-ordered CHANGELOG
(3) Added Makefile in doc/ directory

Version 2.5.29
Mar 19, 2001
(1) Moved examples into separate directories and included output files
(2) Rename potential files from (e.g., nial.pot to nial.txt) and fixed
    example files to include correct potential file from archive
    directory tree.

Version 2.5.29
Jun 15, 2000
(1) Fixed reported Y2K problem, tm_year -> tm_year+1900
(2) Added 'thermal' stress component to stress calculation
    with STRESS THERMAL command

VERSION 2.5.28
Feb 18
(1) Fixed MACROF to accept %d, to give better error message and 
    cddoc.c to report correct usage.

Feb 13
(7) Fixed WRITE EKIN.  Formerly writing (3/2)KT, which didn't
    take into account varying degrees of freedom.  Have now
    replaced GetTemperature() with GetKET(), GetKE() and a
    new GetTemperature().
(8) Fixed ITEMP to correctly apply random velocities to
    constrained system - added ApplyConstraint() command
    just before velocities rescaled to account for constraint

Feb 2
(6) Fixed Y2K problem in cdstate, printed year 2000 as 19100.

VERSION 2.5.27
Jan 7, 2000
(1) Fixed bug with Quench, previously Clamp would be applied
    for each step when potential energy dropped after force calc.
    Not good..
Jan 14, 2000
(1) Added WRITE VAR command and WRITE MASS command
Jan 17, 2000
(1) Converted ClampVelocityTag() and GetTemperature() to use
    number of degrees of freedom based on the type of constraint,
    none, plane or line.
(2) Added velocity to ApplyConstraint() - needed to get correct
    temperature when using constraints.
(3) Have cditemp.c InitialTemp() call ApplyConstraint()
(4) Call CalcTotalDOF() from read_particle(), read_fix(), 
       read_remove(), read_cor(), read_rcv(), read_dup(), 
       read_state(), read_posvel()
Jan 18
(5) Fix strsub.c strlin() to break input lines on \r as well as
    \n (thanks Qikai Li)

VERSION 2.5.26
Nov 16, 1999
(1) Correct read_select so that command "select all;fix off" works
(2) Have macro command echo macro value
Dec 5, 1999
(3) cditemp.c InitialTemp(), divide random velocities by sqrt(mass)
(4) cdrepeat.c, read_repeat(), 'quit' command end program from with
    REPEAT/END loop
(5) Add -d option to turn on debugging
(6) Moved nrand() from cditemp.c to parse.c 
     ! NEEDED TO #include "parse.h" in cditemp.c

VERSION 2.5.25
Sep 28, 199
(1) Have FILL GO command mark neighbor list as invalid.
(2) Add  CALC nrand() command for Emmanuel.
(3) Add  option to read from stdin ('-')

VERSION 2.5.24
June 24, 1999
(1) Fixed notorious state file bug reported by Emmanuel Bournez.
(2) Updated Makefile
(3) Add WRITE [TAG] COR kludge to help Emmanuel plot different
    colors for different groups of atoms using XMDVIEW

VERSION 2.5.23
Jan 25, 1999
(1) Add formula option to doc.
(2) Add VERBOSE INFO command.
(3) In cdcons.c read_constrain() add test for a->cons[]==NULL
    before ALLOCATE()ing it.

			if (*ptype==POT_EMBED || *ptype==POT_DENS)
				{
				if (*type>=NumType_m)
(14) In cdcomm.c read_command() change
        IsComment (cmdstr,..)
     to
        IsComment (cpnt,..)
     Change required when added new Macro Command.

(5)  Call WrapParticles() after end of every MD step.
     This prevent the dependence of trajectory on
     calls to WriteCor() or writercv() (which in turn
     calls WrapParitcles() ).
(6)  Call UpdateNeighborList() whenever writing a STATE file
     so that subsequent trajectory will match that
     of XMD restarted with the STATE file.
(7)  EXTFORCE and EXTSPRING commands now read data in cgs units.
     Previously they read units in eunit/cm and eunit/cm^2.
(8)  Added FORMAT option to WRITE PARTICLE
(9)  In cdwrite.c, add WARNING for when WRITE DISP called without
     first calling DISP.
(10) Add MACROF command.
(11) Add automatic variable->macro substitution, that is if
       calc i=22
       calc var22=100
       write var$i
       write var22
     the 'write var22' and 'write var$i' statements give the 
     same result.
Jan 14, 1999
(12) In plotc.c, change ClipAtom() to ignore atom pairs when
     both atoms outside the box.  In theory this should not
     happen but plot_coord() does this because it is not
     set to handle free surface case when atoms are
     less then 0 or greater than a->bcur[].
Jan 21, 1999
(13) In cdeam.c _parse_pot(), changed t2 to *type in following
     code

VERSION 2.5.22
Nov 3, 1998
(1)  Correct PLOT bug detected by example plot.xm
(2)  Save PRESSURE info in state file.
(3)  In cdwrite.c PrintVectorList(), remove s->eunit factor
     so that Forces and Spring Constant prints in cgs units.
(4)  In cdwrite.c PrintVectorList(), change print out for
     null list from (example) 
         1 0.0 0.0 0.0
     where one is type to 
         1 2.75 2.75 4.25 0 0.0 0.0

Nov 2,1998
(5)  Fix read_pressure() to implement units of MBAR for
     EXTERNAL pressure, not cgs.

(4)  remove SEL option from ROTATE WAVE

(3)  For following commands, 
      - print number of particles changed
      - print warning if no particles selected
    CLAMP (sel) CONSTRAIN DAMP DISP (sel) EXTFOR EXTSPRING
    FIX ITEMP(sel) MASS "PLOT SYMBOL" PSTRAIN ROTATE(sel)
    SET TYPELIST WAVE(sel) WRITE(sel)

(2)  In cdeam.c, check that input potential type does not exceed
     maximum specified in POTENTIAL SET EAM n command.

VERSION 2.5.21
Oct 28, 1998
(1)  CHanged wording for error message from
	     PREVIOUS COMMAND NOT FOUND
     to
   	  ERROR:  PREVIOUS COMMAND NOT FOUND
     so that user can find error message easily in large output file.

VERSION 2.5.20
Oct 5, 1998
(1)  Fixed cdstate.c readstate(), was not setting
     BMA_MotionAlgorithm correctly.

VERSION 2.5.19
Sep 30, 1998
(1)  Added message after CMD or QUENCH command that reports
     final step.  Helpful for debugging when trying to 
     synchronize .xmo files and .e, .s, .b files.


VERSION 2.5.18
Sep 24, 1998
(1)  Changed type of NeighborList from USHORT (unsigned short)
     to int, so now can do 2^32 neighobrs instead of just 2^16,
     which caused havoc with Xiaowei's large 90000+ atom 
     simulation.
(2)  Added ability to have different X,Y,Z pressures for
     Pei's sintering simulations with pressure clamp.  
     Not valid for simulations with Andersen's algorithm.

VERSION 2.5.17
Sep 14, 1998
(1)  In cdeam.c, added warning messages when reading potential (using
     either standard for FORMULA option) without NTABLE, X0 or XN.
(2)  In cdeam.c, corrected error in GetAtomSubset() which omitted the
     last atom when using odd number of aatoms.  This error 
     would have no effect when the last atom in array
     was also the last atom in the neighbor list, in which
     case it wouldn't be needed because it was handled
     as a neighbor of previous atoms.
(3)  For some unknown reason, SELECT ALL became broken, because
     if /else if/ statments not correct, and after SELECT ALL
     code was executed, a later check thought that it wasn't
     and therefore concluded that SELECT ALL was not a correct command.

VERSION 2.5.16
Sep 11, 1998
(1)  Added SELECT KEEP ON|OFF to read_select(), it was missing.
(2)  Have read_select() check that a->np>0 before ALLOCATEing tsel[]
(3)  Have WriteCorFile() check nsel before writing selected coordinates.
     TAG value as 0.

VERSION 2.5.15
Aug 26, 1998
(1)  Correct PARTICLE and FILL GO command to initialize particle
     TAG value as 0.

VERSION 2.5.14
Aug 25, 1998
(1)  Fix FILL BOUNDARY SPHERE and FILL MARGIN interaction, they
     were not working together.

VERSION 2.5.13
Aug 21, 1998
(1) WRITE AVG,MAX,MIN FORCE was mistakenly scaling output by 1e8
    because code was copied from WRITE PARTICLE code.  This is
    now corrected.

VERSION 2.5.12
Aug 11, 1998
(1) Change cdmain.c, cdthread.h, cdthread.c, cdeam.c to use
    macros PTHREAD_MUTEX_T etc instead of pthread_mutex_t.
    This is to prevent name collision on Dec Alpha, because
    on Xiaowei's Dec Alpha pthread_mutex_t etc are defined
    in the default include files, and those definitions are
    incompatible with the substitute dummy pthread library.

Version 2.5.11
July 16, 1998
(1) Change cddoc.c from 
       PRESSURE EXPRESSURE ... 
    to 
       PRESSURE EXTERNAL ...
(2) Change keyword ORTHONORMAL to ORTHORHOBMIC in cddoc.c,
    read_pressure() and in defines BMG_ORTHORHOMBIC
(3) Fixed cdeam.c to make USE_THREAD_CODE the default.

July 13, 1998
Version 2.5.10
(1) Program now prints ERROR if QUENCH called without first 
    initializing MASSes
(2) Corrected stress for STILL algorithm.  Tested with Still2.xm

July 8, 1998
Version 2.5.9
(1) Correct BoxDynamics - in ClampPressure() had
		if (!a->BoxMotionAlgorihtm!=BMA_CLAMP)
			return;
    instead of
		if (a->BoxMotionAlgorihtm!=BMA_CLAMP)
			return;

July 1, 1998
Version 2.5.8
(1) Correct BoxDynamics functions - 
		previously called when a->BoxMotionAlgorithm!=BMA_NONE, 
		now only called when a->BoxMotionAlgorithm==BMA_ANDERSEN

June 12, 1998
Version 2.5.7
(1)  For PARTICLE and POSVEL commands, clear all flags in a->Selection[]
(2)  Added cdfunc.c to do potential functions.
(3)  Created cdpairf.c to allow other models to include pair potential
	  model, cdpairf.c now call cdfunc.c to handle functions.
(4)  Interfaced cdstil.c to cdpairf.c to include pair potential model.

June 12, 1998
Version 2.5.6
(1)  Add commands for R. Ge
        WRITE  [SEL] PARVEL
        PARVEL [ADD] n  

     PRESSURE  ANDERSEN  xmass [ ymass [ zmass ] ] 
     PRESSURE  CLAMP     bulkmodulus [ cstep ]
     PRESSURE  OFF
     PRESSURE  EXTERNAL pressure
     PRESSURE { ISOTROPIC | ORTHORHOMBIC }

June 11, 1998
Version 2.5.5
(1) Increase precision on WRITE EPOT
(2) For Selena, 
        SELECT EATOM lo hi, 
        SELECT VELOCITY [ABS] {X|Y|Z|MAG} lo hi
(3) Test BULKMODULUS before PRESSURECLAMP
(4) Restructure read_pressure() to fit new command syntax

May 28, 1998
Version 2.5.4
DONE
(1) Have PressureClamp respect the a->BoxMotionGeometry==BMG_ISOTROPIC
    setting.
(2) Add VERBOSE { ON | OFF } command for Dr. Ge to remove
    comments from WRITE EATOM
(3) Let macros ignore case
(4) Change PRESSURE PRESSURE <pressure> option 
    to     PRESSURE EXTERNAL <pressure>
(5) Have CALC print error information
(6) Fix POTENTIAL WRITE PAIR 1 command in cdeam.c
     - It was writing POTENTIAL DENS 0 and POTENTIAL EMBED 0
     - It was using incomplete format %13.4 instead of %13.4e
(7) Fix cdeam.c __efn() so that __efn(rcut) is not out of range
    (see comments in cdeam.c)

May 14, 1998
Version 2.5.3
      (1) Error found with particle array allocation, calls
          to crdalloc() used a->np instead of a->NumPartAlloc.
          Have replaced all crdalloc() calls with ALLOCATE and
          replaced a->np with a->NumPartAlloc.
      (2) Write out messages about compile switches that were used.
      (3) added routine GetTemperature() calculates temperature
          of selected atoms (using correct number of free particles)
      (4) WRITE SEL TEMP and WRITE SEL EKIN now use selected atoms.
          Previously, SEL options ignored, and WRITE EKIN wrote
          total kinetic energy including box motion, not the 
          kinetic energy per particle.  Now WRITE SEL EKIN writes 
		    only kinetic energy for particles (NOT Box), and normalized
          only by number of free atoms.
          WRITE EKIN includes BOX kinetic energy, but divided by 
			 all particle (*including* fixed particles).
      (5) Write erorr message when STATE _file_ not found
      (6) Add MACRO capability

May 12, 1998
Version 2.5.2
      (1) Threaded version was giving Selena intermitent errors.
          Found that we needed to initilaze FPU at start of 
          Thread functions ThreadCalcRho() and ThreadCalcForce()
          with statement   asm("finit");
      (2) PLOT now draws filled circles with black border.

May 6, 1998
Version 2.5.1
      (1) mistakenly called free(rho) instead of FREE(rho) in cdeam.c,
          lead to confused "Check" messages and CheckMem* output.
      (2) All allocations like 
             ALLOCATE (a->xxx, xxx, a->np)
          must be changed to
             ALLOCATE (a->xxx, xxx, a->NumPartAlloc)

April 23, 1998
Version 2.5.0
      (1) Created threaded version of EAM force routine.
      (2) Added cdthread.c as a dummy replacement for PTHREAD library
      (3) Corrected WRITE TEMP, was not dividing by number of particles.
      (4) -p option to read number of processors 
		(5) FILL GO now write number of new particles

April 2, 1998
Version 2.4.36
      (1) Fixed FILL GO comand, did not implement orientation
          or alignment correctly.
      (2) Changed sign in external pressure for PRESSURE CLAMP
          dynamics in cdmd.c ClampPressure()