CHANGELOG MCGEN
===============

Version: mcgen-20090103 by cipo@ut.ee

moved connections list output under "verbose_energy" option

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Version: mcgen-20081229 by ciop@ut.ee

added "di12" vdw potential

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Version: mcgen-00.00.40-070404 by cipo@ut.ee

fixed number of required parameters for 'opa2' potential

 vdw energy for uninitialized vdwrecords (vdwkey==EMPTY) is zero
 instead of some random value.

 Optimizing: replaced vector with list in UNITID::instances

Connections debug output made more readable 

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Version: mcgen-00.00.39-070402 by esoolo@ut.ee

Changed again FMCT to avoid going over array edge, this time taking the first
two long-range energy scaling parameters also into account.

Added parity check for the number of FMCT parameters

Changed numbers of parameters in the fieldout.ini file for some potentials.

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Version: mcgen-00.00.38-070402 by cipo@ut.ee

added opa2 dihedral potential:
OPA2 potential: K. Kahn, T. C. Bruice, J. Comp. Chem., 23, 2002, 977-996
"Parameterization of OPLS-AA force field for the conformational analysis 
 of macrocyclic polyketides"
opa2: U(f) = A[0] + A[1]*(1+cos(f))+A[2]*(1-cos(2f))+A[3]*(1+cos(3f))+ \
             A[4]*(1-cos(4f))        
     params order in mcgen DEF-file: 
DIH site1 site2 site3 site4 opa2 7 ES VDW A[0] A[1] A[2] A[3] A[4]

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Version: mcgen-00.00.37-070402 by cipo@ut.ee

restored original FMCT potential

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Version: mcgen-00.00.36-070320 by cipo@ut.ee

added "12-6" vdW potential: U(r)=A12/r^12-A6/r^6

Atoms can be described by labels instead of numbers in UNITS file 

Constraint ID can be a string instead of a number

Bond, Angle and Dihedral labels can be strings

Informatiivsemad veateated

VDW-failis aatomite thistus nimepidi

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Version: mcgen-00.00.35-061004 by cipo@ut.ee

added default zero values for scalar_cou and scalar_vdw in int DEFS::read_bonddef --  learn to program ;)

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Version: mcgen-00.00.34-060824 by cipo@ut.ee

lisatud COSG dihedraal kujul: cosg: U(f) = sum{A[i]*cos(B[i]*f)}, i=1...spec
parameetrid vahelduvad: A[1], B[1], A[2], B[2],..., A[spec], B[spec]

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Version: mcgen-00.00.33-051207

 Laiendasin mned eeldefineeritud unititega sooritatavad tegevused ka
 nhtamatutele unititele.
History kirje on nd xyz-failiga identne.
 Xyz-faili lhevad aatomid ainult tervete unitite kaupa
 (vlja arvatud eeldefineeritud unitis, kust vib kshaaval vlja visata).
 Xyz-faili salvestamata aatomite koordinaadid lhevad dumpi.

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Version: mcgen-00.00.32-051206 by cipo@ut.ee

Salvestasin moltries ja interrupt_done dumpfaili
Coulombi ja Van der Waalsi skaleerimistegureid otsitakse nummerdatud
 juvljaparameetrite seast
Parandused Coulombi ja Van der Waalsi skaleerimisteguritega seoses

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Version: mcgen-00.00.31-051201 by cipo@ut.ee

Lisaks muudele loendajatele suurendatakse ka moltries vrtust mcgen.log-is
suurendatud verisooninumbrit

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Version: mcgen-00.00.30-051130 by cipo@ut.ee

Lisasin funktsiooni protsendi jrgi peaahelast selle uniti lesotsimiseks,
 mille thtajaks genereerimata jmisel tehakse katkestus
chain.cpp: Bugfix: ilma krvalharudeta ahela krvalharude vahekaugust pole vaja
 kontrollida
 Katkestuse sooritamiseks vajalikud uued funktsioonid ja muutujad
mcgen.h unit.cpp: Muudatus exceptionites
genfieldoutini.cpp: Muutujatbi parandus printf jaoks
Lisatud uus loendaja: moltries
Lisatud maksimaalse tulemuse salvestamine eraldi
 Viisin vljundfailide nimed htsesse andmestruktuuri
 Uus sisendandmete kontroll:
 krvalahelate vahe > ettegenereeritavate peaahela llide arv

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Version: mcgen-00.00.29-051101 by cipo@ut.ee

 mcgen.out.FIELD faili lisasin ebastandardsetesse dihedraalidesse
 reavahetused ja kaks 0.0-vrtusega arvu.

 fieldout.ini ja mcgen.out.FIELD failide VDW-osadesse lhevad ainult
 olemasolevate aatomite paarid.

 Lisasin mcgen.out.FIELD failis igasse VDW-ritta he thiku.

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Version: mcgen-00.00.28-051031 by cipo@ut.ee

 Changed number of dihedral force-parameters according to DL_POLY local
changes
 (file dlpoly/2.14/source/CHANGES_LOCAL.txt in CVS module dlpoly).

 New method in UNIT class to
 replace current coordinates of all output-ready atoms
with those read from a given xyz-file.

 Optimised: retr_units_outputting_order instead of
get_units_outputting_order.
 Moved reading of xyz-files from UNIT constructor to new class READXYZ.


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Version: mcgen-00.00.27-051031 by cipo@ut.ee

fieldout.ini output fixes
made EXCLUDE-records active
new feature: GENFIELDOUT class generates a FIELD-file for DL_POLY

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Version: mcgen-00.00.26-051020 by cipo@ut.ee

fixed size_t conversion problem in genxyz.cpp:int GENXYZ::write_file(FILE *_file) method
fixed size_t conversion problem in genfieldoutini.cpp:int GENFIELDOUTINI::write() method
several other bugs fixed by Endel

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Version: mcgen-00.00.25-051017 by cipo@ut.ee

Removed invalid assertion in int UNIT::init_units_outputting_order()

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Version: mcgen-00.00.24-051014 by cipo@ut.ee

added line numbers into error messages
reordered units in history and xyz output files
added genfieldoutini class to output input file for genfield program
compiled against changes in sysutils class
updated version number

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Version: mcgen-00.00.23-050712 by cipo@ut.ee

removed "CROSSES" check for endunits in chains.cpp...

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Version: mcgen-00.00.22-050601 by cipo@ut.ee

updated doc
updated version number
added surefinish parameter to CHAIN record (unittype=end) in chains.ini file...if surefinish>0 the endunit will be added without energy control after surefinish tries...if 0, normal adding process goes on

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Version: mcgen-00.00.21-050525 by cipo@ut.ee

fixed bug in int CHAINS::read_nextfield(const char*) method

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Version: mcgen-00.00.20-050224 by cipo@ut.ee

updated version number after number of unlogged changes and bugfixes

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Version: mcgen-00.00.19-050128 by cipo@ut.ee

fixed logfile.print output bug in connect.cpp:45:CONNECT::CONNECT(CONNECT &_original, int _unitshift): added (int) for output variables

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Version: mcgen-00.00.18-050127 by esoolo@ut.ee

fixed energy calculation for first units of the chain if the backbone is less than 3 atoms long

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Version: mcgen-00.00.17-050121 by cipo@ut.ee

removed forcenr check in double BONDDEF::torsion_energy(const double _tau)
added new potential by Jaanus COSJ with keyword 'cosj'
	// cosj: U(F) = sum{0.5*A[i]*[1-B[i]*cos(if)]}, i=1...3
	//	params (6) order: A[1], A[2], A[3], B[1], B[2], B[3]
added DLPOLY torsion potential COS5 with keyword 'cos5'
	// cos5: U(f) = sum{0.5*A[i]*[1-cos(i*f)]}, i=1...5, 
	//	params (5) order A[1], A[2], A[3], A[4], A[5]
added DLPOLY torsion potential COS with keyword 'cos'
	// cos: U(f) = A[1+cos(mf-s], params (3) order: A, s, m
ANDIARTICLE potential renamed to ANPA
added FORCENR into bonddef.h

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Version: mcgen-00.00.12-041223 by cipo@ut.ee

replaced 'catch(int exception)' by 'catch(int Exception)' in unit.cpp
added #include <math.h> into vdwrecord.h

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Version: mcgen-00.00.11-041209 by endel@ut.ee

 * New parameter in params.ini.
   Keyword FIXED in the end of the RANDOME line obligates mcgen to
   always take back the maximum allowed number of units instead of random
number.
 * Bugfix: replaced undefined variables argv and argnum
   with defined variables arg and argnr in Lennard-Jones potential function.

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Version: mcgen-00.00.10-041104-00 by cipo@ut.ee

added Lennard-Jones' potential, keyword 'lj', 2 parameters: epsilon, sigma

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Version: mcgen-00.00.08-040829-00 by cipo@ut.ee

`uname -i` replaced by `uname -m` in Makefile

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Version: mcgen-00.00.08-040829-00 by cipo@ut.ee

added $HOSTTYPE for library and binary paths

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Version: mcgen-00.00.08-040829-00 by cipo@ut.ee

inserted '#include <cassert>' into textfile.h

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Version: mcgen-00.00.07-040513-00 by cipo@ut.ee

removed '-V' as short argument for output verbose since it's in use for 'version'
fixed input angles count bug in defs.cpp

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Version: mcgen-00.00.06-040322-00 by cipo@ut.ee

fixed some code mistakes...
added new geometrical constraints

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Version: mcgen-00.00.04-031127 by cipo@ut.ee

* changed completely mcgen.cpp structure by involving commline class
* class defs: all input filename types changed to string
* class defs: changed include scheme
* class units: all input filename types changed to string
* class units: changed include scheme
* class params: all input filename types changed to string
* class params: changed include scheme
* in ATOM::torsion_energy: -1 changed to -1.0 (line 353, pow())

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Version: mcgen-00.00.03 by cipo@ut.ee

* RNDM class replaced by RANDOME class (cvs module 'randome')
* changes in the code to reflect changes in randome class

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Version: mcgen-00.00.01 by cipo@ut.ee

* mcgen added into cvs






