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Fix small leaks in do_md cleanup
2018-12-22
Da
v
id van
der
S
p
oel
Re
v
er
t
"Removed t_t
o
p
o
logy f
r
om g
m
x msd"
commit
|
commitdiff
|
tree
2018-12-20
David va
n
der S
p
oel
Removed
t
_topolog
y
from gmx msd
commit
|
commitdiff
|
tree
2018-12-05
David
v
an der Spoel
Added new testin
g
c
o
d
e
for n
o
rmal mode
analysis
.
commit
|
commitdiff
|
tree
2018-12-04
David van
der Spoel
Small update to
m
d
run tests
.
commit
|
commitdiff
|
tree
2018-12-04
David
v
an de
r
S
poe
l
Remov
e
d
gmx morph
commit
|
commitdiff
|
tree
2018-12-04
David van der Spoe
l
Removed gmx
dyndom
commit
|
commitdiff
|
tree
2018-12-04
Dav
i
d van der Sp
o
el
Removed
gmx anadock
commit
|
commitdiff
|
tree
2018-11-21
Da
v
id
van
d
e
r
S
poel
Merge
branch 're
l
e
as
e
-2019'
commit
|
commitdiff
|
tree
2018-11-18
David
va
n
der
Spoel
Added citation for
n
e
w ana
l
y
si
s
f
unc
t
i
o
nality
.
commit
|
commitdiff
|
tree
2018-11-11
Dav
i
d van der Spoel
Fix entropy calc
u
lation in gmx ana
e
ig
commit
|
commitdiff
|
tree
2018-11-09
David van de
r
S
p
o
e
l
Change ge
t
_at
o
m_index to allow multiple molecules
.
commit
|
commitdiff
|
tree
2018-10-11
David van de
r
Spoel
Reinstated quas
i
h
armonic entropy calcul
a
tion i
n
gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
David van der Spoel
Added option to
g
mx nme
i
g to
p
rint
ZPE
.
commit
|
commitdiff
|
tree
2018-06-12
D
a
vid v
a
n
der Sp
o
el
Le
t
gmx n
m
eig print
thermochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
David
v
an der Spoel
Re
n
amed entropy
.
*
to th
e
rmoc
h
e
mistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
D
avid van der Spoel
Split off
entropy calculation
to
s
epar
a
te
f
ile
.
commit
|
commitdiff
|
tree
2017-12-28
Dav
i
d van de
r
Spo
e
l
Fixes an
d
u
p
date
s
fo
r
xplor2gml
.
p
l
and atom_n
o
m
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
D
a
vid van
d
er Spoel
Fi
x
ed
c
heck for water i
n
gen
_
vs
i
t
e
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David
van der
S
poel
N
e
w
m
dp inpu
t
for electric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David
v
an
d
er Spoel
Fixed
m
d
p
o
u
tput from el
e
ct
r
ic fi
e
l
d code
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
Added
option -w
a
ter ti
p
s3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van der
Spoel
Split off
the NMR related analyses
f
r
om
gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
D
a
vid
v
an der Spoel
Fixed
m
issing entries in n
r
n
b arrays
.
commit
|
commitdiff
|
tree
2017-08-15
Da
v
id van der
Spoel
Worked around
m
issing
OpenMP
i
m
plemen
t
ation in ori
r
e
s
.
commit
|
commitdiff
|
tree
2017-08-03
David van der Spoel
Fixed bug in gmx disre
s
indexing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
David
v
an der Spoel
Worked around missing OpenMP implementation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
D
avid van der Spoel
Added
u
nit
-
t
est for ori
e
nta
t
ion
r
e
straints output
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Remove
d
unn
e
c
e
ss
a
ry static d
e
clarati
o
ns for co
m
m
a
nd
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
Davi
d
va
n
der
S
poel
F
i
xed test-
o
rd
e
r dependency in gmxp
r
epr
o
cess tes
t
s
.
commit
|
commitdiff
|
tree
2017-07-19
David va
n
der Spoel
Fix n
o
n-reproducability of c
l
ustsiz
e
tests
.
commit
|
commitdiff
|
tree
2017-05-01
D
a
vid
va
n
d
e
r S
p
o
e
l
Xpm test for gmx clustsize
commit
|
commitdiff
|
tree
2017-03-12
D
av
i
d van der Spoel
Added tests
for gmx clusts
i
z
e
.
commit
|
commitdiff
|
tree
2017-03-04
David van der Spoel
Removes rogue pri
n
ting to x
v
g
fil
e
i
n
gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
Dav
i
d v
a
n der
S
p
oel
Fixes bu
g
in gm
x
sol
v
ate with -shell that yiel
d
ed 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der
S
poel
Fixes SEG
V
in gmx o
r
der
.
commit
|
commitdiff
|
tree
2017-02-02
David va
n
der Spoel
Only print
a
l
l
dangling atoms wi
t
h grompp -v
commit
|
commitdiff
|
tree
2017-01-23
David v
a
n der S
p
oel
A
d
d
ed refere
n
ce for dihedral function in O
P
LS
.
commit
|
commitdiff
|
tree
2016-12-07
D
a
vid
van der Spo
e
l
Couple
of new q
u
otes
commit
|
commitdiff
|
tree
2016-11-18
Davi
d
van der Sp
o
el
Add
e
d
f
i
r
st tests of bonded force functions
.
commit
|
commitdiff
|
tree
2016-10-14
D
avid van der Spoel
Fixes
s
ome
memo
r
y l
e
aks associated with testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avid va
n
d
er Spoel
Modula
r
ize
el
e
c
tric field handl
i
n
g
commit
|
commitdiff
|
tree
2016-09-27
D
avi
d
van der Spoel
Fixe
d
s
cript xplor2gmx
.
pl to work with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David van der Spoel
F
i
xes issue with Release build in correlati
o
n
fun
c
tions
.
commit
|
commitdiff
|
tree
2016-09-20
Davi
d
v
a
n de
r
S
p
oel
Ma
d
e correlatio
n
func
t
ion rout
i
ne
u
s
e
std::vector
commit
|
commitdiff
|
tree
2016-09-05
David v
a
n der Spoel
M
erge "
M
e
r
ge branch rel
e
ase-2016"
commit
|
commitdiff
|
tree
2016-08-24
David van d
e
r
S
p
oel
A
dded d
o
cumentation for shell p
o
te
n
tials
.
commit
|
commitdiff
|
tree
2016-08-03
David v
a
n der Spoe
l
Three
n
ew quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David
v
a
n de
r
Spoel
Merge "M
e
rge
branch
r
e
l
ease-5-
1
into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van der Spoel
Fixes incorrect charges
i
n OP
L
S/AA
-
L
f
or HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
D
avid
v
an der Spoel
Me
r
ge "Merge
branch release-5-1 into rele
a
se-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
Intro
d
uce
fatal error
for too f
e
w frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van
der
Spoel
Made gmx dos work agai
n
.
commit
|
commitdiff
|
tree
2016-06-22
Dav
i
d van der Spoel
Removed s
p
urious
r
_ij in for
c
e for Morse pote
n
tial
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
D
a
v
id va
n
der Spoel
Modify lmfi
t
library t
o
avo
i
d clashes with othe
r
versions
.
commit
|
commitdiff
|
tree
2016-03-23
D
avi
d
van der Spoel
Removed sre
n
ew that
w
as making array smalle
r
incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
Davi
d
va
n
der
Spoel
Fixed division
b
y zer
o
i
n
polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van
der
Spoe
l
C
o
uple
of new quote
s
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoel
Made normal modes work w
i
t
h s
h
ell
s
a
n
d
vsites
commit
|
commitdiff
|
tree
2015-11-24
Da
v
id v
a
n der Spoel
F
i
x
e
s newly introduc
e
d
bug in
m
ake_
n
dx
.
commit
|
commitdiff
|
tree
2015-11-23
Da
v
i
d
v
a
n
d
e
r Spoel
Moved
d
omdec structures out
of commre
c
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van
der Spoe
l
Clea
n
ups in legacyheader/typ
e
s/com
m
rec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged le
g
acyheaders/types/qmmmr
e
c
.
h into mdlib/q
m
mm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David va
n
der
S
poel
Merg
e
d gen
b
o
r
n
.
h
f
rom legacy
h
e
a
ders/
t
y
p
es into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved l
e
gacyhe
a
d
er
s
/types
/
g
r
oup
.
h
to
m
dtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van
der Spoel
Mer
g
ed l
e
gacy
h
ea
d
ers/types/ns
.
h
and
n
b
l
ist
.
h
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Combine
enu
m
s
.
h and names
*
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
a
n
der Spoe
l
Merge
d
lega
c
yheaders/nr
n
b
.
h
and
types/
n
rnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Mov
e
d
mdato
m
.
h from legacyheader
/
types to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Moved
l
ega
c
yheaders/ty
p
e
s
/energ
y
.
h to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-15
David
van der
Sp
o
el
Merg
e
d legacyh
e
aders/
t
ype
s
/input
r
ec
.
h into md
t
ypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David
van
d
er Spoel
M
e
rg
e
d lega
c
yhead
e
rs/typ
e
s/
s
tate
.
h into mdtypes
/
state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David
v
an der Spoe
l
Replaced atom_
i
d by int
.
commit
|
commitdiff
|
tree
2015-11-13
David
van der Spoel
M
o
ved genborn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van
d
er Spoel
Moved txtdump
.
* to
fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Moved co
p
yrite
.
* to fi
l
eio from
gmxlib and l
e
gacyhe
a
ders
.
commit
|
commitdiff
|
tree
2015-11-11
Davi
d
van
der
S
poel
Moved
inputrec
.
* f
r
om gmxlib and legacyh
e
a
d
ers t
o
md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-10
D
avid v
a
n
der Spoel
Removed legac
y
headers/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David
van der Sp
o
e
l
Moved df_h
i
story utility routines from typedefs
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Da
v
id van der Sp
o
e
l
Replaced
NOTS
E
T from typedefs
.
h by local solutions
.
commit
|
commitdiff
|
tree
2015-10-23
David
v
a
n der S
p
oel
Removed energyhist
o
ry c
o
d
e
from typedefs to a separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
M
o
v
e
d
pb
c
/
c
ut-off related uti
l
iti
e
s from
typ
e
defs
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Freed memo
r
y
i
n leg
a
cy sta
t
i
s
ti
c
s routines
.
commit
|
commitdiff
|
tree
2015-10-03
Davi
d
van der Sp
o
el
Remo
v
ed sim
p
le
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
moved
s
imp
l
e
.
h
fro
m
nb_kernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
Removed si
m
p
l
e
.
h f
r
o
m
n
b_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n der Spoel
Remove
d
simple
.
h from nb_
k
ernel_c
a
nd nb_kernel_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n der Spoe
l
R
e
moved
i
nclude simple
.
h from nb_kernel_
a
v
x
_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
moved simpl
e
.
h from nb_kernel_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
v
id van der Spoel
Removed output_env_t, now using gmx_output_env_
t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der Spo
e
l
Removed types/nrnb
.
h f
r
om typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
D
a
vid van der
S
poel
Re
m
oved types/n
b
l
i
st
.
h and types/nsgrid
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Da
v
id van der Spoel
Remov
e
d types/md
a
tom
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Da
v
id v
a
n d
e
r Spoel
Removed types/inputrec
.
h f
r
om typedefs
.
h an
d
r
eleted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van
d
er
Sp
o
e
l
Fix
e
s bug in the com
p
utation o
f
Coeffi
c
ient
of
Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
avid van der
S
poel
Removed
t
y
p
es/for
c
e
r
ec
.
h fr
o
m type
d
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-25
Da
v
id va
n
der Sp
o
el
Removed in
c
lude of
t
y
p
e
s/ifun
c
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Spoel
R
em
o
v
ed
f
our incl
u
des from legacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der
Spo
e
l
Remo
v
e
d
legacyhe
a
ders/types/commrec
_
fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van d
e
r
Spoel
Moved content
f
ro
m
mdrun
.
h to
s
e
p
arat
e
h
ead
e
rs
.
commit
|
commitdiff
|
tree
2015-09-10
D
avid
van der Spoel
Removed <sys/typ
e
s
.
h> and "types/constr
.
h" from
typedefs
commit
|
commitdiff
|
tree
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