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Fix legacy topology memory error
2018-03-21
Davi
d
van der Spoel
Re
n
amed
e
ntropy
.
* to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der Sp
o
el
Split off e
n
t
ropy
c
alculation to separa
t
e f
i
le
.
commit
|
commitdiff
|
tree
2017-12-28
David van der S
p
oel
Fixes
and updates fo
r
x
plor2gm
l
.
pl and atom_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van der S
p
oel
F
ixed check for
wa
t
e
r
in gen_
v
site
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David van der Spoel
New mdp input f
o
r electric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spo
e
l
F
i
xed mdp output fr
o
m e
l
ectric field code
.
commit
|
commitdiff
|
tree
2017-10-30
David van d
e
r
Spoel
Adde
d
option -water tips
3
p
t
o pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van der Spoel
Spli
t
off
the NMR related anal
y
ses from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
David van der
S
poel
F
ixed missing
e
ntrie
s
in nrnb a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-15
David
v
an der
S
p
o
el
W
orked a
r
o
und mis
s
ing Ope
n
M
P
implementatio
n
in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David van d
e
r Spoel
Fix
e
d bug in gmx disres indexi
n
g arrays
.
commit
|
commitdiff
|
tree
2017-08-02
Davi
d
va
n
der S
p
oel
Worked arou
n
d
m
issing Ope
n
M
P
im
p
lementation
i
n orires
.
commit
|
commitdiff
|
tree
2017-07-28
Davi
d
van der Spoel
Adde
d
unit-test f
o
r orientation rest
r
aints out
p
ut
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
R
e
m
o
ved u
n
necessary
s
tatic declarat
i
o
ns for co
m
mand
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David v
a
n
der Spoel
Fixed test-order dependency in gmxpreprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
F
i
x non-
r
eprodu
c
abilit
y
of cl
u
stsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
D
a
vid van d
e
r
S
p
oel
Xpm test for
g
m
x
cl
u
stsi
z
e
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoe
l
Added t
e
sts for gmx clus
t
size
.
commit
|
commitdiff
|
tree
2017-03-04
David
van
der
S
p
oe
l
Remove
s
ro
g
ue printing to xvg
file in gm
x
mindi
s
t
commit
|
commitdiff
|
tree
2017-02-27
David
van der Spoel
Fixes
b
ug in
g
m
x sol
v
a
t
e with -shell that
yi
e
lded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
D
avid van der
Spoe
l
Fixes SEGV in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
Da
v
id van der Sp
o
e
l
Only print all dangling ato
m
s
w
ith grompp -v
commit
|
commitdiff
|
tree
2017-01-23
Davi
d
van der Spoel
Added refer
e
nce for d
i
hedral func
t
i
o
n in OP
L
S
.
commit
|
commitdiff
|
tree
2016-12-07
Dav
i
d
v
a
n der Spoel
Couple of
n
ew quote
s
commit
|
commitdiff
|
tree
2016-11-18
Davi
d
van der Spoe
l
A
dded fi
r
st
t
ests o
f
bonded force fu
n
ctions
.
commit
|
commitdiff
|
tree
2016-10-14
David van
der Spoel
Fixes
some memor
y
leaks associated
w
ith
testing appl
i
ed
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avid van der Spo
e
l
Modul
a
rize elect
r
ic field
h
andling
commit
|
commitdiff
|
tree
2016-09-27
David van
d
er Spoel
Fixed script
x
p
l
or2gmx
.
pl to wor
k
with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
D
avi
d
v
a
n der Spoel
Fixes is
s
ue with Release
build
i
n correlation functi
o
ns
.
commit
|
commitdiff
|
tree
2016-09-20
David van der Spoel
M
a
de
c
orrelation function routine use std::vector
commit
|
commitdiff
|
tree
2016-09-05
David van der Spoel
Merge
"
Mer
g
e
b
ranc
h
release-2016"
commit
|
commitdiff
|
tree
2016-08-24
David van der Spoel
Added
d
ocumentat
i
on for sh
e
ll pote
n
tials
.
commit
|
commitdiff
|
tree
2016-08-03
David van de
r
S
poel
Three new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David van
der Spoel
Mer
g
e
"Mer
g
e branc
h
release-5-1
i
n
t
o
r
e
lease-
2
0
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
D
a
v
i
d v
a
n der Spoel
Fixes incorre
c
t char
g
es in OPLS/AA-L for H
I
SD and
H
ISE
commit
|
commitdiff
|
tree
2016-07-08
Davi
d
van de
r
Spo
e
l
Merge "Merge
branch release-5-1
i
n
to release-2016
"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Dav
i
d v
a
n der S
p
oel
Introduce fatal
e
rror for too
few
f
r
a
mes
i
n gmx do
s
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made g
m
x d
o
s
wor
k
a
g
ain
.
commit
|
commitdiff
|
tree
2016-06-22
Da
v
id van
d
er
Spo
e
l
Removed
s
purious r_ij in f
o
rce for Mor
s
e potenti
a
l
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Da
v
id
v
a
n der Spoel
Mod
i
fy lmfit l
i
b
rary to avoid cla
s
hes w
i
th
o
ther versions
.
commit
|
commitdiff
|
tree
2016-03-23
David van der
Sp
o
el
Removed srenew
t
hat
was ma
k
i
n
g array smalle
r
incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
D
avid va
n
der
Spoel
Fixed
d
ivis
i
on by zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Spoel
Couple
o
f new quotes
commit
|
commitdiff
|
tree
2016-01-07
David
v
a
n d
e
r Spoel
Made
n
o
rmal mo
d
es wo
r
k
w
ith
s
hells
a
nd vs
i
tes
commit
|
commitdiff
|
tree
2015-11-24
D
a
vi
d
van
der Spoel
Fixes newly introduced bug in make_
n
dx
.
commit
|
commitdiff
|
tree
2015-11-23
Da
v
i
d
van de
r
Sp
o
el
Moved domdec structures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
D
a
vid van
d
er Spoel
C
leanups in legacyheader/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
id van der Spoel
Me
r
ged
l
egacyhe
a
d
e
rs/types/qmmm
r
e
c
.
h i
n
to mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged genborn
.
h from legacyhe
a
der
s
/types int
o
mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spo
e
l
Moved l
e
gac
y
h
eade
r
s/types/group
.
h to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der
S
poel
Merged legacyheaders/ty
p
es/ns
.
h and nblist
.
h to md
t
ype
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
d
er Spoel
Combine e
n
ums
.
h a
n
d name
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van der Spoel
Merg
e
d legacyheaders/nrnb
.
h a
n
d types/n
r
nb
.
h to gmxli
b
.
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
Spoel
Move
d
mdatom
.
h from legac
y
header
/
types t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van
der Spoel
Move
d
legacyheaders/t
y
p
e
s
/
energy
.
h to md
t
y
pe
s
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
v
i
d
v
an der
Spoe
l
Merged legacyheaders
/
t
ypes/
i
nputrec
.
h in
t
o mdt
y
pes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
D
avid va
n
de
r
Sp
o
el
Merged legacyheaders/types
/
state
.
h into mdtyp
e
s/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d va
n
de
r
Sp
o
el
Re
p
laced atom
_
id by int
.
commit
|
commitdiff
|
tree
2015-11-13
Da
v
id van der
S
poel
Moved genbo
r
n
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van
d
e
r
Spoel
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van d
e
r Spoel
Moved copyrite
.
* to filei
o
from
g
mxlib
and l
e
gacyhe
a
ders
.
commit
|
commitdiff
|
tree
2015-11-11
David van
d
e
r
Spoel
M
o
ved inputrec
.
*
f
rom gmxlib and legacyhead
e
rs to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Sp
o
e
l
Removed legac
y
hea
d
er
s
/typede
f
s
.
h
commit
|
commitdiff
|
tree
2015-11-03
Davi
d
v
a
n
der
Sp
o
el
Mo
v
ed df
_
history
u
tilit
y
ro
u
tines from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
a
vid van der S
p
o
el
Replaced NO
T
SET fro
m
typedef
s
.
h b
y
local solu
t
ions
.
commit
|
commitdiff
|
tree
2015-10-23
David van der Spoel
Remove
d
energyhistory code from typed
e
fs
to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
Da
v
id van der
Spoel
Mov
e
d pbc/cut-off related utilitie
s
from typ
e
defs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Fr
e
ed me
m
ory in legacy statistics rout
i
ne
s
.
commit
|
commitdiff
|
tree
2015-10-03
David van der
Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id va
n
der
Spoel
Removed simple
.
h from nb_kernel_
s
se4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
emoved
simple
.
h fr
o
m nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed simple
.
h
f
rom nb_ke
r
nel_c a
n
d n
b
_kernel_sparc64
_
hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
D
avid van der Spoel
Remov
e
d
i
nc
l
ude si
m
ple
.
h from nb_kernel_avx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van der Spoel
Remov
e
d
simpl
e
.
h from nb_kernel_av
x
_256_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid van der S
p
oel
Removed output_env_t
,
now using gmx_outpu
t
_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David
van der Spoel
Re
m
o
ved typ
e
s
/n
r
nb
.
h
from
ty
p
ede
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
D
a
vid van der Spoel
Removed types/n
b
list
.
h and types/nsgri
d
.
h
f
rom typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
a
vid van der Spoel
Removed types/
m
datom
.
h
f
rom typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
D
avid van der Spoel
Removed
t
ypes/
i
n
p
utrec
.
h
from ty
p
edefs
.
h an
d
rel
e
ted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Dav
i
d van de
r
Spoel
Fix
e
s bug in the
c
omputat
i
on
o
f Coeffic
i
en
t
of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der Spoe
l
R
emoved
t
ypes/forcerec
.
h fro
m
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
Da
v
id van der Spoel
Removed i
n
clude of t
y
pes/ifunc
.
h
from ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Spoel
R
e
moved f
o
ur includes from legacy
h
eaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David
van de
r
Spoel
Removed legacyheader
s
/
t
ype
s
/commr
e
c_fwd
.
h f
r
om t
y
ped
e
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Moved
c
ontent from md
r
un
.
h t
o
separ
a
te headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spo
e
l
Removed
<
sys/ty
p
e
s
.
h> and
"types
/
constr
.
h" from
t
ypedefs
commit
|
commitdiff
|
tree
2015-09-09
David van de
r
Spo
e
l
Rem
o
ved f
i
leio/trx
.
h from ty
p
e
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-08
D
avi
d
van der
Spoel
Moved functions op
e
rating on forc
e
rec to separa
t
e
header
.
commit
|
commitdiff
|
tree
2015-08-28
Dav
i
d van der Spoel
Added
energy (edr) fil
e
t
y
pe
to Options headers
.
commit
|
commitdiff
|
tree
2015-08-28
David van de
r
Spoel
Adde
d
ad
d
itional constru
c
tor t
o
StringStr
e
am class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
D
a
vid van de
r
Spo
e
l
Made output
f
rom dumping
n
e
i
g
htborlists easier
to
r
ead
.
commit
|
commitdiff
|
tree
2015-07-31
David van der Spoel
Change initia
l
p
a
rameters
f
or
t
esting expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoel
Cod
e
for checking xvg files in
testut
i
ls
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spoel
Updated
exponential fitting
t
o ma
k
e it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoe
l
Clarified comments for time-depe
n
den
t
electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van d
e
r
Spoel
Fixed incorre
c
t output of gb
_
algorith as sa_a
l
gorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van
d
er
S
poel
U
pdat
e
d docu
m
ent
a
tion
for el
e
c
t
ric
fields
.
commit
|
commitdiff
|
tree
2014-12-13
David van der
Spoel
Four new q
u
ot
e
s from around t
h
e
w
o
rld
.
commit
|
commitdiff
|
tree
2014-11-28
Davi
d
va
n
der
Sp
o
el
Fixes r
e
cently
intro
d
uced bug i
n
gmx analyze
.
commit
|
commitdiff
|
tree
2014-11-24
David van der Spoe
l
Added warnings for ewald-geome
t
ry and
s
ur
f
ac
e
-epsil
o
n
commit
|
commitdiff
|
tree
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