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Convert gmx_stochd_t to C++
2018-12-28
Kev
i
n
B
oyd
C
o
n
vert
g
mx_stochd_t t
o
C++
commit
|
commitdiff
|
tree
2018-12-27
Szilár
d
Páll
Use std::
s
w
ap
i
n LINC
S
commit
|
commitdiff
|
tree
2018-12-27
Be
r
k Hess
U
se
A
tom
P
a
i
r f
o
r LIN
C
S indexing
commit
|
commitdiff
|
tree
2018-12-27
Artem Zhmurov
The tests for LINCS and SHAKE constra
i
nts
.
commit
|
commitdiff
|
tree
2018-12-27
Be
r
k He
s
s
Use a
r
rayref in LINCS
commit
|
commitdiff
|
tree
2018-12-27
Kevin
B
oyd
Use std::vec
t
or for trotter_seq
commit
|
commitdiff
|
tree
2018-12-27
Kev
i
n Bo
y
d
Make all thread-mpi thr
e
ads release cr
st
r
ucture
commit
|
commitdiff
|
tree
2018-12-26
Kevin
Bo
y
d
F
i
x small leaks in
do_
m
d cleanup
commit
|
commitdiff
|
tree
2018-12-22
David v
a
n der
Spoe
l
Rev
e
rt "Removed
t_top
o
logy fro
m
gmx m
s
d"
commit
|
commitdiff
|
tree
2018-12-05
Da
v
id van der Spoel
A
dded new testing code for n
o
rmal
m
ode analysis
.
commit
|
commitdiff
|
tree
2018-12-04
David van d
e
r
S
poel
Small update to mdrun tests
.
commit
|
commitdiff
|
tree
2018-12-04
David van d
e
r Spoel
Remo
v
ed gmx morph
commit
|
commitdiff
|
tree
2018-12-04
Da
v
i
d
van de
r
S
poel
Removed
gmx
d
yndom
commit
|
commitdiff
|
tree
2018-12-04
D
a
vi
d
va
n
d
e
r Spoel
Remov
e
d gmx
an
a
dock
commit
|
commitdiff
|
tree
2018-11-21
David van der S
p
oel
M
erg
e
branch
'rel
e
ase-201
9
'
commit
|
commitdiff
|
tree
2018-11-19
Mark
Abraham
Fi
x
i
ne
f
fici
e
nt sh
e
l
l
m
inimizat
i
on
commit
|
commitdiff
|
tree
2018-11-18
David van der
S
poe
l
Added
citation for new analysis function
a
lity
.
commit
|
commitdiff
|
tree
2018-11-08
Paul Bauer
Actuall
y
f
ix g
m
x
h
elix segmentation fa
u
lt
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
Improv
e
robustness of end-t
o
-e
n
d testing
commit
|
commitdiff
|
tree
2018-06-22
Mark Abraham
Updat
e
energy and trajec
t
ory f
r
ame
typ
e
s
commit
|
commitdiff
|
tree
2018-06-12
Mar
k
Abr
a
ham
P
repare
f
or GROMACS 2019 r
e
leas
e
notes
commit
|
commitdiff
|
tree
2018-06-12
David van der Spoel
Let
g
m
x n
m
eig
p
r
i
n
t therm
o
c
hemistry
.
commit
|
commitdiff
|
tree
2018-03-16
David van de
r
Spoel
Split off entropy c
a
lculation t
o
separate file
.
commit
|
commitdiff
|
tree
2018-01-04
Erik
Lindahl
Improve fram
e
time/step handli
n
g in
trjconv
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindahl
Fi
x
tr
j
conv for tdump
<
frame timeste
p
commit
|
commitdiff
|
tree
2018-01-01
Erik Lindahl
Fix gmx density
for non-mass calcul
a
tion
s
commit
|
commitdiff
|
tree
2017-12-28
David
v
an der Spoel
Fixes
a
nd
updates for x
p
lor2gml
.
pl and atom
_
nom
.
tb
l
commit
|
commitdiff
|
tree
2017-10-17
D
avid van der
S
p
o
el
Fixed missi
n
g entries in nrnb arrays
.
commit
|
commitdiff
|
tree
2016-10-01
Be
r
k
H
ess
Fix inputrec initialization
i
n
4 tool
s
commit
|
commitdiff
|
tree
2016-08-24
David van der
S
p
o
e
l
Added document
a
tion for shell potentials
.
commit
|
commitdiff
|
tree
2016-06-27
David van
d
er
S
poel
Made gmx dos work again
.
commit
|
commitdiff
|
tree
2016-03-23
David van der Spoel
Removed
s
renew that
w
a
s
making a
r
r
a
y
smaller in
c
orrectly
.
commit
|
commitdiff
|
tree
2016-01-20
Dav
i
d va
n
d
er
Spoel
C
ouple of new quotes
commit
|
commitdiff
|
tree
2015-11-24
Dav
i
d van de
r
Spoel
Fix
e
s
n
ewly
i
ntroduced bug
in m
a
ke_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
D
a
vi
d
van der Spoel
Moved domdec
structures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-21
David
v
an
d
er
Spoel
Me
r
g
e
d legacyheaders/typ
e
s/q
m
m
mrec
.
h
into
mdl
i
b/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id va
n
der Spoel
Mo
v
ed
legacy
h
eaders/t
y
pes/group
.
h to mdtyp
e
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Merged legacyhea
d
ers/type
s
/ns
.
h and n
b
lis
t
.
h
t
o
m
dtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der Spoel
Combine e
n
ums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Merged legacyheaders/
n
rnb
.
h
a
nd types/nrnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved
m
datom
.
h
from legacyheade
r
/ty
p
es
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der
Spoe
l
Merged legacyhea
d
ers/types/stat
e
.
h in
t
o md
t
ypes/s
t
ate
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van
der S
p
oel
Moved genborn
.
h
t
o mdlib
commit
|
commitdiff
|
tree
2015-11-12
Dav
i
d van
der Spoel
Moved t
x
tdump
.
*
t
o fileio
.
commit
|
commitdiff
|
tree
2015-10-15
David van der
S
poe
l
Fre
e
d me
m
ory in leg
a
cy
s
t
atistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David
v
an der Sp
o
e
l
R
em
o
ved simpl
e
.
h
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d van der Spoel
R
e
moved types
/
nblist
.
h
a
nd types/
n
sgri
d
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der
Spoel
Rem
o
v
ed t
y
p
es/mdatom
.
h
from typ
e
def
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
D
avid van der Spoel
R
e
moved t
y
pes/
i
nputrec
.
h from typedefs
.
h
and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
v
an der S
p
o
e
l
Fixes bu
g
in the comput
a
tion o
f
Coeffi
c
ient of
T
her
m
al
.
.
.
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid van de
r
Spoel
Removed l
e
gacyheaders/types
/
commrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
a
n der Spoel
Removed <sy
s
/
ty
p
es
.
h> and "types/
c
onstr
.
h"
from typedefs
commit
|
commitdiff
|
tree
2015-09-08
David van d
e
r Spoel
Moved function
s
operatin
g
on f
o
rcerec to separate header
.
commit
|
commitdiff
|
tree
2015-09-04
Rossen A
p
ostolo
v
C
o
nverte
d
esse
n
tialdynamic
s
m
odule to C++
.
commit
|
commitdiff
|
tree
2015-09-02
Béla Voß
Avoi
d
integer overf
l
o
w
in gmx_wh
a
m by
u
sing g
m
x_int64_t
.
commit
|
commitdiff
|
tree
2015-08-03
David van der S
p
oe
l
Mad
e
output f
r
o
m dumping neight
b
orlists
easier to read
.
commit
|
commitdiff
|
tree
2015-07-29
E
r
ik Lindahl
Moved anothe
r
bunch of mdli
b
utils to C+
+
commit
|
commitdiff
|
tree
2015-07-24
Teemu Mu
r
t
o
la
Rename tr
n
io
.
* to trrio
.
*
commit
|
commitdiff
|
tree
2015-05-12
Jochen H
u
b
O
p
enM
P
parallel
i
zation of
g_wha
m
commit
|
commitdiff
|
tree
2015-04-09
David van der
S
poel
Clarified c
o
mmen
t
s
for time-dependent e
l
ectric fie
l
ds
.
commit
|
commitdiff
|
tree
2015-04-08
David
v
an der Spoe
l
Fixed incorr
e
ct output
of gb
_
algorith
a
s sa_algorithm
.
commit
|
commitdiff
|
tree
2014-10-28
Da
v
id
v
an der Spoel
Eve
n
more
r
efreshing quot
e
s
.
commit
|
commitdiff
|
tree
2014-09-17
David van der Spoel
Merge relea
s
e-5-0
in
t
o mast
e
r
commit
|
commitdiff
|
tree
2014-08-30
David van der Spoel
Fixes iss
u
e
with v
s
iten and v
e
r
l
et buffers
.
commit
|
commitdiff
|
tree
2014-06-25
David van d
e
r Sp
o
el
Added check for
domain deco
m
posit
i
on and
s
hells
.
commit
|
commitdiff
|
tree
2014-06-22
David van der Spoel
Implemente
d
fa
t
al error for n
s
tca
l
cenergy
!
=1
wi
t
h shells
.
commit
|
commitdiff
|
tree
2014-06-11
D
avid van der Spoel
Fixes bug where -e and -dt
flags d
i
d not work anymore
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lu
n
d
b
o
rg
Fix bug w
r
iting
T
NG output from dump
.
commit
|
commitdiff
|
tree
2014-05-24
Mark
Ab
r
aha
m
Mo
v
e
tool
s
co
d
e
to where i
t
is
u
sed
commit
|
commitdiff
|
tree
2014-05-16
David van der S
p
oel
Fixe
s
a
c
o
mplic
a
ted bug
in g
_
anae
i
g
.
commit
|
commitdiff
|
tree
2014-02-10
David v
a
n der Spoel
M
o
ved condit
i
onal
cmake code for vmdio
.
commit
|
commitdiff
|
tree
2013-12-23
David van der Spoel
Fixed compi
l
at
i
on issue
d
ue to gcc4
.
8
commit
|
commitdiff
|
tree
2013-07-24
Da
v
id van der
S
poel
F
i
xes #1312 u
n
ini
t
ialized error
i
n g_ene
m
at
.
commit
|
commitdiff
|
tree
2013-05-16
David
v
an der Spoel
Fi
x
ed two co
m
p
ilat
i
on issues
.
commit
|
commitdiff
|
tree
2013-05-02
David v
a
n der Spoel
Fixes
#
123
8
g_hydorder doe
s
not c
a
ll set_pb
c
.
commit
|
commitdiff
|
tree
2013-03-07
David van der Spo
e
l
Fixes #1183
PBC bug in g_
m
indist
commit
|
commitdiff
|
tree
2013-02-13
David v
a
n
d
er S
p
oel
Pla
i
n
text quotes
.
commit
|
commitdiff
|
tree
2012-11-26
Da
v
id va
n
der Spoel
Fixe
s
#1035 NaN in g_cluster outpu
t
.
commit
|
commitdiff
|
tree
2012-11-20
David van der S
p
oel
F
ixes b
u
g in g
_
hbond
t
h
a
t
mak
e
s it produce fatal error
.
commit
|
commitdiff
|
tree
2012-10-21
D
a
vid
v
an der Spoel
Fixed Bug
#
5
93 a
b
o
u
t
mem
o
ry hole in trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
Dav
i
d van de
r
Spo
e
l
S
e
t
r
etu
r
n value to FALSE (0
)
in estimate_d
t
in lib
x
drf
.
c
commit
|
commitdiff
|
tree
2012-09-07
D
a
vid van der Spoel
Adapted
N
MR related
data to new pdb for
m
at
.
commit
|
commitdiff
|
tree
2012-09-04
David van
d
er
S
poel
Made
tutorial s
l
ightl
y
less confusing
.
commit
|
commitdiff
|
tree
2012-08-16
Davi
d
van der Spoe
l
Opti
o
nal c
o
mp
u
ta
t
i
o
n
o
f fluct
.
props in g_energy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
David van der Spoel
Fixe
d
bug in free energy calcul
a
tion fo
r
Morse potentials
commit
|
commitdiff
|
tree
2012-06-21
David
v
an der
S
poel
Fixes #961 - Shake repor
t
s wrong
e
rror
commit
|
commitdiff
|
tree
2012-03-17
David
van der Spoel
R
e
moved qhop files from t
h
is
b
ra
n
ch
.
commit
|
commitdiff
|
tree
2012-03-10
Da
v
id van der Spoel
Vibration spectra from velocity ACF or Normal mod
e
s
.
commit
|
commitdiff
|
tree
2012-01-31
David
v
a
n
d
er Spoel
Changed
o
r
der o
f
parameters i
n
top file
commit
|
commitdiff
|
tree
2012-01-25
Davi
d
va
n
der Spo
e
l
A
d
d
e
d two new bonded f
u
ncti
o
ns
.
commit
|
commitdiff
|
tree
2012-01-17
D
av
i
d
van der Spoel
Replace
s
tde
r
r
b
y
stdout in editconf terminal
o
utput
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
David van der Spoel
Intr
o
duced
fa
t
al error in grompp for incorrect use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spo
e
l
Commented ou
t
p
a
r
t
of this new program that was
n
ot
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der
Spoel
Fix
e
d documen
t
ation issue describe
d
i
n
r
e
dmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
D
avid va
n
de
r
Spoel
Fixed
d
ocumentation issu
e
described in redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
David
van der Spoel
Fixed compilatio
n
issues
commit
|
commitdiff
|
tree
2011-09-19
David van der Sp
o
el
R
e
solved gerrit issue h
t
tps://g
e
r
r
i
t
.
groma
c
s
.
org/#change,12
6
commit
|
commitdiff
|
tree
2011-09-13
Dav
i
d va
n
der
Sp
o
e
l
Ad
d
ed warning line
.
commit
|
commitdiff
|
tree
2011-05-23
D
avid van d
e
r
Sp
o
e
l
Re-i
m
plemen
t
ed
the fluctua
t
ion analysis,
b
ased o
n
Enthal
p
y
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
D
avi
d
van de
r
Spoe
l
Re-i
m
pl
e
men
t
ed t
h
e
f
l
uctua
t
io
n
an
a
lysis, base
d
on Ent
h
alpy
.
.
.
commit
|
commitdiff
|
tree
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