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OpenMP parallelization of g_wham
2015-05-12
J
o
c
hen Hub
O
p
en
M
P parallelizatio
n
o
f
g_wham
commit
|
commitdiff
|
tree
2015-04-09
Davi
d
van der Spoel
Cla
r
i
f
ied comme
n
t
s
for
t
ime-dependent
electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
Dav
i
d van der Spoel
Fixed incorre
c
t
ou
t
put of
gb_algorith as sa_algorithm
.
commit
|
commitdiff
|
tree
2014-10-28
Dav
i
d
van
d
er Spo
e
l
Ev
e
n mo
r
e refreshi
n
g
quotes
.
commit
|
commitdiff
|
tree
2014-09-22
Ma
r
k Abraham
M
o
re quotes
commit
|
commitdiff
|
tree
2014-09-22
Erik Lindahl
M
o
re q
u
otes
commit
|
commitdiff
|
tree
2014-09-19
Teem
u
Murtola
Add support for cum
u
lative histog
r
am
s
commit
|
commitdiff
|
tree
2014-09-17
Dav
i
d van de
r
Spoel
Merg
e
re
l
ea
s
e-5-0 into master
commit
|
commitdiff
|
tree
2014-08-30
Da
v
id van der
S
poel
Fixes issu
e
w
i
t
h vsiten
a
nd verlet buffers
.
commit
|
commitdiff
|
tree
2014-06-25
David
van der
Spoel
A
dded check for dom
a
i
n
de
c
ompositio
n
and
s
h
e
lls
.
commit
|
commitdiff
|
tree
2014-06-22
Davi
d
van
d
er Spoel
I
mplemented fatal error for
n
st
c
alcenergy!=1
w
ith shells
.
commit
|
commitdiff
|
tree
2014-06-13
Berk
Hess
Made sh
e
lls wo
r
k
w
ith the Ver
l
et sch
e
me
commit
|
commitdiff
|
tree
2014-06-12
Berk Hess
Made gmxcheck
-
r
msd work again with
f
orces
commit
|
commitdiff
|
tree
2014-06-12
Eri
k
Lindah
l
Mak
e
sur
e
genrestr uses
the disre_u
p
2
para
m
e
t
er
commit
|
commitdiff
|
tree
2014-06-12
Er
i
k Li
n
dahl
Rem
o
ved undocumented -map and -mdata options fr
o
m g_sham
.
commit
|
commitdiff
|
tree
2014-06-12
E
rik Lindah
l
Always write output fr
o
m
g
en
i
o
n
commit
|
commitdiff
|
tree
2014-06-11
David v
a
n d
e
r Spoel
Fixes b
u
g
where
-e
a
nd -dt flags d
i
d n
o
t work
a
nymore
.
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
M
ade repl
_
ex ti
m
e st
e
p
m
ore
r
eada
b
le
commit
|
commitdiff
|
tree
2014-06-07
T
eemu Murt
o
l
a
Impr
o
ve
(
S
election|Fi
l
eName)Optio
n
Ma
n
ager h
a
ndling
commit
|
commitdiff
|
tree
2014-06-07
Te
e
mu Murt
o
la
Repla
c
e
a
l
l comma
n
d
l
in
e
parsing with Opti
o
ns
commit
|
commitdiff
|
tree
2014-06-07
T
eemu Mur
t
ola
Move
r
esiduety
p
e handling to
i
t
s
own file
.
commit
|
commitdiff
|
tree
2014-06-07
Teemu Murtola
Rem
o
ve support for
"
old"
i
ndex file format
commit
|
commitdiff
|
tree
2014-05-31
Mag
n
us
Lundborg
F
i
x bug writing TN
G
output from
dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Bug fix
i
n
the TNG
l
ib
r
ary to improve readin
g
.
commit
|
commitdiff
|
tree
2014-05-24
Mark
Abraham
Move tools code to w
h
ere it is use
d
commit
|
commitdiff
|
tree
2014-05-18
Teemu Murtola
Move 3
d
view
.
*
to p
r
ograms/view
/
commit
|
commitdiff
|
tree
2014-05-16
David van der Spo
e
l
Fixes a
c
omplicated bug in
g
_anaeig
.
commit
|
commitdiff
|
tree
2014-03-17
Teemu Murtola
U
pda
t
e manual
analysi
s
sectio
n
commit
|
commitdiff
|
tree
2014-02-21
N
ina Fischer
Add
e
d new amber99sb-ildn-
b
sc0 force fiel
d
.
commit
|
commitdiff
|
tree
2014-02-10
Da
v
id
van
d
er Spo
e
l
Moved conditional
c
make c
o
de
for vm
d
io
.
commit
|
commitdiff
|
tree
2014-01-19
Mark Abraham
Cl
e
a
n up after gmxcpp
commit
|
commitdiff
|
tree
2013-12-23
Da
v
id van d
e
r Spo
e
l
Fixed c
o
mpilation issue due to gc
c
4
.
8
commit
|
commitdiff
|
tree
2013-07-24
David
van der
S
poe
l
Fixes
#
1312
u
ninitial
i
zed error in g_enemat
.
commit
|
commitdiff
|
tree
2013-05-16
D
a
v
i
d va
n
de
r
Spoel
Fixed t
w
o
compilat
i
on issues
.
commit
|
commitdiff
|
tree
2013-05-02
David
v
a
n
d
er Spoel
F
i
xes #1238 g_hydorder does not
c
all set_pbc
.
commit
|
commitdiff
|
tree
2013-03-07
D
avid van
der S
p
oel
F
ixes #1183 PBC bug in g_mindist
commit
|
commitdiff
|
tree
2013-02-13
David v
a
n der S
p
oel
Plain text quotes
.
commit
|
commitdiff
|
tree
2012-11-26
Davi
d
van der Spoel
Fixes
#
1035
N
a
N
in g
_
c
luster output
.
commit
|
commitdiff
|
tree
2012-11-20
David
van der Spoel
F
i
x
e
s bug in g
_
h
bond tha
t
makes it produce fatal error
.
commit
|
commitdiff
|
tree
2012-10-21
David van
d
er Spoel
F
i
xed Bug
#593 about m
e
m
ory h
o
l
e
in trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
David
v
an d
e
r
Spo
e
l
S
e
t retu
r
n value to FALSE (0)
i
n
es
t
i
m
ate_dt in libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-07
Da
v
id van der S
p
oel
A
d
apted
N
M
R re
l
a
te
d
dat
a
to
new pdb f
o
rmat
.
commit
|
commitdiff
|
tree
2012-09-04
Da
v
id van der
S
p
oel
M
ad
e
t
utorial slightly l
e
ss confusing
.
commit
|
commitdiff
|
tree
2012-08-16
D
avid van der Spoel
O
ptional co
m
putation o
f
f
l
u
c
t
.
props in g_energy
.
F
i
x
e
s
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
D
avi
d
van
d
e
r Spoel
Fi
x
ed
b
ug in fre
e
ene
r
gy calculati
o
n for Morse pote
n
t
i
als
commit
|
commitdiff
|
tree
2012-06-21
David
v
a
n
der S
p
o
e
l
Fixes #961 -
S
hake repo
r
ts wrong error
commit
|
commitdiff
|
tree
2012-03-17
Davi
d
van der Spoel
Removed
q
hop
f
iles f
r
om
this b
r
a
n
ch
.
commit
|
commitdiff
|
tree
2012-03-10
Davi
d
van de
r
Spoel
Vibrati
o
n sp
e
ctra from velo
c
ity ACF or Normal
mo
d
es
.
commit
|
commitdiff
|
tree
2012-01-31
Dav
i
d
v
a
n
d
e
r S
p
oel
Change
d
o
r
d
e
r of
p
a
r
a
meter
s
i
n t
o
p file
commit
|
commitdiff
|
tree
2012-01-25
David v
a
n der Spoel
Added two
n
ew
b
o
n
d
e
d
f
unctions
.
commit
|
commitdiff
|
tree
2012-01-17
David v
a
n der Spoe
l
Re
p
lace stderr by std
o
ut
in e
d
itconf terminal output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
Davi
d
v
a
n
d
er S
p
oel
Introd
u
c
ed f
a
tal er
r
or i
n
grompp for incorr
e
ct
u
s
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Davi
d
van
d
er Spoel
C
o
m
mented o
u
t part of this
n
ew program
t
hat
w
as not
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spoel
Fixed do
c
umentation issue
d
e
s
cribed in
redmi
n
e issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David
van der Spoel
Fixed do
c
umentation issue described in redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
D
a
v
id van der Spoel
Fixed
compilation issues
commit
|
commitdiff
|
tree
2011-09-19
David va
n
d
er
S
poel
Re
s
o
l
v
ed
gerrit
i
s
sue https://gerrit
.
g
rom
a
cs
.
org/#chan
g
e,126
commit
|
commitdiff
|
tree
2011-09-13
David
v
an der S
p
oel
Added warning line
.
commit
|
commitdiff
|
tree
2011-07-20
David van d
e
r Spoel
Merge branch 'release
-
4-5-pa
t
ches' of g
i
t@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
D
avid van der Spoe
l
Added initiali
z
ation o
f
ar
r
ays afte
r
srenew call
.
commit
|
commitdiff
|
tree
2011-07-20
David van der Spo
e
l
Added i
n
itia
l
ization of arra
y
s after
s
ren
e
w
call
.
commit
|
commitdiff
|
tree
2011-07-02
David van
d
er Spoel
Merge branch 'maste
r
' o
f
g
it@git
.
g
r
oma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2011-07-02
David
van der
Spoel
Compilati
o
n fixes in gmx_density
.
c and histogram
.
cpp
commit
|
commitdiff
|
tree
2011-07-01
David van de
r
Sp
o
e
l
Merge br
a
nch
'
r
e
l
ea
s
e-
4
-5-
p
at
c
hes' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Dav
i
d van
der Spoel
Merge branch '
r
elease-
4
-5-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van der Spoel
Added g_
d
os
tar
g
et
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
i
d v
a
n der Spoel
Further patc
h
es to fluct
u
ation code and density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
van der S
p
oel
Added
compu
t
ation of A and U
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
Upd
a
ted,
m
ade
d
efault tolerance fo
r
bisect
o
r more
s
tringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id van der Spoel
Fixed weigh
t
functions and add
e
d -dump op
t
ion (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
i
d
van der Spo
e
l
Updat
e
d
.
Fixed
c
omputation of
f
req
u
ency
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
U
p
dated the eqn for
c
o
m
puting D
e
lta
.
N
o
w get rough
l
y
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der S
p
oel
Multiplied the
D
oS b
y
th
e
tim
e
s
t
ep (between
f
rames)
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
der
S
poel
Updated
.
No
w
computes dif
f
us
i
o
n
f
rom the VAC
F
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
der Spoe
l
Fixed
x
-axis to be in
r
ec
i
procal cm
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van de
r
Spoel
Further upd
a
tes
.
St
i
ll not perfect
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id van
d
er Spoel
Added
stuff to compu
t
e cP and S
.
Not comple
t
e
y
et
.
commit
|
commitdiff
|
tree
2011-05-31
D
avid v
a
n der Spoel
Updated to
c
o
m
pute the fluidicity
.
A
dd
e
d refs
f
or citation
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
d
e
r
Spoel
Up
d
at
e
d
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der Spoel
New
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
F
urther patche
s
to
fluctuation
c
ode an
d
d
ensity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoe
l
M
erg
e
branch
'
master' o
f
git@git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2011-05-31
David van der
Spoe
l
Added q
u
ote
.
commit
|
commitdiff
|
tree
2011-05-31
David
v
a
n der Spo
e
l
Further p
a
tches to fluctuati
o
n code and density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der
Spoel
A
d
d
ed
quote
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
Mer
g
e branch 'releas
e
-4
-
5-
p
atche
s
' of git@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
D
a
vi
d
van d
e
r Spoe
l
Merge branch 're
l
ea
s
e-4-5-
p
atches'
of git@git
.
g
roma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van der Spoel
Re-i
m
plemented
the
fl
u
ctuation a
n
alysis, based
on
Enthal
p
y
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van der Spoel
Re-implemented
the f
l
u
ctuation a
n
alysis, b
a
sed on Entha
l
py
.
.
.
commit
|
commitdiff
|
tree
2011-05-07
Dav
i
d van der
Spoel
Added computatio
n
of A a
n
d U
.
commit
|
commitdiff
|
tree
2011-05-06
David v
a
n der Spoe
l
Updated, made
default tolerance f
o
r b
i
sector mo
r
e stringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
D
a
vid van der Spoel
Fixed w
e
i
ght fun
c
tions and added
-
d
u
mp
o
pt
i
o
n
(hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
David van der Spoel
Updated
.
Fixed co
m
putation
o
f frequency
.
commit
|
commitdiff
|
tree
2011-05-06
D
a
vi
d
v
an der
Spoel
Merge branch '
r
ele
a
s
e
-4-5-pat
c
hes' of git
@
git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-02
David va
n
der
S
poel
Updated the eqn for com
p
ut
i
ng
D
e
l
t
a
.
Now get roughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-01
D
avid v
a
n der Sp
o
el
Multiplied th
e
DoS by the tim
e
st
e
p
(between
f
r
a
mes)
.
commit
|
commitdiff
|
tree
2011-04-26
David van der
Spoel
Upd
a
ted
.
No
w
computes diffusion f
r
o
m
the
V
A
C
F
.
commit
|
commitdiff
|
tree
2011-04-23
Davi
d
van der Spoel
Fixed x-axis to be in reci
p
r
oca
l
cm
.
commit
|
commitdiff
|
tree
2011-04-23
Davi
d
van
d
e
r Spoel
Further updates
.
Still not
p
erfect
.
commit
|
commitdiff
|
tree
2011-04-22
D
a
vid van der Spoel
Added
stuff
to
c
ompute cP and
S
.
Not co
m
plete
y
et
.
commit
|
commitdiff
|
tree
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