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Removed unnecessary static declarations for command-line parsing
2017-07-19
David van der Spoel
Remov
e
d unnecessary
sta
t
ic de
c
larations for
c
ommand
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fi
x
ed
test-
o
rder
dependen
c
y in gmxpr
e
process t
e
sts
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid van der Spoel
Fix non-rep
r
oducabili
t
y of clus
t
s
i
ze tests
.
commit
|
commitdiff
|
tree
2017-05-01
David
v
an der
S
poel
Xpm
test
f
or gmx
c
lustsi
z
e
commit
|
commitdiff
|
tree
2017-03-12
David v
a
n
der S
p
o
e
l
Added te
s
ts for
g
mx c
l
ust
s
i
ze
.
commit
|
commitdiff
|
tree
2017-03-04
David v
a
n der Spoel
R
em
o
ves
r
ogue print
i
ng to xv
g
file in gmx m
i
ndist
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoel
F
i
xes
b
ug in gmx so
l
vate with
-
s
h
e
ll that yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
D
a
v
id
v
a
n der Spoel
Fixes SEGV in gmx orde
r
.
commit
|
commitdiff
|
tree
2017-02-02
David
van der Spoel
Only print all dangling ato
m
s with grompp
-v
commit
|
commitdiff
|
tree
2017-01-23
David van der Spoel
Added reference for
d
ihedral f
u
nctio
n
i
n
OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der
S
poel
C
o
uple of new q
u
ote
s
commit
|
commitdiff
|
tree
2016-11-18
D
a
vid van der S
p
oel
Added first tes
t
s of bonded force functions
.
commit
|
commitdiff
|
tree
2016-10-14
D
a
v
i
d van der Spo
e
l
Fixes some m
e
mory leaks ass
o
c
iate
d
with
test
i
n
g
appli
e
d
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avid van der
S
p
o
e
l
Modu
l
arize electric
f
ield han
d
ling
commit
|
commitdiff
|
tree
2016-09-27
David v
a
n der Spo
e
l
Fixed scr
i
pt
x
plor2gm
x
.
pl to work with GMX
D
ATA
commit
|
commitdiff
|
tree
2016-09-26
D
avid va
n
der
Spoel
F
ixes issue with Re
l
ease build i
n
correlation func
t
ions
.
commit
|
commitdiff
|
tree
2016-09-20
David
van
d
er Spoel
Made corr
e
lation f
u
nction rout
i
ne use std::ve
c
t
o
r
commit
|
commitdiff
|
tree
2016-09-05
David van der
Spoel
Merge "
M
erge branch rele
a
se-2
0
16"
commit
|
commitdiff
|
tree
2016-08-24
Davi
d
v
an der Spoel
Added documentati
o
n f
o
r shell
p
ote
n
tials
.
commit
|
commitdiff
|
tree
2016-08-03
D
avid
v
an der
S
poel
Three new
q
uotes
.
commit
|
commitdiff
|
tree
2016-07-31
D
a
vi
d
van
d
e
r Spoel
Merg
e
"Merge branch
release-5-1
into release
-
2
0
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David
van der
S
p
o
el
Fi
x
es
inc
o
rr
e
ct charges
i
n
OPLS/A
A
-L for HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
David van d
e
r Spoel
Merge "Merge br
a
nch releas
e
-5
-
1 into r
e
lease-20
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Dav
i
d
v
an de
r
Spo
e
l
I
ntr
o
duce fata
l
er
r
o
r
for
t
oo few frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David
v
an
d
er
Spoel
Made gmx
dos work again
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
vid van de
r
Spoe
l
R
e
moved spurious r_ij in force fo
r
Morse
potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Davi
d
v
an der Spoel
Modify lm
f
it lib
r
a
r
y
t
o avoid clashes
w
ith other versions
.
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d
v
an der S
p
oel
R
e
move
d
srenew
that was
making array
s
malle
r
i
n
corr
e
ctly
.
commit
|
commitdiff
|
tree
2016-03-18
D
avid van der
Spoel
Fixed
division by zero in polariz
e
.
commit
|
commitdiff
|
tree
2016-01-20
David v
a
n
der Spoel
Coup
l
e of n
e
w quotes
commit
|
commitdiff
|
tree
2016-01-07
D
a
vid van der S
p
o
el
Made normal mod
e
s work
with
shells and
vsite
s
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
Fi
x
es newly introduced bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David
v
an de
r
Sp
o
el
Moved domdec
struct
u
res
o
u
t of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der
Spoel
Cle
a
nups
i
n l
e
gac
y
header/ty
p
es/commre
c
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
avid van de
r
S
poel
Mer
g
ed
l
egacyhead
e
r
s
/t
y
pe
s
/q
m
m
m
rec
.
h into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
avid
v
an der Spoel
Mer
g
ed genborn
.
h
from legacyheaders/types
into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
va
n
der Spo
e
l
Moved
leg
a
cyhead
e
rs/types/group
.
h to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Merged legac
y
heade
r
s/typ
e
s/ns
.
h
and nblist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid van der Spoel
Combine enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
M
e
r
g
ed
l
egacyhead
e
rs/nrnb
.
h
and types/nr
n
b
.
h
t
o gmxl
i
b
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spo
e
l
Moved
mdato
m
.
h fr
o
m legacyh
e
ader/types
to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der Spoe
l
M
oved legacyheaders/ty
p
es/e
n
e
rgy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van
d
e
r
S
poel
Merge
d
lega
c
yh
e
a
d
ers/types/inputre
c
.
h i
n
t
o
md
t
yp
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van der
S
poel
Me
r
ged legacyheaders/types/st
a
te
.
h
into mdtypes/
s
tate
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van
de
r
Spoel
Replac
e
d a
t
om_
i
d by int
.
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Moved genborn
.
h t
o
mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
M
o
ved txtdump
.
*
to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der Sp
o
el
Moved co
p
yrite
.
* t
o
fil
e
io
from gmxlib and legacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
Da
v
id van der S
p
oel
Moved inputrec
.
*
f
r
o
m
g
mxl
i
b a
n
d
legacyheaders to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Sp
o
el
Removed legacyhead
e
r
s
/type
d
efs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van de
r
Spoe
l
Moved
d
f_history
u
tilit
y
routi
n
es
fro
m
typ
e
defs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
a
vid van der
S
poel
Replaced NOTSET from typedefs
.
h by loca
l
solutions
.
commit
|
commitdiff
|
tree
2015-10-23
David
van der Sp
o
el
Removed energyh
i
story
c
ode f
r
om typedefs t
o
a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
Moved pbc/cut-
o
ff related utilities from type
d
efs
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
D
a
vid van
d
er Spoe
l
Freed memor
y
in leg
a
cy st
a
tistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David v
a
n der Spoel
Re
m
oved simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n der Sp
o
el
Removed simple
.
h fro
m
nb_kernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David
v
an
d
er Spoel
R
e
moved
simple
.
h
from nb_k
e
rnel_
s
se2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed s
i
mple
.
h from nb_kern
e
l_c an
d
nb
_
kernel_sparc64
_
hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed include s
i
mple
.
h f
r
om nb_kernel
_
avx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
Dav
i
d
v
a
n
der Spoel
R
emove
d
simple
.
h from
n
b
_
k
ern
e
l_avx_2
5
6
_
XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remove
d
ou
t
put_env_t,
n
ow
us
i
ng
gmx_output_e
n
v_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der Spoel
Removed types/n
r
nb
.
h
from typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
Davi
d
van der S
p
oel
Removed types/nblist
.
h
and types/nsgrid
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
a
v
id v
a
n
d
er Spo
e
l
Removed ty
p
es/mdatom
.
h from typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
Remo
v
ed types/i
n
putrec
.
h
from ty
p
e
defs
.
h and re
l
e
ted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
D
a
vid van
d
e
r Spoel
Fixe
s
bug
i
n
t
he computation of
C
oeff
i
cient
o
f Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
a
vid
v
a
n
der Spoel
Rem
o
ved types/forcerec
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David va
n
d
e
r Spo
e
l
Re
m
oved include of types/ifu
n
c
.
h from
t
ypede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
id van
d
er S
p
oel
R
e
moved fou
r
in
c
l
udes
f
rom lega
c
y
h
eaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David va
n
der Spo
e
l
Removed lega
c
y
h
eaders/types/commrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van der Sp
o
e
l
Mov
e
d
c
o
n
tent from mdrun
.
h t
o
sepa
r
ate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David va
n
der Spoel
R
e
moved
<
sys/types
.
h> and
"
types/c
o
nstr
.
h" from typede
f
s
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoe
l
Removed fileio/trx
.
h f
r
om typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van d
e
r
Spoel
Moved functions
operati
n
g on for
c
erec
t
o
separate
h
eader
.
commit
|
commitdiff
|
tree
2015-08-28
David van de
r
Spoel
Added energy
(edr) fil
e
t
ype to Opti
o
ns head
e
rs
.
commit
|
commitdiff
|
tree
2015-08-28
Dav
i
d van de
r
Spoel
Added
a
dditi
o
nal construct
o
r to StringStream
c
lass
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David va
n
der Spoel
Made out
p
ut fr
o
m
d
umping ne
i
ghtborli
s
ts easier t
o
rea
d
.
commit
|
commitdiff
|
tree
2015-07-31
D
a
vid van
de
r
S
poel
C
h
ange
in
i
tial
pa
r
ame
t
ers for testing expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van de
r
Spoel
Code for
c
h
ecking xvg
fi
l
es in
tes
t
utils
.
commit
|
commitdiff
|
tree
2015-04-17
D
a
vid van
d
er Spoel
U
pdated expone
n
t
i
al fitting to make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
Dav
i
d van d
e
r Spoel
C
l
ari
f
i
ed comments
f
or time-depende
n
t ele
c
tri
c
fiel
d
s
.
commit
|
commitdiff
|
tree
2015-04-08
David van der
Spoel
Fixe
d
inc
o
rrect
out
p
ut of gb_algor
i
th
a
s sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van
d
er
Spoel
Updated documentation for electric fiel
d
s
.
commit
|
commitdiff
|
tree
2014-12-13
David v
a
n
der Sp
o
el
Four
new quotes
f
rom around the world
.
commit
|
commitdiff
|
tree
2014-11-28
Da
v
i
d
van d
e
r
Spoel
Fixes recently introduced bug
in gmx analyze
.
commit
|
commitdiff
|
tree
2014-11-24
Dav
i
d van der Spoel
A
dde
d
wa
r
ning
s
for ewald-geometry and s
u
rface-ep
s
ilon
commit
|
commitdiff
|
tree
2014-10-28
David van der
Spo
e
l
Even
m
ore refreshing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
David
van der Spoel
Reorganizing
a
nalysi
s
of c
o
r
r
elat
i
o
n
f
un
c
tions
.
commit
|
commitdiff
|
tree
2014-09-23
D
avid van de
r
Spoel
Fi
x
e
s potential bug in
n
eighborse
a
rching
.
commit
|
commitdiff
|
tree
2014-09-17
David
van der Spoe
l
Merge relea
s
e-5-0
i
nto master
commit
|
commitdiff
|
tree
2014-09-10
David van d
e
r
Spoe
l
R
emov
e
.
tpa,
.
tpb,
.
tpx,
.
trj files
.
Part of #1500
.
commit
|
commitdiff
|
tree
2014-08-30
D
avid van der Spoe
l
Fixes i
s
sue
with vsiten and verle
t
bu
f
fe
r
s
.
commit
|
commitdiff
|
tree
2014-07-05
David
v
an d
e
r
S
p
oel
Fixed inc
o
nsi
s
tency in block
a
handling
.
commit
|
commitdiff
|
tree
2014-06-29
Davi
d
van d
e
r Spo
e
l
Fi
x
es #153
2
,
SEGV in g_
c
ur
r
ent
.
commit
|
commitdiff
|
tree
2014-06-25
David
van der
Sp
o
el
Added che
c
k f
o
r domai
n
d
e
compos
i
tion a
n
d sh
e
lls
.
commit
|
commitdiff
|
tree
2014-06-24
D
a
vid van
der Spoel
Added check i
n
grompp
for shells and i
n
putrec issues
.
commit
|
commitdiff
|
tree
2014-06-22
David v
a
n der Spoe
l
Implemented fata
l
error
f
or nstcalcenergy!=1 with
s
hells
.
commit
|
commitdiff
|
tree
2014-06-13
David van de
r
Spoel
Fix memory-usage error in
g_chi
commit
|
commitdiff
|
tree
2014-06-11
Dav
i
d van der Spoel
Fixes bug where -e and
-
dt flags
did
n
o
t
work a
n
ymore
.
commit
|
commitdiff
|
tree
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