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Fix erroneous PME GPU "step" namings
2017-10-30
D
a
vid van der Spo
e
l
Fixed mdp o
u
tput
f
rom
e
lec
t
ric field code
.
commit
|
commitdiff
|
tree
2017-10-30
David van der
Sp
o
e
l
Added opt
i
on -wate
r
t
i
ps3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David v
a
n der Spoel
S
plit off the
NMR relate
d
a
nalyses from gm
x
energ
y
.
commit
|
commitdiff
|
tree
2017-10-17
D
a
v
i
d van
der Spoel
Fixed missi
n
g
en
t
ries in nrnb
a
rrays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoe
l
Worked ar
o
u
n
d missing Open
M
P
impl
e
men
t
ation in orires
.
commit
|
commitdiff
|
tree
2017-08-03
Dav
i
d
van de
r
Spoel
Fixed bug in
gmx disres
i
ndexi
n
g ar
r
ays
.
commit
|
commitdiff
|
tree
2017-08-02
David
v
an der Spoel
Worked around missi
n
g
Op
e
nMP i
m
p
le
m
ent
a
ti
o
n in orires
.
commit
|
commitdiff
|
tree
2017-07-28
Da
v
i
d
van
d
er S
p
o
e
l
Added
unit-test for o
r
ientat
i
on restr
a
in
t
s
o
utput
.
commit
|
commitdiff
|
tree
2017-07-19
D
avid van
d
er Spoel
R
e
moved unneces
s
ary static declarati
o
ns for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van
d
e
r
S
poel
Fi
x
e
d
test
-
or
d
er dependency
in gmxprepro
c
ess test
s
.
commit
|
commitdiff
|
tree
2017-07-19
D
avid
van d
e
r Sp
o
el
Fi
x
non-reprod
u
c
a
bility
o
f clustsize
t
e
sts
.
commit
|
commitdiff
|
tree
2017-05-01
David van der
Spoel
Xpm
test for
g
mx cl
u
stsize
commit
|
commitdiff
|
tree
2017-03-12
David van der
Spoel
Added test
s
f
o
r
gmx clustsi
z
e
.
commit
|
commitdiff
|
tree
2017-03-04
David van der Spoel
Removes
rogue prin
t
ing to xvg fi
l
e
in gmx
m
indist
commit
|
commitdiff
|
tree
2017-02-27
David van
de
r
S
p
oe
l
Fi
x
es bug in gmx so
l
vate
w
ith -shell
t
hat
y
ie
l
ded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David
v
an d
e
r
Spo
e
l
Fixes SEGV in
g
mx o
r
de
r
.
commit
|
commitdiff
|
tree
2017-02-02
David
van der Spoel
Only print al
l
dangling atoms with
grompp -
v
commit
|
commitdiff
|
tree
2017-01-23
D
a
vid van de
r
Spoel
A
d
ded referen
c
e for
d
ihedr
a
l function in OP
L
S
.
commit
|
commitdiff
|
tree
2016-12-07
David
v
a
n
d
e
r Spoel
Couple of new qu
o
tes
commit
|
commitdiff
|
tree
2016-11-18
Davi
d
van der Sp
o
el
A
d
ded first tes
t
s o
f
bond
e
d force functions
.
commit
|
commitdiff
|
tree
2016-10-14
D
avid van der Spoel
Fixes some memory lea
k
s
asso
c
i
ated with testing a
p
plied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avid van d
e
r Spoel
Modularize electric field handling
commit
|
commitdiff
|
tree
2016-09-27
David van d
e
r Spoel
Fixe
d
script
xpl
o
r2
g
mx
.
pl
to work
with GMXDA
T
A
commit
|
commitdiff
|
tree
2016-09-26
David van der Spoel
Fixes
issue
w
i
t
h
Re
l
ease bui
l
d in correlation func
t
i
o
n
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van d
e
r Spoel
Made
c
o
r
r
e
latio
n
fu
n
cti
o
n rout
i
ne us
e
std::vector
commit
|
commitdiff
|
tree
2016-09-05
David van d
e
r Spoel
Merge "Merge branch re
l
eas
e
-2
0
16"
commit
|
commitdiff
|
tree
2016-08-24
David van
d
er Spoel
A
dded doc
u
men
t
a
ti
o
n for
s
h
e
ll potentials
.
commit
|
commitdiff
|
tree
2016-08-03
Davi
d
van der Spoel
T
h
ree new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David van der Spoe
l
M
e
rg
e
"Merge branch
release-5-1
i
nto
r
e
l
ease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van der Sp
o
el
Fixes incorre
c
t c
h
arges i
n
OPLS/AA-L fo
r
HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van der
Spoel
Merge
"Merge branch release-5-1 into re
l
ease-2
0
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Dav
i
d v
a
n der
S
poel
Int
r
o
duce fatal e
r
ror for
too fe
w
frames i
n
gmx do
s
.
commit
|
commitdiff
|
tree
2016-06-27
D
avid van d
e
r Spoel
M
a
de gmx dos
w
ork
a
gain
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
vi
d
van der Spoel
Removed spurious r_ij in forc
e
for Mo
r
se potentia
l
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Dav
i
d van der Spo
e
l
Modify lmfit lib
r
ary to
a
void clashes wit
h
othe
r
ve
r
sions
.
commit
|
commitdiff
|
tree
2016-03-23
Da
v
id van
d
er Spoel
R
emo
v
e
d srenew t
h
a
t was
maki
n
g array
s
mal
l
e
r
in
c
orrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David van
der Spoel
Fixed divisi
o
n by
z
ero in
polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van der
S
p
o
e
l
Couple o
f
new qu
o
tes
commit
|
commitdiff
|
tree
2016-01-07
David va
n
der Spoel
Made norma
l
m
odes wo
r
k
w
ith
shells and vsites
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
Fixes newly introduce
d
bug in ma
k
e_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
D
avi
d
van der Spoel
Moved domdec
structures o
u
t of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David
van
d
er Spo
e
l
Clea
n
ups in
l
egacyheader/types/com
m
rec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van der Spoel
Merged
lega
c
yheaders/types
/
qmmm
r
ec
.
h i
n
to mdlib/qmm
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vid van
d
er Spoel
Merged g
e
n
b
o
rn
.
h from legac
y
headers/types
int
o
md
l
ib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
Spoel
Moved legacyheaders/ty
p
es/grou
p
.
h
to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r Spoel
Me
r
g
e
d legacyh
e
a
ders/types/ns
.
h a
n
d nblist
.
h to mdt
y
p
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Combine enums
.
h and na
m
es*
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Merged l
e
gacyheaders/nr
n
b
.
h and types/
n
rnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Moved mdatom
.
h from legacyheader/t
y
pes
t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van der Sp
o
el
Moved legacyheader
s
/types/energy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van
der Spoel
Me
r
g
e
d legacyheader
s
/ty
p
es
/
inpu
t
rec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Sp
o
el
Merged legacyheade
r
s
/
types
/
state
.
h into mdty
p
es/
s
tate
.
h
commit
|
commitdiff
|
tree
2015-11-13
David
van
d
er Spoel
Repl
a
c
ed a
t
om_
i
d
by int
.
commit
|
commitdiff
|
tree
2015-11-13
Davi
d
van der
S
p
oel
Moved
ge
n
born
.
h
t
o
mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Moved txtdump
.
* t
o
fi
l
eio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der
Spoel
Moved copyr
i
te
.
* to fileio from gmxlib a
n
d
legacyhead
e
r
s
.
commit
|
commitdiff
|
tree
2015-11-11
Davi
d
v
a
n
der Spoe
l
M
oved inp
u
tr
e
c
.
* fr
o
m gmxlib and legacyheader
s
t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van
der Spoel
Removed legacyhea
d
ers/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van
der Spoel
Moved df_history u
t
il
i
ty
routines
f
rom typed
e
fs
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Dav
i
d
v
an der
S
p
oel
Repl
a
ced NOTSET
f
rom
t
ype
d
efs
.
h by loc
a
l
solutions
.
commit
|
commitdiff
|
tree
2015-10-23
David van der Sp
o
el
Removed en
e
rgyhi
s
t
o
r
y
c
ode fro
m
typedef
s
to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
Da
v
id van
der Sp
o
e
l
M
oved pbc/
c
ut-off related utilities from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David
van der Spoel
Fr
e
ed
memory in legacy statis
t
i
c
s
r
o
utines
.
commit
|
commitdiff
|
tree
2015-10-03
D
a
vid van der
S
po
e
l
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
D
a
v
id van der
S
p
o
e
l
R
e
m
oved si
m
pl
e
.
h from nb_k
e
rnel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
emov
e
d
s
im
p
l
e
.
h from
n
b_kernel
_
sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
i
d
van der Spoel
Removed s
i
mple
.
h
from nb_kern
e
l_
c
and nb_kernel_sp
a
r
c
64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
Removed i
n
clu
d
e s
i
mp
l
e
.
h fr
o
m n
b
_kernel_avx_128_
f
ma_XX
commit
|
commitdiff
|
tree
2015-10-02
David
van
d
er Spoel
Removed simpl
e
.
h
from nb_k
e
rnel
_
avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n der
S
p
oel
Removed output_env_t, now us
i
ng
gm
x
_output_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der Spoel
Remov
e
d typ
e
s/nrn
b
.
h fro
m
typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van de
r
Sp
o
el
Removed types/nbli
s
t
.
h a
n
d types/n
s
grid
.
h from typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David v
a
n der S
p
oel
R
e
mo
v
ed
t
ypes/mdato
m
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David va
n
der Spo
e
l
Remove
d
types/in
p
utre
c
.
h from ty
p
e
defs
.
h a
n
d releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoe
l
F
i
xes bu
g
i
n
the
co
m
putat
i
on of Coeffi
c
ient of The
r
m
a
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der Spoel
Removed types/forcerec
.
h from t
y
ped
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der Spoel
Re
m
oved in
c
lude of
typ
e
s/ifunc
.
h
from ty
p
ede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Davi
d
van d
e
r Spoel
Removed fo
u
r includes from legacyhe
a
ders/t
y
pede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
i
d van
d
er Spoel
R
emoved legac
y
head
e
r
s
/types/commrec_fwd
.
h from typ
e
d
e
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
an der Spoel
Moved content from m
d
r
u
n
.
h to sep
a
rate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David
v
an
der Spoel
Re
m
oved
<sys/types
.
h> and "types/c
o
nstr
.
h" from t
y
pedefs
commit
|
commitdiff
|
tree
2015-09-09
David v
a
n d
e
r Spoel
Removed
f
ileio/trx
.
h from t
y
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
van d
e
r Spoel
Moved fun
c
tions
o
p
erati
n
g on
f
orce
r
e
c
t
o
separate
h
eader
.
commit
|
commitdiff
|
tree
2015-08-28
David v
a
n der Spoel
Added e
n
ergy (edr)
f
il
e
type to O
p
t
ion
s
headers
.
commit
|
commitdiff
|
tree
2015-08-28
David
v
an der
S
poel
A
d
ded
a
ddit
i
on
a
l con
s
tr
u
ctor to
S
tringStream
class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
Dav
i
d van
der Spoe
l
M
a
de
o
utput from
dumping neigh
t
b
orlist
s
easier to read
.
commit
|
commitdiff
|
tree
2015-07-31
Davi
d
van der
S
p
oel
Chan
g
e
i
nitial par
a
meters for tes
t
ing expfit
.
commit
|
commitdiff
|
tree
2015-07-29
D
avid
v
an der Spoel
Cod
e
f
or c
h
ecking xvg files
in testutils
.
commit
|
commitdiff
|
tree
2015-04-17
D
a
vid van
d
er Sp
o
el
Updated
exponential
f
itt
i
ng to make it
r
obust
.
commit
|
commitdiff
|
tree
2015-04-09
D
avid
van der Spoel
Clarifi
e
d comme
n
t
s
f
or time-depende
n
t
e
l
e
c
t
ric
fi
e
lds
.
commit
|
commitdiff
|
tree
2015-04-08
David van der Spoel
Fixed incorr
e
ct output of gb_algorith as sa
_
algori
t
hm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der Spoel
Upd
a
ted documentation for electric
fie
l
ds
.
commit
|
commitdiff
|
tree
2014-12-13
David van der Sp
o
el
Four new
q
uotes from aro
u
n
d the world
.
commit
|
commitdiff
|
tree
2014-11-28
D
a
vid van der Spoel
Fixes r
e
c
ently introduced b
u
g in gmx
a
nalyze
.
commit
|
commitdiff
|
tree
2014-11-24
D
a
v
i
d
van
d
e
r
S
p
oel
Added
warning
s
for ewald-geometry an
d
surface-epsilon
commit
|
commitdiff
|
tree
2014-10-28
D
avi
d
van d
e
r
Spoel
E
v
e
n
more refreshing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
D
a
vid van de
r
Spoel
Reorganizing analysis of c
o
rrelation fun
c
tions
.
commit
|
commitdiff
|
tree
2014-09-23
David van der Sp
o
el
Fixes
p
otential bug in neighborsearch
i
n
g
.
commit
|
commitdiff
|
tree
2014-09-17
David van der Spoe
l
Merge
r
elease-5-0 in
t
o master
commit
|
commitdiff
|
tree
2014-09-10
David van der Spo
e
l
Remove
.
tpa,
.
tpb,
.
tpx,
.
trj files
.
P
a
rt of
#
15
0
0
.
commit
|
commitdiff
|
tree
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