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Fixed bug in gmx disres indexing arrays.
2017-08-03
David
v
an der Spo
e
l
Fixed bug in gmx disres
i
ndexi
n
g
a
rra
y
s
.
commit
|
commitdiff
|
tree
2017-08-02
Dav
i
d
van der Spoel
Work
e
d aro
u
nd missing OpenMP
i
mpleme
n
tation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
D
avid van
d
er Spoel
Added un
i
t-t
e
s
t
for ori
e
ntation r
e
straints
out
p
ut
.
commit
|
commitdiff
|
tree
2017-07-19
David van der
S
poel
Re
m
ove
d
unn
e
cessar
y
s
tatic declarations fo
r
co
m
m
a
nd
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der
S
p
o
el
F
ixed test
-
order d
e
pendency in gmxpreprocess
tests
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fix non-reproducability of clustsi
z
e tests
.
commit
|
commitdiff
|
tree
2017-05-01
David van
der Spoel
X
p
m
test for gmx
clus
t
s
ize
commit
|
commitdiff
|
tree
2017-03-12
David
v
an der Spoel
A
dded tests for gmx clustsi
z
e
.
commit
|
commitdiff
|
tree
2017-03-04
David van
de
r
Spoel
Remov
e
s ro
g
ue printing t
o
xvg file in
gmx mindi
s
t
commit
|
commitdiff
|
tree
2017-02-27
David van
de
r
Spoel
Fixes bug in gmx
solvate with -sh
e
ll
t
hat y
i
e
l
ded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Spoel
F
i
xes SEGV in
gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
Davi
d
van der Sp
o
el
Only print
all
dangling atoms
wit
h
grom
p
p -
v
commit
|
commitdiff
|
tree
2017-01-23
Dav
i
d v
a
n
der Spoel
A
dded referenc
e
fo
r
dihedral function in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der
Sp
o
el
Couple of n
e
w quotes
commit
|
commitdiff
|
tree
2016-11-18
D
avid va
n
d
e
r
S
p
oel
Adde
d
first te
s
ts of bonded f
o
r
ce
fu
n
ct
i
o
ns
.
commit
|
commitdiff
|
tree
2016-10-14
D
a
vid v
a
n der
S
poe
l
Fixes
some memory leaks associated with testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
a
v
id va
n
der
Sp
o
e
l
Modulari
z
e electric fi
e
ld handlin
g
commit
|
commitdiff
|
tree
2016-09-27
D
avid van der Spoel
Fixed script xplor2gmx
.
p
l
to work with GMXDAT
A
commit
|
commitdiff
|
tree
2016-09-26
D
avid van der Spoel
Fixes issue w
i
th Release build i
n
co
r
r
e
l
a
t
i
o
n functions
.
commit
|
commitdiff
|
tree
2016-09-20
Da
v
id van der Spoel
Made cor
r
elation functio
n
routine use st
d
::vect
o
r
commit
|
commitdiff
|
tree
2016-09-05
Da
v
id van der S
p
oel
Merge "Merge branch
releas
e
-2016"
commit
|
commitdiff
|
tree
2016-08-24
D
avid van
der Spoel
Added documentation fo
r
s
hell p
o
ten
t
ials
.
commit
|
commitdiff
|
tree
2016-08-03
David va
n
der Spoel
Three
new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
D
a
v
id van
der Spoel
Merge
"Merge branch
r
e
leas
e
-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van d
e
r
S
poel
F
ixes incorrect
cha
r
ges in
O
PLS/AA-L for HISD an
d
HISE
commit
|
commitdiff
|
tree
2016-07-08
David van der
Spoel
Merge "Me
r
g
e
b
ranc
h
rel
e
ase
-
5-1 in
t
o
re
l
ea
s
e-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David
v
an der Spoel
Introduce
f
atal error for too few
frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made g
m
x do
s
work again
.
commit
|
commitdiff
|
tree
2016-06-22
David van
d
er
S
poel
Removed spu
r
ious
r_ij in
f
orc
e
for Mo
r
se poten
t
ial
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Da
v
i
d v
a
n
der Spoel
Modify lmfit libra
r
y to avoid
clashes with other versio
n
s
.
commit
|
commitdiff
|
tree
2016-03-23
D
a
vi
d
va
n
de
r
Spoel
R
e
moved srenew that was m
a
king ar
r
ay smaller incorr
e
ctly
.
commit
|
commitdiff
|
tree
2016-03-18
David van
der
S
poel
Fixed di
v
i
s
i
o
n by zer
o
i
n
polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Sp
o
el
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
D
a
vid
van der Spoel
Made normal modes work with s
h
ell
s
a
n
d vsite
s
commit
|
commitdiff
|
tree
2015-11-24
Da
v
id va
n
der Sp
o
el
Fixes
ne
w
ly introd
u
ced
bug
i
n
make_nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
D
a
vid
van der
S
p
oel
Moved domdec structures out
of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Davi
d
van der Spoel
Cle
a
nups in legacyheader/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged legacyheader
s
/type
s
/qmmmrec
.
h into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van
d
e
r Spoel
Merged genborn
.
h f
r
om legacyhe
a
ders/typ
e
s int
o
mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Move
d
legacyhea
d
ers/types/group
.
h to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id
van
d
er S
p
oel
Merge
d
legacyhea
d
ers/types/ns
.
h and nb
l
ist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Combine enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der
Spoel
M
e
r
ged l
e
g
a
cyheade
r
s
/nrnb
.
h
and type
s
/nrnb
.
h
t
o gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David v
a
n
der S
p
oel
Mov
e
d md
a
tom
.
h
f
rom le
g
a
cyheader/types to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der
S
p
o
e
l
Moved lega
c
y
h
e
aders/types/energy
.
h to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-15
David
v
an der Spoel
Merged legacyheaders/types/inputrec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
v
an der
S
p
oel
Merged
l
e
g
acyheaders/ty
p
e
s/st
a
te
.
h int
o
mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
R
ep
l
ace
d
atom_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
David
v
an der Spoel
Mo
v
ed gen
b
orn
.
h to m
d
li
b
commit
|
commitdiff
|
tree
2015-11-12
D
a
vid van der S
p
o
e
l
Moved txtdump
.
* t
o
fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Mo
v
ed co
p
yrite
.
* to file
i
o
from gmxli
b
a
nd legacyhe
a
ders
.
commit
|
commitdiff
|
tree
2015-11-11
Da
v
i
d
van
d
er Spoe
l
Moved inputrec
.
* fr
o
m gm
x
lib and leg
a
cyhead
e
rs to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-10
Da
v
id van der Spo
e
l
Removed legacyheaders/typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-11-03
D
a
vid van der Spo
e
l
Move
d
d
f
_
history util
i
ty routine
s
f
r
om typede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Da
v
i
d
van der S
p
oel
Replace
d
NOTSET
fro
m
t
y
pedefs
.
h b
y
local so
l
utions
.
commit
|
commitdiff
|
tree
2015-10-23
David
v
an
d
er Spoel
Removed energyhistory code
f
r
om typedefs to
a
separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
Moved
p
bc/
c
ut-of
f
relate
d
utilities
f
rom
typedefs
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David
van der
Spoel
F
reed mem
o
ry in le
g
acy s
t
atistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David van de
r
Spoel
Removed simpl
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der S
p
oel
Rem
o
ved simple
.
h from n
b
_
k
ernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
d
e
r Spo
e
l
Removed
s
i
mpl
e
.
h from nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remov
e
d simple
.
h from nb
_
kernel_c and nb_ke
r
n
e
l_sp
a
rc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n der S
p
o
e
l
R
e
moved
include simple
.
h from
n
b_kern
e
l_
a
vx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
Dav
i
d van
der Spoel
Rem
o
ved
s
imple
.
h from nb
_
kernel_
a
vx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
David
van der Sp
o
el
Remo
v
ed
o
u
tpu
t
_env_t, now using
g
m
x
_output_env_t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van
d
er
S
po
e
l
Removed ty
p
es/nrnb
.
h fr
o
m
t
yped
e
fs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d van der
Spoel
Remove
d
types/n
b
lis
t
.
h and type
s
/nsgrid
.
h from typede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der
S
p
o
el
Re
m
oved t
y
p
e
s/m
d
atom
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
R
emoved t
y
pes/inputrec
.
h from
typedefs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der Spo
e
l
Fixes bug in the computation of Coeffic
i
ent of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
a
vid van der
Spoel
Rem
o
ved types/forcerec
.
h fr
o
m
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David
van der S
p
oe
l
Re
m
o
ve
d
i
nclude of types/ifun
c
.
h from typ
e
de
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid van d
e
r Spoel
Removed four incl
u
de
s
from legacyhea
d
ers/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David v
a
n
d
er Spo
e
l
Removed
l
egacyhead
e
rs/ty
p
es/commrec_fwd
.
h from type
d
ef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
van der S
p
o
el
Moved conte
n
t
f
rom
m
dr
u
n
.
h to separate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David
v
an de
r
Sp
o
e
l
Removed
<
sys/types
.
h
>
and "types/constr
.
h"
f
rom
typedefs
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoel
Re
m
oved fileio/trx
.
h from typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
v
an der Spoel
M
ov
e
d functions op
e
r
ating on force
r
e
c
to separate
h
eader
.
commit
|
commitdiff
|
tree
2015-08-28
David v
a
n
d
e
r
Spoel
A
dded energy
(edr) file type to Options headers
.
commit
|
commitdiff
|
tree
2015-08-28
David van
der Spoel
Added additional c
o
nstructor t
o
St
r
ingS
t
r
e
am class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David va
n
der Spoel
M
a
de output fro
m
dum
p
ing neigh
t
borlists eas
i
er to read
.
commit
|
commitdiff
|
tree
2015-07-31
David van
de
r
Spoel
Change initial parameters for testing expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoel
Code for
checki
n
g xvg file
s
in testutils
.
commit
|
commitdiff
|
tree
2015-04-17
David
v
an der Spoel
U
pd
a
ted exponential fitting
to
make i
t
robust
.
commit
|
commitdiff
|
tree
2015-04-09
D
a
v
id
van
der Spoel
C
larified comments for tim
e
-depend
e
nt electr
i
c fields
.
commit
|
commitdiff
|
tree
2015-04-08
D
a
vid van
d
er
S
poel
Fixed incorrect output of gb_algorith as sa_algori
t
hm
.
commit
|
commitdiff
|
tree
2015-03-02
Dav
i
d van d
e
r Spoel
Up
d
ated
documentation for
electric
f
ields
.
commit
|
commitdiff
|
tree
2014-12-13
Dav
i
d van der Spoel
F
o
ur new quo
t
es from a
r
ound the
w
orld
.
commit
|
commitdiff
|
tree
2014-11-28
David van der
S
poel
Fixes recently i
n
tr
o
d
u
c
e
d
bu
g
in g
m
x
analyze
.
commit
|
commitdiff
|
tree
2014-11-24
David
v
an
der Spoe
l
Added
warning
s
for ewal
d
-geometry and surface-e
p
silon
commit
|
commitdiff
|
tree
2014-10-28
D
a
vid v
a
n
der Spoel
E
ven mor
e
refreshing quote
s
.
commit
|
commitdiff
|
tree
2014-10-14
David van der Spoel
Re
o
rganizing analysis of correl
a
tion
f
uncti
o
ns
.
commit
|
commitdiff
|
tree
2014-09-23
David van der Spoel
Fix
e
s
potentia
l
bug in ne
i
g
h
borsea
r
c
hing
.
commit
|
commitdiff
|
tree
2014-09-17
David
van
d
er Spo
e
l
M
e
r
g
e release-5-0
i
nto master
commit
|
commitdiff
|
tree
2014-09-10
Da
v
id van der Spoel
Remove
.
t
p
a
,
.
t
p
b,
.
tpx,
.
trj files
.
Par
t
of #1500
.
commit
|
commitdiff
|
tree
2014-08-30
David van
der Spo
e
l
Fixes issue
wi
t
h
vsiten and verlet
buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David van der Sp
o
el
Fixed inc
o
n
s
istency in blocka handling
.
commit
|
commitdiff
|
tree
2014-06-29
D
a
v
id van der Spoel
Fix
e
s #1532,
SEGV
i
n g_curr
e
n
t
.
commit
|
commitdiff
|
tree
2014-06-25
Dav
i
d van der Spo
e
l
Added
check f
o
r domain decompo
s
iti
o
n and shells
.
commit
|
commitdiff
|
tree
2014-06-24
David van der Spoe
l
A
d
d
ed check i
n
gr
o
mpp for sh
e
ll
s
and input
r
ec
issues
.
commit
|
commitdiff
|
tree
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