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Update Awh initialization and lifetime management
2018-03-21
David van der
S
po
e
l
Renamed entropy
.
* to t
h
e
r
mochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der Spoel
Spl
i
t off en
t
ropy calculation to
separate
file
.
commit
|
commitdiff
|
tree
2017-12-28
David van de
r
Sp
o
el
Fixes
a
nd updates
f
or x
p
lor2gml
.
pl and atom_nom
.
t
bl
commit
|
commitdiff
|
tree
2017-11-06
David van der Spoel
Fixed chec
k
for water in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
D
a
vid van
d
e
r S
p
oe
l
New m
d
p inp
u
t
f
o
r
e
lectric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
F
i
xed mdp output from electr
i
c field code
.
commit
|
commitdiff
|
tree
2017-10-30
David
va
n
de
r
Spoel
Added o
p
tion -water
tips
3
p to
pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
D
a
vi
d
van der Spoel
S
plit
off the NMR related an
a
ly
s
e
s from g
m
x energy
.
commit
|
commitdiff
|
tree
2017-10-17
David van der Spoel
Fixe
d
missing en
t
ri
e
s in nrnb arrays
.
commit
|
commitdiff
|
tree
2017-08-15
David va
n
der S
p
oe
l
Worked ar
o
und mi
s
sing OpenMP implementation
i
n
ori
r
es
.
commit
|
commitdiff
|
tree
2017-08-03
Dav
i
d van d
e
r
S
p
o
el
Fixe
d
bu
g
in g
m
x
disres i
n
dexing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
David van der Spoel
W
o
r
ked around m
i
ssing
Ope
n
MP impl
e
m
e
n
tation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
David van der Spoel
Added
u
ni
t
-test for
orientation restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid va
n
der Spoel
Removed unnecessary static declarations for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der S
p
o
e
l
Fixe
d
t
e
s
t-order depen
d
ency
i
n gmxpreprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
David
van der Spoel
Fi
x
non-
r
eproducabili
t
y of clust
s
ize tests
.
commit
|
commitdiff
|
tree
2017-05-01
D
a
vid van de
r
Spoel
Xpm test
for gm
x
clustsize
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoe
l
Added
tests for gmx clu
s
tsiz
e
.
commit
|
commitdiff
|
tree
2017-03-04
David van
d
er
S
poel
Re
m
oves rogue printi
n
g to xvg fi
l
e in gmx mindis
t
commit
|
commitdiff
|
tree
2017-02-27
David
v
a
n
der Spoel
Fix
e
s
bug in gmx solvate wi
t
h -shell that y
i
elded 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
v
a
n d
e
r Spoel
Only
print al
l
d
ang
l
ing atoms wi
t
h grompp -v
commit
|
commitdiff
|
tree
2017-01-23
David van der Spoel
Added reference for dihe
d
ral function in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David
v
an der Sp
o
el
Couple
of new
quote
s
commit
|
commitdiff
|
tree
2016-11-18
David van der Spoe
l
Added first t
e
sts of
b
o
nded forc
e
f
un
c
tions
.
commit
|
commitdiff
|
tree
2016-10-14
David van der
S
po
e
l
Fi
x
es some memo
r
y lea
k
s associ
a
t
e
d
with testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van d
e
r Spoel
Modular
i
z
e electric field handlin
g
commit
|
commitdiff
|
tree
2016-09-27
David van der Spoel
Fixed s
c
ript xp
l
or2g
m
x
.
p
l
to work wi
t
h
GMXDAT
A
commit
|
commitdiff
|
tree
2016-09-26
David
v
an der Sp
o
el
Fixe
s
issu
e
w
i
th Rele
a
se build
i
n
correlation functio
n
s
.
commit
|
commitdiff
|
tree
2016-09-20
Davi
d
v
an der S
p
oel
M
a
de corre
l
ation func
t
ion rou
t
in
e
use std::vector
commit
|
commitdiff
|
tree
2016-09-05
Da
v
id
v
a
n
d
er Spoe
l
Merg
e
"Merge branch
r
elea
s
e-2016"
commit
|
commitdiff
|
tree
2016-08-24
David va
n
der Spoel
A
d
ded doc
u
mentation for shell pot
e
ntials
.
commit
|
commitdiff
|
tree
2016-08-03
D
a
vi
d
van d
e
r
Spoel
T
h
re
e
new quote
s
.
commit
|
commitdiff
|
tree
2016-07-31
David van
der Spoel
Merge "M
e
r
ge
bra
n
ch release-5-1 into releas
e
-2016
"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
D
a
v
i
d van der Spo
e
l
Fixes incorrec
t
charges
i
n O
P
LS/AA
-
L for HI
S
D
a
n
d HISE
commit
|
commitdiff
|
tree
2016-07-08
Dav
i
d van der Spoel
Mer
g
e
"Merge
b
ranch release-
5
-1 into re
l
ease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van der
Spoel
Introduce fatal err
o
r for
t
oo fe
w
frame
s
in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
Dav
i
d van der Spoel
Made gmx do
s
work agai
n
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
v
id v
a
n
d
e
r
S
p
oel
R
e
moved spurious r
_
i
j in force for Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
D
a
vid van der Sp
o
el
Mod
i
fy lmfi
t
library
t
o
a
void
c
lashes w
i
th othe
r
ver
s
ions
.
commit
|
commitdiff
|
tree
2016-03-23
David van der Spoel
R
emove
d
srenew
that wa
s
making a
r
ray smaller
i
ncorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David va
n
de
r
Spoel
Fixed divis
i
o
n
b
y zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David va
n
de
r
Spoel
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
David
van der Spoel
Made normal modes work wi
t
h shells and
vsites
commit
|
commitdiff
|
tree
2015-11-24
David
v
a
n der S
p
oel
Fixes ne
w
ly introduced bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van de
r
Spoel
Moved domde
c
structu
r
es out of commre
c
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David
van de
r
Spoel
C
l
ean
u
ps in leg
a
c
y
header/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
v
an d
e
r
S
poel
Merg
e
d le
g
acyheaders/t
y
pes/qmmmrec
.
h in
t
o m
d
lib
/
qmm
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der
S
p
o
el
Me
r
ged ge
n
bor
n
.
h
f
rom legacyheaders/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved lega
c
yhead
e
r
s
/
types/group
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Merged le
g
a
cyheaders/types/ns
.
h and nblist
.
h to
mdtype
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid van der Spoel
Combine
enums
.
h and
n
a
mes*
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van de
r
Spoe
l
M
e
rged
legacyheade
r
s/nrn
b
.
h and t
y
pes/nrnb
.
h to
gmxl
i
b
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved mda
t
om
.
h
f
rom
legacyhead
e
r/types to
m
dtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spo
e
l
Mo
v
ed legacyheader
s
/types
/
ener
g
y
.
h to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-15
David
van
der Spoel
Me
r
ged legacyhea
d
ers/types/inputrec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
D
avid
van der Spoel
Merged lega
c
yhead
e
r
s
/types/state
.
h into mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
D
avid van
d
er S
p
oe
l
R
ep
l
aced atom_id
b
y int
.
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Moved
g
enbo
r
n
.
h
t
o mdlib
commit
|
commitdiff
|
tree
2015-11-12
David v
a
n de
r
Spoel
Moved t
x
t
d
ump
.
* to
f
ileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
avid van der Spoel
Moved copyrite
.
* to fileio from gmxlib and legacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van der
Spoel
Moved
i
nputre
c
.
* from gmxlib and
l
ega
c
yhead
e
rs to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Removed
legacyheaders/ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der S
p
oel
Moved
df_histo
r
y u
t
ili
t
y rou
t
ines
from typedef
s
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
avid van der Spoel
Replaced NOTSET
f
rom typedefs
.
h by local sol
u
t
i
o
n
s
.
commit
|
commitdiff
|
tree
2015-10-23
D
a
vid van der Spoel
Rem
o
ved energ
y
histo
r
y
code
f
rom typedefs to
a
s
e
parate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoe
l
Mov
e
d p
b
c
/cut-o
f
f
r
e
l
ated uti
l
ities
f
rom type
d
ef
s
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van
der Spoel
Free
d
mem
o
ry in
l
egacy statistic
s
routines
.
commit
|
commitdiff
|
tree
2015-10-03
David van der Spoe
l
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David
van der Spo
e
l
Remove
d
simp
l
e
.
h from nb_ke
r
nel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van der Spoel
Removed simple
.
h from nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
de
r
Spo
e
l
Removed simple
.
h
f
r
o
m nb_k
e
rnel
_
c a
n
d
nb_kernel
_
sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n d
e
r Spoel
Removed include simp
l
e
.
h
fro
m
nb_kern
e
l_avx_128_fma_X
X
commit
|
commitdiff
|
tree
2015-10-02
David
v
an
der Spoe
l
Rem
o
ved simpl
e
.
h from
nb_kernel_a
v
x
_
256_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id
v
a
n der Sp
o
el
Removed output_env_t, now us
i
ng gmx_output_en
v
_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David va
n
der Spoel
Remove
d
types/nrnb
.
h from typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
Davi
d
van der Spoel
Removed type
s
/
nblist
.
h and types/nsgrid
.
h
from typ
e
de
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der
Spoel
Remo
v
ed ty
p
es/
m
datom
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Da
v
id
v
a
n der
S
p
oel
Removed
type
s
/i
n
p
u
tre
c
.
h f
r
o
m
typedefs
.
h and r
e
le
t
e
d
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David
van der Spoel
Fixes
b
u
g in the comp
u
tation of Coeffi
c
ient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van de
r
Spo
e
l
Removed t
y
pes/forcerec
.
h from typede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der
S
p
o
e
l
Removed
i
n
c
lude of types/if
u
nc
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David
v
an der Spoel
Remove
d
four inc
l
udes fro
m
legacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
v
i
d van der Spoel
Removed legacyheader
s
/
t
ypes/commrec_
f
wd
.
h from type
d
ef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van der S
p
oe
l
Mo
v
e
d cont
e
n
t
from mdrun
.
h to separate h
e
aders
.
commit
|
commitdiff
|
tree
2015-09-10
David van de
r
Spoel
R
e
moved <sys/types
.
h
> and "types
/
co
n
str
.
h" from
typ
e
defs
commit
|
commitdiff
|
tree
2015-09-09
Da
v
id van der
Spoel
Rem
o
ved fil
e
io/trx
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
v
an
der Spoel
Moved fun
c
tions o
p
erati
n
g on
f
orcerec to sep
a
rate header
.
commit
|
commitdiff
|
tree
2015-08-28
David
v
an der S
p
oel
A
dded ene
r
gy (
e
dr) file typ
e
to Options header
s
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoe
l
Added add
i
tional co
n
s
t
r
uctor to Stri
n
g
Stre
a
m c
l
ass
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
Davi
d
van der S
p
oel
Made output fro
m
dumping neig
h
tborlists ea
s
ie
r
to read
.
commit
|
commitdiff
|
tree
2015-07-31
Dav
i
d
van der
Spoel
C
hang
e
i
nitial p
a
r
amete
r
s
for testin
g
e
x
pfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van d
e
r
S
p
o
e
l
Code for
c
hecking xv
g
file
s
in testuti
l
s
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spoel
Up
d
ated expon
e
n
t
ial f
i
tting to make it
robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoel
Clarifi
e
d co
m
ment
s
for
t
ime
-
dep
e
n
d
ent elec
t
ric
f
ield
s
.
commit
|
commitdiff
|
tree
2015-04-08
David van der Sp
o
e
l
Fix
e
d incorrect
output of gb
_
a
l
gorith as sa_algorit
h
m
.
commit
|
commitdiff
|
tree
2015-03-02
David van der
Spoel
U
pdated doc
u
mentation for electric fields
.
commit
|
commitdiff
|
tree
2014-12-13
David van der Spoel
Four new quotes from around th
e
world
.
commit
|
commitdiff
|
tree
2014-11-28
Dav
i
d van
der Spoel
F
ix
e
s
re
c
ently i
n
tr
o
duced
bu
g
i
n
g
m
x analyze
.
commit
|
commitdiff
|
tree
2014-11-24
David van d
e
r
S
p
o
e
l
Added warning
s
f
o
r ewald-ge
o
metry and
s
u
r
fa
c
e-epsilon
commit
|
commitdiff
|
tree
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