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Rename atomGroups in gmx_domdec_t to atomGrouping
2018-06-12
David van der
Spoel
Let gmx nmeig print t
h
ermochemist
r
y
.
commit
|
commitdiff
|
tree
2018-03-21
David v
a
n
der Spoel
Renamed entro
p
y
.
* to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David va
n
der Spoe
l
Split
o
ff e
n
tropy calculatio
n
to
s
eparat
e
file
.
commit
|
commitdiff
|
tree
2017-12-28
David v
a
n der Spoel
F
ixes and u
p
dates fo
r
x
p
lor2gml
.
pl
a
nd
at
o
m_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
D
avi
d
van der Spoel
F
i
xed check f
o
r w
a
ter in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David va
n
der
S
poel
New mdp input fo
r
electric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David v
a
n der Spoe
l
Fixe
d
mdp outp
u
t from electr
i
c
field code
.
commit
|
commitdiff
|
tree
2017-10-30
Dav
i
d
van der Spoel
Added option -water tips3
p
to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
Dav
i
d van der Spoel
S
p
li
t
off the NMR related analy
s
e
s fro
m
gmx
e
n
e
rgy
.
commit
|
commitdiff
|
tree
2017-10-17
David van der Spoel
Fixed mis
s
i
n
g entrie
s
in nrnb
a
r
r
ays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der
S
poel
W
o
rked
around m
i
ssing O
p
enM
P
impleme
n
ta
t
ion in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David
v
an der Spoel
Fixed bug in gmx disres index
i
ng a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-02
David van der Spoel
Wo
r
ke
d
around missing OpenMP implementatio
n
in orires
.
commit
|
commitdiff
|
tree
2017-07-28
David van der Spoel
Added uni
t
-t
e
st for
o
rie
n
tati
o
n
rest
r
ain
t
s output
.
commit
|
commitdiff
|
tree
2017-07-19
David van
der Spoel
Removed unne
c
essary static declara
t
ions for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fi
x
ed test-order dependency i
n
gmxpreproce
s
s
t
est
s
.
commit
|
commitdiff
|
tree
2017-07-19
David van der
Spoel
Fix no
n
-repro
d
ucabili
t
y of cl
u
stsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
Dav
i
d van
der Spoel
Xpm test for gmx clu
s
tsize
commit
|
commitdiff
|
tree
2017-03-12
Davi
d
va
n
d
e
r
Spoel
Added
t
ests for
gmx
c
lu
s
tsize
.
commit
|
commitdiff
|
tree
2017-03-04
D
avid van der Spoel
Removes ro
g
u
e
pri
n
ting t
o
xvg
file in gmx mindi
s
t
commit
|
commitdiff
|
tree
2017-02-27
David va
n
der
Spoel
F
i
xes
b
ug in
gmx solvate with -shell that y
i
elded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David
v
an der
Spoel
Fixes S
E
GV in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
Da
v
i
d
v
a
n der
S
poe
l
Only print all
dangling ato
m
s with gr
o
mpp -v
commit
|
commitdiff
|
tree
2017-01-23
David van d
e
r
Spoel
Adde
d
refere
n
ce for dihe
d
ral
functio
n
in O
P
LS
.
commit
|
commitdiff
|
tree
2016-12-07
Dav
i
d
v
an de
r
Sp
o
e
l
Couple of ne
w
quotes
commit
|
commitdiff
|
tree
2016-11-18
David van der
S
poel
A
d
ded first tests of bonded fo
r
ce f
u
nctions
.
commit
|
commitdiff
|
tree
2016-10-14
David van der Spoel
Fixes some memo
r
y leaks asso
c
iated with testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
a
vid van der Sp
o
e
l
M
odularize elec
t
r
i
c f
i
eld handlin
g
commit
|
commitdiff
|
tree
2016-09-27
David van der
Spoe
l
Fi
x
ed script xplor2
g
mx
.
p
l
to work with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David van der Spoel
F
i
xes i
s
sue with Release build in c
o
rrelation
function
s
.
commit
|
commitdiff
|
tree
2016-09-20
D
a
vid van der Spoel
Made correlati
o
n function routin
e
use std::v
e
ct
o
r
commit
|
commitdiff
|
tree
2016-09-05
D
a
vid van der Spo
e
l
Me
r
ge "Mer
g
e branc
h
rele
a
se-2
0
1
6
"
commit
|
commitdiff
|
tree
2016-08-24
David va
n
der Spoel
Added document
a
tion for
s
hell p
o
tentials
.
commit
|
commitdiff
|
tree
2016-08-03
David
van de
r
Spoel
Three
new qu
o
t
e
s
.
commit
|
commitdiff
|
tree
2016-07-31
David v
a
n der Spoel
Merge "Merge branch release-5-1 into r
e
lease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van der Sp
o
el
Fi
x
es inc
o
r
r
ect charges in OPLS/AA
-
L for HISD and
HISE
commit
|
commitdiff
|
tree
2016-07-08
D
avid van
d
er Spoel
Merge "Merg
e
branch release-5
-
1 i
n
to release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van d
e
r Spoel
Introduce
f
atal error fo
r
too few frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made gmx dos work ag
a
in
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
vid van der Spoel
Removed spurious r_ij in fo
r
ce for Morse p
o
t
e
ntial
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David
van der S
p
o
el
Mo
d
ify lm
f
it li
b
rary to avoid clashes with other versions
.
commit
|
commitdiff
|
tree
2016-03-23
Davi
d
van de
r
S
p
oel
Removed sre
n
ew
that
w
as making arr
a
y smaller incorrect
l
y
.
commit
|
commitdiff
|
tree
2016-03-18
David van
d
e
r
Spoel
Fix
e
d division by zero in po
l
ari
z
e
.
commit
|
commitdiff
|
tree
2016-01-20
D
avid van der Spoel
Couple of
n
e
w quotes
commit
|
commitdiff
|
tree
2016-01-07
D
avid va
n
der
Spoe
l
M
ade normal modes work
w
ith shel
l
s and vsites
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
F
ixe
s
newly introduced bug i
n
m
a
k
e_nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
Da
v
id
v
a
n der Spoel
Moved domdec structures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spoel
Cleanups in legacyhead
e
r/types/co
m
m
rec
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vid van der
S
poel
M
erged legacyheaders/types/qmmmrec
.
h int
o
m
d
lib/qmm
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
David v
a
n
d
e
r
Spoel
Merg
e
d
genborn
.
h f
r
om lega
c
y
h
ea
d
ers/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Mo
v
ed
le
g
a
c
y
headers/types/gro
u
p
.
h to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid van der Spoel
Merg
e
d legacyheaders/ty
p
es/ns
.
h and nblist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der
Spoe
l
C
om
b
ine enums
.
h and na
m
es*
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id va
n
der Spoel
Merged legacyhea
d
ers/nrnb
.
h and types/nrnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David v
a
n der Sp
o
el
Mo
v
ed mdatom
.
h from leg
a
cy
h
eader/
t
yp
e
s to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
d
e
r
Spoel
Moved
legacyh
e
ade
r
s/types/ener
g
y
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David
v
an
d
er Sp
o
el
M
erged
l
e
g
acy
h
eaders/t
y
pes/inputrec
.
h into
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van d
e
r Spoel
Me
r
ged leg
a
cyheaders/types/state
.
h into mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van
de
r
Spoel
Replaced atom
_
id b
y
int
.
commit
|
commitdiff
|
tree
2015-11-13
David van
der
S
poel
Moved
g
enbor
n
.
h t
o
m
d
lib
commit
|
commitdiff
|
tree
2015-11-12
David van
der Spoel
M
oved t
x
tdump
.
* t
o
fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der S
p
oel
Moved
c
opyrit
e
.
* to filei
o
from gmxlib and legacyhea
d
er
s
.
commit
|
commitdiff
|
tree
2015-11-11
David van der Spoel
Moved inputrec
.
* from g
m
xlib and legacyhead
e
rs to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Removed legac
y
header
s
/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
D
avid
van der Spoel
Moved df_hist
o
ry utility r
o
utines fro
m
t
y
pede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der
S
po
e
l
Replac
e
d
N
O
T
SET from typedefs
.
h by
l
ocal sol
u
tions
.
commit
|
commitdiff
|
tree
2015-10-23
David van d
e
r Spo
e
l
R
e
moved e
n
e
rgyhistory code from t
y
pedefs t
o
a separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David
van der Spoel
M
o
ved
p
bc
/
cu
t
-off
r
e
l
a
t
e
d
utilities from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David va
n
de
r
Spoel
Freed memory in legacy st
a
tistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
Davi
d
van
d
er Spo
e
l
R
emove
d
simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van
der Spoel
Remove
d
simple
.
h
f
rom nb_ke
r
nel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van
d
er Spoel
Removed s
i
mple
.
h
f
rom nb_k
e
rnel_ss
e
2
_XX
commit
|
commitdiff
|
tree
2015-10-02
David
v
an de
r
Spoel
Re
m
oved
simple
.
h
fr
o
m nb_
k
e
r
nel_c a
n
d n
b
_k
e
r
n
el_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid van der Spoe
l
Removed include simple
.
h
from nb_kernel_av
x
_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van
d
er Spoel
Remo
v
ed simple
.
h from nb_
k
ernel_avx_256_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoe
l
Remo
v
ed output_env_t
,
now using gmx_output_en
v
_t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Dav
i
d van
d
er Spoel
Remo
v
ed types/nrnb
.
h from
type
d
e
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
D
a
v
i
d van
d
e
r
S
p
oel
Removed types/
n
blis
t
.
h and types/nsg
r
id
.
h fr
o
m
t
y
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der S
p
oe
l
Removed ty
p
e
s
/mdatom
.
h
f
rom t
y
p
e
de
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
Da
v
id
v
an der Spoel
Removed type
s
/in
p
utrec
.
h
fro
m
typedef
s
.
h and
releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
van der
S
poel
Fixes bug
in
t
he computat
i
on
o
f Coef
f
ic
i
ent o
f
Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
Davi
d
van der Spo
e
l
Re
m
oved t
y
pes/for
c
erec
.
h f
r
om t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
Dav
i
d
v
an der S
p
o
e
l
Removed include of type
s
/ifu
n
c
.
h from
ty
p
ed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der
Spoel
Re
m
oved f
o
ur includes fr
o
m legacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid van
de
r
Spoe
l
R
e
m
o
ved
l
e
gacyheaders/type
s
/commrec_fwd
.
h
f
rom typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van der Spo
e
l
M
o
ve
d
content from
m
drun
.
h t
o
s
eparat
e
headers
.
commit
|
commitdiff
|
tree
2015-09-10
David
van der Spo
e
l
Removed
<
sys/typ
e
s
.
h> and "types/const
r
.
h
" f
r
om
t
ypedef
s
commit
|
commitdiff
|
tree
2015-09-09
David
v
an
der Spoel
R
e
moved
f
i
l
eio/trx
.
h
f
rom
t
y
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
Davi
d
van der Spoel
M
oved fu
n
c
t
i
o
ns operating on
f
orcerec to separate
h
eade
r
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoe
l
Added energy
(edr) file t
y
pe
to Options headers
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spo
e
l
Added ad
d
i
ti
o
nal constr
u
ctor to Str
i
n
gStream class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David v
a
n
d
er S
p
o
el
M
a
de o
u
tput from d
u
mping neightborl
i
st
s
easier to rea
d
.
commit
|
commitdiff
|
tree
2015-07-31
David van
d
er
S
po
e
l
Change
i
nitial pa
r
ameters for te
s
ting
expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van d
e
r Spoel
Code for checking xvg
f
iles in
t
es
t
utils
.
commit
|
commitdiff
|
tree
2015-04-17
David van d
e
r Spoel
Updated exponential fitting
t
o make it r
o
bust
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoel
Clarifie
d
comments
fo
r
time-depend
e
nt e
l
ec
t
ric
f
iel
d
s
.
commit
|
commitdiff
|
tree
2015-04-08
David van
der Spo
e
l
Fixed inco
r
rect output of gb_a
l
go
r
ith as s
a
_algo
r
ithm
.
commit
|
commitdiff
|
tree
2015-03-02
D
a
v
i
d van
der S
p
oel
Update
d
documenta
t
ion for electric
fields
.
commit
|
commitdiff
|
tree
2014-12-13
David v
a
n
d
e
r Spoel
Four
new quote
s
f
ro
m
around the w
o
r
l
d
.
commit
|
commitdiff
|
tree
2014-11-28
David van
d
e
r
Spo
e
l
Fix
e
s recently introduced b
u
g
in
gmx
a
nalyze
.
commit
|
commitdiff
|
tree
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