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Partial conversion of gmx_domdec_t to C++
2018-06-12
Dav
i
d
va
n
d
er
Spoel
Let gmx nmeig print th
e
r
m
o
chemistry
.
commit
|
commitdiff
|
tree
2018-03-21
D
a
vid van der Sp
o
el
Rename
d
entrop
y
.
* to thermochem
i
stry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van de
r
Spo
e
l
Split
o
f
f
e
ntropy calc
u
lation t
o
separate
f
i
le
.
commit
|
commitdiff
|
tree
2017-12-28
Davi
d
v
an der
Spoel
Fixes and up
d
a
tes for xplor2gml
.
pl and a
t
om_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
D
avid va
n
d
er
S
poel
F
i
xed
c
heck fo
r
wa
t
e
r
i
n gen
_
vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David van
der Spoel
Ne
w
mdp input for ele
c
tric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
F
ixed m
d
p out
p
ut fro
m
ele
c
tric field code
.
commit
|
commitdiff
|
tree
2017-10-30
Da
v
id
van
d
er Spoel
Added option -water tips3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van
der Spoel
S
plit
o
f
f
the NMR related
analyses from gmx
e
nergy
.
commit
|
commitdiff
|
tree
2017-10-17
David van
der Spoel
Fixe
d
missing
e
n
t
r
i
es in
nrnb
arrays
.
commit
|
commitdiff
|
tree
2017-08-15
Da
v
id van d
e
r Spoel
Worke
d
around missing
O
penMP implemen
t
ation in or
i
res
.
commit
|
commitdiff
|
tree
2017-08-03
David van
der
Spoel
Fixed bug in gmx disres inde
x
i
n
g arrays
.
commit
|
commitdiff
|
tree
2017-08-02
David van der
Spoel
Worked
a
roun
d
missing OpenMP
i
mplementati
o
n in orir
e
s
.
commit
|
commitdiff
|
tree
2017-07-28
Da
v
id van der S
p
oel
Adde
d
u
n
it
-
test for orienta
t
ion restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
v
id van
d
e
r S
p
oel
Rem
o
ved unnecessa
r
y static
d
ecl
a
rati
o
n
s for com
m
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
D
avi
d
v
a
n
d
er Spoel
Fixed te
s
t-order depend
e
ncy in gmxpreprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
Davi
d
van der Spoel
Fix non-re
p
roducability o
f
clustsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
Davi
d
van
der
S
poel
Xpm t
e
st f
o
r g
m
x clustsiz
e
commit
|
commitdiff
|
tree
2017-03-12
Da
v
id va
n
der Spoel
A
dded tests
for
g
mx clu
s
t
s
ize
.
commit
|
commitdiff
|
tree
2017-03-04
Da
v
id
van
d
er Spoel
Removes r
o
g
u
e printing to xvg fil
e
in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
David van der
Spoel
Fixes bug in gm
x
s
o
lvate w
i
t
h
-shell th
a
t yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Spoel
Fi
x
es SEGV
i
n gm
x
or
d
er
.
commit
|
commitdiff
|
tree
2017-02-02
David
v
an d
e
r Spoel
Onl
y
print all da
n
g
l
ing atoms
w
ith gro
m
pp -v
commit
|
commitdiff
|
tree
2017-01-23
D
a
vid van der Spoel
Added
referen
c
e fo
r
dihedr
a
l fu
n
ct
i
on in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
Dav
i
d
van der
S
p
o
el
Coupl
e
of new
quotes
commit
|
commitdiff
|
tree
2016-11-18
Da
v
id va
n
d
e
r
Spoe
l
Added
f
ir
s
t tests of
b
onded force
f
unctio
n
s
.
commit
|
commitdiff
|
tree
2016-10-14
David van de
r
Spoel
Fixes some memory leak
s
associ
a
te
d
with t
e
st
i
ng applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avid van der
Spoel
Modu
l
arize electric f
i
eld h
a
ndling
commit
|
commitdiff
|
tree
2016-09-27
D
avid van der
Spoel
Fixed sc
r
ipt xpl
o
r2gmx
.
pl to wo
r
k with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
D
a
vi
d
van der Spoel
Fixes issue with Rel
e
ase build in correlation functi
o
ns
.
commit
|
commitdiff
|
tree
2016-09-20
David van der
Spoel
Ma
d
e correla
t
ion fun
c
t
ion rout
i
ne
use s
t
d:
:
vector
commit
|
commitdiff
|
tree
2016-09-05
David
van
der Spoel
Merge "Merge b
r
a
nch release-
2
016"
commit
|
commitdiff
|
tree
2016-08-24
David
v
an
der Spoel
Added docu
m
entati
o
n for s
h
ell
potentials
.
commit
|
commitdiff
|
tree
2016-08-03
Da
v
id van der
S
poel
Three
new quot
e
s
.
commit
|
commitdiff
|
tree
2016-07-31
David van
d
er Sp
o
el
Merg
e
"Merge branch rel
e
ase-5-1
into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
Dav
i
d van der Spoel
F
i
xes incorrect
c
harges in OPLS/AA-L for
H
ISD an
d
HISE
commit
|
commitdiff
|
tree
2016-07-08
David van der S
p
oel
Merge "Merg
e
branch release-5-1
i
nto
release-2
0
16"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van der Spoel
I
ntrodu
c
e fatal error for too few f
r
am
e
s in gm
x
dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van der
S
poel
Mad
e
gm
x
dos work again
.
commit
|
commitdiff
|
tree
2016-06-22
D
avid va
n
der
S
p
oel
R
emoved
spurious r_ij in force
f
or
M
orse potent
i
al
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David
va
n
der Spoel
M
o
dif
y
lm
f
it libr
a
r
y
to avoi
d
clashes with othe
r
versi
o
ns
.
commit
|
commitdiff
|
tree
2016-03-23
D
a
vid v
a
n der
Spoel
Removed srenew
t
hat was
m
aking array smaller in
c
o
rrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der
S
poel
Fixe
d
division by zero in
p
olarize
.
commit
|
commitdiff
|
tree
2016-01-20
Davi
d
v
a
n der Spo
e
l
Couple of new q
u
otes
commit
|
commitdiff
|
tree
2016-01-07
David
v
an der
S
p
o
e
l
Made normal modes
w
ork with shells and
v
si
t
es
commit
|
commitdiff
|
tree
2015-11-24
David va
n
der Spoel
F
ixes newly intro
d
uc
e
d
bug in m
a
ke_nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
David v
a
n der Spoel
Moved domdec structure
s
out of
c
omm
r
ec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Davi
d
van der S
p
oel
Cleanups in legacyh
e
ad
e
r/typ
e
s/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der S
p
oel
Merged leg
a
cyheaders/types/
q
mmmrec
.
h in
t
o
mdlib/qmm
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der
Spoel
Merged genb
o
rn
.
h from legacyheaders/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved leg
a
cyhe
a
d
ers/types/group
.
h to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der Spoel
Mer
g
ed
l
e
gacyheaders/t
y
pes
/
ns
.
h and nblist
.
h to md
t
ypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Sp
o
el
Combin
e
enums
.
h a
n
d
na
m
e
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
v
i
d
van der
S
p
oel
Me
r
ged lega
c
yheaders/nrnb
.
h and t
y
p
es
/
n
rnb
.
h to gmx
l
ib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
oel
M
o
ved
mdato
m
.
h from legacyh
e
ader/types to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
oel
Moved l
e
ga
c
yheaders/types
/
energy
.
h to
m
dtypes
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van d
e
r Sp
o
e
l
Merge
d
l
e
gacyheaders
/
types/inputrec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
D
avi
d
van der Spoel
M
e
rged legacyheader
s
/types/state
.
h
in
t
o md
t
ypes/s
t
ate
.
h
commit
|
commitdiff
|
tree
2015-11-13
Da
v
i
d
van der Spoel
R
e
pl
a
ced atom_id
by i
n
t
.
commit
|
commitdiff
|
tree
2015-11-13
Da
v
id van der
Spoel
Moved genbo
r
n
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David v
a
n
der Spoe
l
Moved txtd
u
mp
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
avid va
n
der S
p
oel
Moved cop
y
rite
.
* to fileio from gmxlib
a
nd l
e
ga
c
yheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van de
r
S
poe
l
Moved
i
nputrec
.
* from gmxlib and legacyhe
a
ders
to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-10
D
avid van
der Spoel
Rem
o
ved
l
ega
c
y
headers/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
D
a
vi
d
van der Spoe
l
Move
d
d
f_history utility routines from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
avid van der
S
po
e
l
Replac
e
d NOTSET f
r
o
m
typedefs
.
h b
y
l
o
cal
solutions
.
commit
|
commitdiff
|
tree
2015-10-23
D
a
v
id va
n
der Spoel
Removed e
n
ergyhistory cod
e
f
r
om typed
e
fs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spo
e
l
Mo
v
ed pbc/cut-of
f
related utilities f
r
om typedefs
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
Davi
d
van der
S
poel
Freed me
m
or
y
in legacy st
a
t
isti
c
s rout
i
n
es
.
commit
|
commitdiff
|
tree
2015-10-03
D
a
vid va
n
der Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David
va
n
der Spoe
l
R
e
moved simple
.
h from n
b
_
k
er
n
el_s
s
e4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van d
e
r
Spoel
Remo
v
ed simple
.
h
f
rom
n
b
_
kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n
der Sp
o
el
Rem
o
ved simpl
e
.
h from
n
b_k
e
rnel_c and
n
b_kernel_sp
a
rc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van der Spo
e
l
Re
m
ove
d
i
nclu
d
e simple
.
h
from
n
b_kernel_
a
vx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
R
e
moved simple
.
h from nb_kernel
_
avx_
2
5
6
_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
R
emoved output
_
en
v
_t, n
o
w us
i
ng
g
mx_output_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David
van
d
e
r Spoel
Removed types/n
r
n
b
.
h from typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van
d
e
r Spoel
Rem
o
ved
t
ypes/nb
l
ist
.
h and types/ns
g
rid
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van d
e
r Spoel
Removed type
s
/
m
d
a
t
om
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
D
a
v
i
d
v
an der
S
po
e
l
R
e
m
oved t
y
p
e
s/inputrec
.
h from typed
e
fs
.
h
a
nd releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
D
avid van der Sp
o
el
Fixes bug in the
computation
of Co
e
fficient of Ther
m
al
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der Spoel
Removed types/forcerec
.
h from
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
D
a
vid van d
e
r Spoel
Remove
d
i
n
c
lude of types/ifunc
.
h
f
rom typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David va
n
der S
p
oel
Removed four includes from legacyheaders/
t
ype
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
avid van d
e
r Spoel
Remov
e
d
legacyheader
s
/types/commrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
D
a
v
i
d van der Spoel
Moved conten
t
f
r
om mdrun
.
h
to
s
e
parate hea
d
ers
.
commit
|
commitdiff
|
tree
2015-09-10
David van de
r
Spo
e
l
Re
m
oved <sys/ty
p
e
s
.
h>
a
nd "typ
e
s
/con
s
t
r
.
h" from ty
p
e
def
s
commit
|
commitdiff
|
tree
2015-09-09
David van der
S
poel
R
emoved fil
e
io/t
r
x
.
h fro
m
typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van der Spoel
Mo
v
e
d
functions operating
on forcere
c
to separate he
a
der
.
commit
|
commitdiff
|
tree
2015-08-28
Da
v
id van
d
er Spoe
l
Add
e
d energy (
e
dr) file type to Opti
o
ns headers
.
commit
|
commitdiff
|
tree
2015-08-28
Davi
d
van
d
er S
p
oel
Adde
d
ad
d
itiona
l
constructor to Str
i
ngS
t
ream class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
Da
v
id van der Spoel
Mad
e
output from d
u
mp
i
n
g
n
eight
b
o
r
list
s
eas
i
e
r
t
o read
.
commit
|
commitdiff
|
tree
2015-07-31
David
van de
r
Spoel
Change initi
a
l par
a
meters for t
e
sting expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spo
e
l
Cod
e
for c
h
ecki
n
g
x
vg files in testu
t
i
l
s
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spoel
Update
d
ex
p
on
e
ntial fittin
g
to make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David
v
a
n der Spo
e
l
Clarified comments f
o
r time-depen
d
ent ele
c
tric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van der Spoel
F
i
xed incorrect
o
utpu
t
of
gb_algorit
h
as sa_al
g
orit
h
m
.
commit
|
commitdiff
|
tree
2015-03-02
David van der Sp
o
el
Update
d
do
c
umentation for
e
l
ectric fiel
d
s
.
commit
|
commitdiff
|
tree
2014-12-13
David
v
an der Sp
o
el
Four new quotes from around the world
.
commit
|
commitdiff
|
tree
2014-11-28
David van der
S
poel
Fi
x
es
r
ecent
l
y introd
u
c
ed
b
ug in gmx an
a
lyze
.
commit
|
commitdiff
|
tree
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