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Refactor cj preload in the nonbonded OpenCL kernels
2018-03-21
David van d
e
r Spoel
Ren
a
med entropy
.
*
to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
D
a
v
i
d van der S
p
oel
S
p
lit off entrop
y
calcula
t
i
o
n to separate file
.
commit
|
commitdiff
|
tree
2017-12-28
Da
v
id van der
Spoe
l
Fixes and updates for xplor2g
m
l
.
pl
a
nd
atom
_
nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
Dav
i
d
van der Spoel
Fixed ch
e
ck
for wate
r
in gen_vsi
t
e
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
Dav
i
d van
der
Spoel
N
e
w mdp in
p
ut for
e
lectric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David
v
a
n der Spoel
F
ixed m
d
p
o
u
t
put from electri
c
fiel
d
code
.
commit
|
commitdiff
|
tree
2017-10-30
David
v
a
n
der Spoel
Added o
p
tio
n
-w
a
ter t
i
ps3
p
to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
Da
v
id van der Spoel
Split off the NM
R
relate
d
analyses from gmx e
n
erg
y
.
commit
|
commitdiff
|
tree
2017-10-17
David van der Spo
e
l
Fixed
m
i
ssing entr
i
es
i
n
nrnb ar
r
ays
.
commit
|
commitdiff
|
tree
2017-08-15
David va
n
d
e
r
Spoel
Worked a
r
ound
m
i
ssing
OpenM
P
implementation i
n
orires
.
commit
|
commitdiff
|
tree
2017-08-03
David v
a
n der
S
p
o
e
l
Fixed bug in gmx
disres inde
x
ing arra
y
s
.
commit
|
commitdiff
|
tree
2017-08-02
David van der
Sp
o
e
l
W
o
rked around missing OpenMP implementation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
Dav
i
d van
d
e
r
Spoe
l
A
dded un
i
t-test for orie
n
tat
i
o
n
r
e
straints output
.
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id van d
e
r Spoel
Removed unnecessary static
declarations for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
Dav
i
d van d
e
r Sp
o
el
F
ixed
t
e
st-order dep
e
ndency in
gmxprepr
o
c
e
ss tests
.
commit
|
commitdiff
|
tree
2017-07-19
David v
a
n der
S
po
e
l
F
i
x non-reproducabil
i
ty of clustsize
t
est
s
.
commit
|
commitdiff
|
tree
2017-05-01
D
a
vid van de
r
S
p
oel
Xpm
t
e
st for gmx clust
s
ize
commit
|
commitdiff
|
tree
2017-03-12
Dav
i
d van der S
p
oe
l
Add
e
d tests for g
m
x clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David van der Spoel
Removes rogu
e
prin
t
ing to
x
vg f
i
le in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
David
van d
e
r Spoel
Fixes
bu
g
in gmx so
l
vate
with
-
shell tha
t
yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Sp
o
el
Fixes SEGV in gmx o
r
der
.
commit
|
commitdiff
|
tree
2017-02-02
D
avid van
d
er Spoe
l
Only print all dangling a
t
oms with grompp
-
v
commit
|
commitdiff
|
tree
2017-01-23
Dav
i
d v
a
n
d
er Spoel
Added reference for d
i
hedral func
t
i
on
in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der Spoel
Coup
l
e of new quotes
commit
|
commitdiff
|
tree
2016-11-18
D
avid van
der Spoel
A
d
ded
first tests of bonded force
f
unction
s
.
commit
|
commitdiff
|
tree
2016-10-14
D
avid van der Spo
e
l
Fix
e
s
s
ome memor
y
lea
k
s associated
w
it
h
testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van der Spoel
M
o
dularize
electric
f
ield handling
commit
|
commitdiff
|
tree
2016-09-27
David van der Spoel
Fixed scrip
t
xplor
2
gmx
.
pl to wor
k
with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David va
n
de
r
Spoel
Fixes is
s
ue with Rel
e
ase buil
d
in correlation funct
i
on
s
.
commit
|
commitdiff
|
tree
2016-09-20
David
v
an der Spoel
Made correlation fun
c
tion
routine use std::vector
commit
|
commitdiff
|
tree
2016-09-05
D
avid v
a
n der Spoel
Merge "Merge branch r
e
lease
-
201
6
"
commit
|
commitdiff
|
tree
2016-08-24
D
a
vid
van der Spoe
l
A
dded do
c
umen
t
ation
for s
h
ell p
o
tential
s
.
commit
|
commitdiff
|
tree
2016-08-03
D
avi
d
van der Spoel
T
h
ree
n
ew quo
t
es
.
commit
|
commitdiff
|
tree
2016-07-31
David
va
n
der Spo
e
l
Me
r
ge "Merge branch release-
5
-1 in
t
o releas
e
-
2
0
16"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David
v
an der Spoel
Fixes in
c
o
rrect
charges
i
n OPLS/A
A
-
L fo
r
HI
S
D
a
nd HISE
commit
|
commitdiff
|
tree
2016-07-08
D
av
i
d van
d
er S
p
oe
l
Merge "Merg
e
branch re
l
ease-5-1 int
o
release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van
der S
p
oel
Introdu
c
e
fat
a
l e
r
ror for too f
e
w fr
a
mes
in gmx d
o
s
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made
g
mx dos
w
ork agai
n
.
commit
|
commitdiff
|
tree
2016-06-22
Davi
d
van
der Spoel
Remo
v
ed
s
purious r_ij in force
for Mors
e
potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van der Spoel
Modify lmfit librar
y
to avoid clas
h
es with othe
r
versions
.
commit
|
commitdiff
|
tree
2016-03-23
Da
v
id van
d
er S
p
oel
Removed srenew that wa
s
making array smaller in
c
o
r
rec
t
l
y
.
commit
|
commitdiff
|
tree
2016-03-18
D
a
vid van
d
er Spoel
Fixed divisio
n
b
y
z
e
r
o in
p
olari
z
e
.
commit
|
commitdiff
|
tree
2016-01-20
Davi
d
van der Spoe
l
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
David
van der Spo
e
l
Made normal
mode
s
w
ork with shells and vsites
commit
|
commitdiff
|
tree
2015-11-24
David va
n
d
e
r Sp
o
el
Fixes newly introduced bug
i
n
make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der S
p
oel
Moved domdec st
r
uctures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spo
e
l
Cleanup
s
i
n
legacyheader/types
/
comm
r
ec
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
avid
va
n
der Spoe
l
Merged legacyheaders/types/qmmmrec
.
h
into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der
S
po
e
l
Merged genborn
.
h
f
rom l
e
gac
y
heade
r
s/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
va
n
de
r
Spoel
M
o
ved
l
egacyheaders/ty
p
es/gro
u
p
.
h to mdtyp
e
s
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van de
r
Spoel
M
e
rge
d
legacyheaders/t
y
pes/ns
.
h a
n
d
n
b
list
.
h to md
t
ype
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Sp
o
el
Combine enums
.
h a
n
d names*
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vi
d
van der S
p
oe
l
Merged legacyhead
e
r
s/nrnb
.
h and
types/nrn
b
.
h to
gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid
v
a
n d
e
r Spo
e
l
Moved
m
datom
.
h from leg
a
cyheader/ty
p
e
s to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id
v
a
n der Spo
e
l
Moved legacyheade
r
s/types
/
energy
.
h
t
o
m
dt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-15
David
van
d
er
S
poel
M
erged legacyheade
r
s/t
y
p
e
s/inputrec
.
h into
m
dtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Merged
l
egacyh
e
a
ders/typ
e
s/st
a
te
.
h int
o
mdty
p
es/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Replac
e
d atom
_
id by int
.
commit
|
commitdiff
|
tree
2015-11-13
David van de
r
Spoel
M
o
ved
g
e
n
b
o
rn
.
h to m
d
lib
commit
|
commitdiff
|
tree
2015-11-12
David
v
a
n
d
er
S
poel
Move
d
txtdump
.
*
t
o
fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David
v
an der Sp
o
el
M
o
ved c
o
pyr
i
te
.
* to file
i
o from gmxlib a
n
d
l
eg
a
cy
h
eaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van
der Spoel
Moved inputrec
.
* f
r
om gmxlib and le
g
a
c
y
h
e
aders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David va
n
der S
p
oel
Removed legacyheader
s
/type
d
efs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David va
n
d
er Spoel
Moved
d
f_histor
y
utili
t
y ro
u
t
in
e
s from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David v
a
n d
e
r Spoel
Replaced NOTSET fr
o
m typedefs
.
h by
loc
a
l solutions
.
commit
|
commitdiff
|
tree
2015-10-23
David van
der
S
poel
Remove
d
energyhi
s
to
r
y code from typedefs
t
o
a sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van
d
er Spoel
Move
d
pbc/cut-off relat
e
d util
i
ties f
r
om t
y
ped
e
f
s
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Sp
o
el
Freed memo
r
y in le
g
a
c
y s
t
a
t
is
t
ics
r
outines
.
commit
|
commitdiff
|
tree
2015-10-03
Dav
i
d van der Spoel
R
e
moved simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der S
p
o
e
l
Removed si
m
ple
.
h
fr
o
m nb_k
e
r
n
e
l_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Sp
o
el
Remov
e
d simp
l
e
.
h from
nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
der Spoe
l
Removed
s
im
p
le
.
h from n
b
_kernel_c and nb_kerne
l
_spa
r
c64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van der Spoel
R
e
moved inc
l
ude simpl
e
.
h from nb_k
e
rnel_avx_128_f
m
a_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van
de
r
Spo
e
l
Remov
e
d simple
.
h
from nb_
k
e
r
n
el_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid van der Spoel
Removed outpu
t
_en
v
_t, now usi
n
g gmx_
o
utp
u
t_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van
d
er
S
poel
Remove
d
types/nrnb
.
h
fro
m
typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van
der Spoel
Removed types/nblist
.
h and types/nsgrid
.
h
fro
m
t
ypedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Da
v
id van der Spoel
Remo
v
ed ty
p
es/mdatom
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David
van der Spoel
Remove
d
types/inputrec
.
h from typedefs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David v
a
n d
e
r
Spoel
Fixes bug in the co
m
p
utation of Coefficient of T
h
ermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
Dav
i
d
van der
Sp
o
el
Removed typ
e
s/forcer
e
c
.
h
from ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van
d
e
r
Spoe
l
Remov
e
d include of types/ifunc
.
h f
r
o
m
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van d
e
r
Spoel
Removed
f
o
ur includes f
r
o
m
legacyheaders/typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Spoel
Removed legacy
h
eaders/typ
e
s/commrec_fwd
.
h from type
d
e
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
D
a
vid van der Spoel
Moved c
o
ntent from
mdr
u
n
.
h to s
e
par
a
te headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Removed <sys/types
.
h> and "types/constr
.
h"
from ty
p
edefs
commit
|
commitdiff
|
tree
2015-09-09
David
v
a
n der Spo
e
l
Removed
fi
l
eio/trx
.
h from typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
David v
a
n d
e
r Spoel
Moved function
s
operat
i
ng
o
n forcerec to
separate header
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spo
e
l
Added ener
g
y
(edr) fil
e
type to Opt
i
ons headers
.
commit
|
commitdiff
|
tree
2015-08-28
Da
v
id v
a
n der
S
p
o
el
Add
e
d
additional cons
t
ruc
t
or
to StringStream c
l
a
s
s
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van de
r
Spoel
Made outpu
t
from
dumping
n
ei
g
ht
b
orlists easier to read
.
commit
|
commitdiff
|
tree
2015-07-31
D
a
vi
d
van
d
er Spoel
Chan
g
e initial paramet
e
rs f
o
r testing exp
f
it
.
commit
|
commitdiff
|
tree
2015-07-29
Davi
d
van der Spoel
Code for che
c
king
xvg
f
iles in testutils
.
commit
|
commitdiff
|
tree
2015-04-17
D
avid van
d
er
Spo
e
l
U
pda
t
ed exponential fitting
to make it
robust
.
commit
|
commitdiff
|
tree
2015-04-09
Da
v
id van der
Sp
o
el
C
larified com
m
ents for time-depende
n
t elec
t
ric fields
.
commit
|
commitdiff
|
tree
2015-04-08
Davi
d
v
an
d
er
Spoel
Fixed inc
o
rrec
t
output of
gb
_
algorith as sa_
a
lgorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der Spoel
Upda
t
ed documenta
t
ion for electric
f
i
elds
.
commit
|
commitdiff
|
tree
2014-12-13
D
a
v
id van de
r
Spoel
F
o
ur
n
ew
q
uotes from around the world
.
commit
|
commitdiff
|
tree
2014-11-28
D
a
vid
van de
r
Spoel
Fixes rece
n
tl
y
introduced bug
i
n gmx analyze
.
commit
|
commitdiff
|
tree
2014-11-24
D
a
vid van
d
er Spoel
Add
e
d
warnings for ewald-
g
e
ometry and s
u
rface-epsilon
commit
|
commitdiff
|
tree
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