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Refactored set_pbc_dd
2015-11-24
Da
v
id van
d
er Spoel
Fixes newly
i
n
t
r
oduced bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
Davi
d
van der
S
poel
Moved domdec stru
c
tures out of
commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der
S
poel
Cle
a
nups
i
n
legacyhead
e
r/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged
legacyhead
e
rs/types/qmmmrec
.
h
i
nto md
l
i
b/q
m
mm
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
i
d van der Spoel
Me
r
ged genborn
.
h
f
r
om legacyheaders/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
oel
Moved legacyhead
e
rs/typ
e
s/gro
u
p
.
h to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Merged l
e
g
a
cyheader
s
/
types/
n
s
.
h and nblis
t
.
h
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der Spoel
Combine enu
m
s
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
oel
Merg
e
d legacyheaders/nrnb
.
h and
t
ypes/nrnb
.
h to
gmxl
i
b
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid
v
a
n
der
Spoe
l
Moved mda
t
om
.
h
from legacyhe
a
d
e
r/typ
e
s to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an de
r
S
p
o
el
M
oved
legacyheaders/types/energy
.
h to
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der
S
poel
Merg
e
d le
g
acyheaders/type
s
/inputrec
.
h
into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David
v
an der Spo
e
l
Merged legacyheaders/t
y
pes/state
.
h into mdtypes/s
t
ate
.
h
commit
|
commitdiff
|
tree
2015-11-13
D
avid van de
r
Spoel
Replaced atom_id
b
y i
n
t
.
commit
|
commitdiff
|
tree
2015-11-13
David v
a
n
d
er S
p
oel
Moved
g
e
nborn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
a
v
id van der Spoel
M
o
ved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van d
e
r Spoel
Mov
e
d
copyr
i
t
e
.
* to
f
ileio
from
g
mxlib and l
e
ga
c
yheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van
d
er S
p
oel
Moved inputrec
.
* from gmxlib
a
nd
legacyhead
e
rs to
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Remove
d
legacyheaders/typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David va
n
der Spoel
Moved
df_history utility rout
i
nes from typedef
s
to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der
Spoel
Rep
l
ac
e
d NO
T
SET
f
rom
t
y
pedefs
.
h
b
y
local solut
i
ons
.
commit
|
commitdiff
|
tree
2015-10-23
David van der Sp
o
el
Removed energyhistory code from typedefs t
o
a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David
v
an der Spoe
l
Moved pb
c
/cut-off r
e
l
a
ted utilities f
r
om
t
ypede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David va
n
der Spoel
Freed memo
r
y in leg
a
cy
stati
s
tics rout
i
ne
s
.
commit
|
commitdiff
|
tree
2015-10-03
David
van der Spo
e
l
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Rem
o
v
ed simple
.
h from
nb_k
e
r
n
el_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van der Spoel
Removed
si
m
ple
.
h fr
o
m nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Sp
o
el
Removed
s
i
m
ple
.
h from nb
_
k
e
rnel_c
a
nd nb_kernel_
s
parc64_
h
pc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
va
n
der Spoel
Rem
o
ved include
simpl
e
.
h from nb
_
kernel_avx_128
_
f
ma_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van d
e
r Spoel
Remove
d
si
m
ple
.
h f
r
om nb_kernel_a
v
x_256_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
R
emoved output_env_t, now using gmx_output_e
n
v
_
t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
D
a
vid van der
S
p
o
el
Removed types/nrnb
.
h fr
o
m
typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David va
n
der S
p
o
e
l
Removed types/
n
blist
.
h and types/nsgrid
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David
va
n
der S
p
oel
R
emov
e
d
t
ypes/m
d
atom
.
h fro
m
t
yped
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
David
van de
r
S
p
o
el
Removed
types/inputrec
.
h
f
rom
t
y
p
ed
e
f
s
.
h an
d
r
e
leted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Dav
i
d
van der Spoel
Fixes
b
ug
i
n the com
p
u
t
a
tion of Coefficient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van
der Spoe
l
Removed types/forcerec
.
h f
r
o
m
typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David
v
an der Sp
o
el
Rem
o
v
e
d include o
f
types/ifunc
.
h f
r
om typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
David va
n
d
e
r
Spo
e
l
Removed four in
c
lu
d
e
s f
r
o
m
legac
y
h
e
aders/typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid van der Spoel
Re
m
o
ved leg
a
cyhe
a
ders/typ
e
s/c
o
m
m
rec_fwd
.
h from ty
p
edef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Moved content from mdrun
.
h
to
separa
t
e
headers
.
commit
|
commitdiff
|
tree
2015-09-10
D
avid van der
S
poel
Removed <sys/types
.
h>
a
nd "types/con
s
tr
.
h
"
from typedefs
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoel
Removed fileio/t
r
x
.
h
fr
o
m typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
Davi
d
van de
r
Spoel
Moved functions
o
perating on forcerec to
s
eparate
header
.
commit
|
commitdiff
|
tree
2015-08-28
D
avid van der Spoel
A
d
ded energy
(edr) file type
t
o Options headers
.
commit
|
commitdiff
|
tree
2015-08-28
Da
v
id van der
Spoel
Added additional construc
t
or to StringStream
c
l
a
s
s
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van der
S
poel
Made output
from dumping neightbo
r
lis
t
s e
a
sier to
r
ead
.
commit
|
commitdiff
|
tree
2015-07-31
David v
a
n der Spoel
C
h
ange initial para
m
eter
s
f
or testi
n
g exp
f
it
.
commit
|
commitdiff
|
tree
2015-07-29
D
a
vid
van der Spoel
Code for checking
xvg f
i
les in testut
i
ls
.
commit
|
commitdiff
|
tree
2015-04-17
Da
v
id van der Sp
o
el
Upd
a
t
ed exponen
t
ial fitting
to ma
k
e it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoel
Clarified comments for
t
im
e
-dependen
t
electric field
s
.
commit
|
commitdiff
|
tree
2015-04-08
David
v
an der Sp
o
el
Fi
x
ed
incor
r
e
c
t outpu
t
of gb_
a
lgorith as sa_algorith
m
.
commit
|
commitdiff
|
tree
2015-03-02
David van der
Spo
e
l
Updated documentation for el
e
ct
r
ic fields
.
commit
|
commitdiff
|
tree
2014-12-13
David
van der Spoel
Four
n
ew qu
o
tes from around the w
o
r
l
d
.
commit
|
commitdiff
|
tree
2014-11-28
Dav
i
d van
d
er
S
p
oel
Fixes recently i
n
troduced b
u
g in gmx analyze
.
commit
|
commitdiff
|
tree
2014-11-24
David van der Spoe
l
Added warnings for ewald-g
e
o
metry and sur
f
ace-epsilon
commit
|
commitdiff
|
tree
2014-10-28
D
a
vid
van der Spoe
l
Ev
e
n
more r
e
freshing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
Da
v
id
van der Spoel
Re
o
r
g
anizing analysis of correlation
f
unct
i
ons
.
commit
|
commitdiff
|
tree
2014-09-23
David van der Spoel
Fix
e
s potential
bug
in neighborsearching
.
commit
|
commitdiff
|
tree
2014-09-17
D
a
vid van der
S
p
o
el
M
e
r
g
e
r
eleas
e
-
5
-
0
into mast
e
r
commit
|
commitdiff
|
tree
2014-09-10
David van der Spoel
R
e
move
.
tp
a
,
.
t
pb,
.
tpx,
.
trj files
.
Part of #1
5
00
.
commit
|
commitdiff
|
tree
2014-08-30
David v
a
n der Spoel
Fixes issu
e
with vsiten and verlet buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David van der
S
poel
Fixed
i
nc
o
nsistency in
b
locka handling
.
commit
|
commitdiff
|
tree
2014-06-29
David van d
e
r Spoel
Fixes #1532
,
SEGV i
n
g_
c
urrent
.
commit
|
commitdiff
|
tree
2014-06-25
David van der S
p
oel
Adde
d
check for domain d
e
composition an
d
sh
e
l
l
s
.
commit
|
commitdiff
|
tree
2014-06-24
David van der Sp
o
el
A
d
ded check
i
n gr
o
mpp for shells and inputrec issue
s
.
commit
|
commitdiff
|
tree
2014-06-22
David
van
der
Spoel
Impleme
n
ted fatal
e
rror for nstcalce
n
er
g
y!=1 with s
h
ells
.
commit
|
commitdiff
|
tree
2014-06-13
David v
a
n der Spoel
Fix memory-usage
e
rror in g_chi
commit
|
commitdiff
|
tree
2014-06-11
D
a
vid va
n
d
e
r
S
p
oel
Fixes bu
g
wher
e
-
e and -dt flags did
not work an
y
more
.
commit
|
commitdiff
|
tree
2014-06-07
David van
d
er Spo
e
l
Me
r
g
e
"Me
r
ge releas
e
-5-0 into master"
commit
|
commitdiff
|
tree
2014-06-07
D
avi
d
v
an der
Spoel
Merge release-
5
-0 int
o
master
commit
|
commitdiff
|
tree
2014-06-02
David van
d
e
r
Spoel
F
i
xed wrong
j
our
n
al ref
e
rence in manua
l
commit
|
commitdiff
|
tree
2014-05-31
Da
v
id va
n
de
r
S
p
o
e
l
P
ermit trjconv to
read and write
v
elocities w
i
th TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David van der
S
poe
l
Fixes
a
complicated
b
u
g in g_a
n
aeig
.
commit
|
commitdiff
|
tree
2014-05-15
D
avid v
a
n der
S
poel
Added c
m
ake p
r
ofiling support
commit
|
commitdiff
|
tree
2014-04-02
Dav
i
d
van der Spoel
Removed possibility of com
p
iling with GSL
.
commit
|
commitdiff
|
tree
2014-03-31
D
av
i
d van der Spoel
Fixed com
p
i
l
ation iss
u
e in fgr
i
d
.
c
pp due to int/enum
commit
|
commitdiff
|
tree
2014-03-06
David van der Spoel
Six new quotes from classic literature
.
commit
|
commitdiff
|
tree
2014-02-11
David van der S
p
o
el
Fixed anot
h
er vmdio issue
.
commit
|
commitdiff
|
tree
2014-02-10
David v
a
n der Spoel
Moved conditional cmake cod
e
f
or vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
David van der Spoel
Moved random number
g
enerator code to
s
eparate d
i
r
.
commit
|
commitdiff
|
tree
2014-01-18
David van de
r
Spoel
This patc
h
mov
e
s the
statisti
c
s library to its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
D
a
vid v
a
n
der Spoel
This
p
a
t
c
h m
o
ves preproc
e
ssing h
e
ad
e
rs
t
o gmxp
r
eprocess
commit
|
commitdiff
|
tree
2014-01-15
D
a
vid van der Spoel
This patc
h
moves the nra
m
a
.
[c
h
] to the gmx
a
n
a
dir
.
commit
|
commitdiff
|
tree
2014-01-13
D
a
v
id
van der Spoel
Cleaned
u
p
list
o
f
GROMACS authors
commit
|
commitdiff
|
tree
2014-01-09
David van der Spo
e
l
Fixed p
r
ecisi
o
n in ther
m
al
e
xpansion coe
f
ficient calc
.
commit
|
commitdiff
|
tree
2013-12-23
David van der Spoel
Fixed compila
t
ion issue
d
u
e to
g
cc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
David v
a
n d
e
r Spoel
M
o
re No
b
e
l quotes
a
nd oth
e
rs
commit
|
commitdiff
|
tree
2013-11-07
D
a
vi
d
van der Spoe
l
12 new quotes
commit
|
commitdiff
|
tree
2013-09-30
David van der Spoel
C
hange name of gmxdump to dump a
n
d gmxcheck to check
commit
|
commitdiff
|
tree
2013-09-29
David van d
e
r Spo
e
l
Fixes bug
i
n process
i
ng virtual
_
s
i
t
e
s
n
i
n
grompp
.
commit
|
commitdiff
|
tree
2013-09-26
David van
der Spo
e
l
Mad
e
MW
o
f the V
s
i
te
part
i
cle
t
ype
.
commit
|
commitdiff
|
tree
2013-09-21
David van der Spo
e
l
M
o
ved n
g
mx to C++, rena
m
ed it t
o
v
i
e
w
.
commit
|
commitdiff
|
tree
2013-08-30
Da
v
i
d
van der Spoel
Updated g_cluster
commit
|
commitdiff
|
tree
2013-07-24
D
a
vid van der Spoel
Fi
x
es #1312 uninitialized error i
n
g_e
n
emat
.
commit
|
commitdiff
|
tree
2013-07-17
D
a
vid v
a
n d
e
r Spoel
Adde
d
cit
a
tion to free volume p
a
per
.
commit
|
commitdiff
|
tree
2013-06-14
Dav
i
d van der Sp
o
el
New analys
i
s t
o
ol to compute the free v
o
lume and total
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
David van d
e
r Spoel
Fixes #1194 error readin
g
4
.
5
.
5 tp
r
files
w
ith
dihres
commit
|
commitdiff
|
tree
2013-05-16
D
a
vid
van der Spoel
Fixed two co
m
p
ilation
i
s
s
ues
.
commit
|
commitdiff
|
tree
2013-05-02
Da
v
id van der Spoel
Fixes #1238 g_hydo
r
d
er does not ca
l
l set_pbc
.
commit
|
commitdiff
|
tree
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