Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
docking
ocladock
Commits
20cf44f1
Commit
20cf44f1
authored
Jun 04, 2018
by
lvs
Browse files
added first working fire implementation
parent
3bf4482e
Changes
6
Expand all
Hide whitespace changes
Inline
Side-by-side
Makefile
View file @
20cf44f1
...
...
@@ -51,7 +51,8 @@ K2_NAME="gpu_sum_evals"
K3_NAME
=
"perform_LS"
K4_NAME
=
"gpu_gen_and_eval_newpops"
K5_NAME
=
"gradient_minimizer"
K_NAMES
=
-DK1
=
$(K1_NAME)
-DK2
=
$(K2_NAME)
-DK3
=
$(K3_NAME)
-DK4
=
$(K4_NAME)
-DK5
=
$(K5_NAME)
K6_NAME
=
"gradient_minFire"
K_NAMES
=
-DK1
=
$(K1_NAME)
-DK2
=
$(K2_NAME)
-DK3
=
$(K3_NAME)
-DK4
=
$(K4_NAME)
-DK5
=
$(K5_NAME)
-DK6
=
$(K6_NAME)
# Kernel flags
KFLAGS
=
-DKRNL_SOURCE
=
$(KRNL_DIR)
/
$(KRNL_MAIN)
-DKRNL_DIRECTORY
=
$(KRNL_DIR)
-DKCMN_DIRECTORY
=
$(KCMN_DIR)
$(K_NAMES)
...
...
@@ -205,8 +206,8 @@ PDB := 3ce3
NRUN
:=
200
POPSIZE
:=
500
TESTNAME
:=
test
TESTLS
:=
sd
NUM_LSIT
:=
30
TESTLS
:=
fire
NUM_LSIT
:=
30
0
test
:
odock
$(BIN_DIR)
/
$(TARGET)
-ffile
./input/
$(PDB)
/derived/
$(PDB)
_protein.maps.fld
-lfile
./input/
$(PDB)
/derived/
$(PDB)
_ligand.pdbqt
-nrun
$(NRUN)
-psize
$(POPSIZE)
-resnam
$(TESTNAME)
-gfpop
1
-lsmet
$(TESTLS)
-lsit
$(NUM_LSIT)
-smooth
0.5
...
...
device/calcenergy.cl
View file @
20cf44f1
...
...
@@ -658,3 +658,4 @@ raw_intraE_sol = ((dspars_S_const[atom1_typeid] +
#
include
"kernel3.cl"
#
include
"calcgradient.cl"
#
include
"kernel_gradient.cl"
#
include
"kernel_fire.cl"
device/kernel_fire.cl
0 → 100644
View file @
20cf44f1
This diff is collapsed.
Click to expand it.
host/src/getparameters.cpp
View file @
20cf44f1
...
...
@@ -147,7 +147,8 @@ void get_commandpars(const int* argc,
// unsigned long num_of_ls
strcpy
(
mypars
->
ls_method
,
"sw"
);
// "sw": Solis-Wetts,
// "sd": Steepest-Descent",
// "sd": Steepest-Descent",
// "fire": FIRE", https://www.math.uni-bielefeld.de/~gaehler/papers/fire.pdf
// "bfgs": Broyden-Fletcher-Goldfarb-Shanno (to be implemented)
mypars
->
smooth
=
0.5
f
;
mypars
->
tournament_rate
=
60
;
// 60%
...
...
@@ -304,8 +305,11 @@ void get_commandpars(const int* argc,
else
if
(
strcmp
(
temp
,
"sd"
)
==
0
)
{
strcpy
(
mypars
->
ls_method
,
temp
);
}
else
if
(
strcmp
(
temp
,
"fire"
)
==
0
)
{
strcpy
(
mypars
->
ls_method
,
temp
);
}
else
{
printf
(
"Warning: value of -lsmet argument ignored. Value must be a valid string:
\"
sw
\"
,
\"
sd
\"
.
\n
"
);
printf
(
"Warning: value of -lsmet argument ignored. Value must be a valid string:
\"
sw
\"
,
\"
sd
\"
,
\"
fire
\"
.
\n
"
);
}
}
...
...
host/src/performdocking.cpp
View file @
20cf44f1
This diff is collapsed.
Click to expand it.
stringify_ocl_krnls.sh
View file @
20cf44f1
...
...
@@ -20,6 +20,7 @@ IN_KERNEL3=$KERNEL_DIR/"kernel3.cl"
IN_KERNEL4
=
$KERNEL_DIR
/
"kernel4.cl"
IN_KERNELb
=
$KERNEL_DIR
/
"calcgradient.cl"
IN_KERNEL5
=
$KERNEL_DIR
/
"kernel_gradient.cl"
IN_KERNEL6
=
$KERNEL_DIR
/
"kernel_fire.cl"
echo
" "
echo
"Stringified input kernel-files: "
...
...
@@ -31,6 +32,7 @@ echo $IN_KERNEL3
echo
$IN_KERNEL4
echo
$IN_KERNELb
echo
$IN_KERNEL5
echo
$IN_KERNEL6
# output file
OUT
=
host/inc/stringify.h
...
...
@@ -58,6 +60,7 @@ sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL3 >> $TMP
sed
's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/'
$IN_KERNEL4
>>
$TMP
sed
's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/'
$IN_KERNELb
>>
$TMP
sed
's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/'
$IN_KERNEL5
>>
$TMP
sed
's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/'
$IN_KERNEL6
>>
$TMP
echo
";"
>>
$TMP
echo
"#endif // End of STRINGIFY_H"
>>
$TMP
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment