From 9c4c16370ba2dd7b8a40fdd9d54703dfc984d9ec Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 20 Sep 2018 14:39:17 -0500
Subject: [PATCH] Updated nonbonded code so that it caches fits to
"jj-nar-dna-pmf-100Mg.dat"
---
mrdna/config.py | 4 ++
mrdna/model/nbPot.py | 124 ++++++++++++++++---------------------------
2 files changed, 51 insertions(+), 77 deletions(-)
diff --git a/mrdna/config.py b/mrdna/config.py
index 8a7862b..ec7f2f2 100644
--- a/mrdna/config.py
+++ b/mrdna/config.py
@@ -10,6 +10,10 @@ _USER_CONF_DIR = Path(appdirs.user_data_dir())
_USER_CONF_DIR.mkdir(parents=True, exist_ok=True)
_USER_CONF = _USER_CONF_DIR / "mrdna.conf"
+CACHE_DIR = _USER_CONF_DIR / "mrdna.cache"
+CACHE_DIR.mkdir(parents=True, exist_ok=True)
+
+
if _USER_CONF.exists():
with open(_USER_CONF) as ch:
config = json.load(ch)
diff --git a/mrdna/model/nbPot.py b/mrdna/model/nbPot.py
index b93bcee..c421778 100644
--- a/mrdna/model/nbPot.py
+++ b/mrdna/model/nbPot.py
@@ -6,9 +6,11 @@ from scipy.signal import savgol_filter as savgol
from mrdna.model.nonbonded import NonbondedScheme
from mrdna import get_resource_path
+from mrdna.config import CACHE_DIR
+
dxParam = -1
-def maxForce(x,u0,maxForce=40):
+def _maxForce(x,u0,maxForce=40):
maxForce = maxForce * 0.014393265 # convert pN to kcal_mol/AA
dx = np.diff(x)
f = -np.diff(u0)/dx
@@ -27,7 +29,6 @@ def maxForce(x,u0,maxForce=40):
assert( np.isnan(u).sum() == 0 )
return u
-# d = np.loadtxt("resources/jj-nar-dna-pmf-20Mg-200Na.dat")
d = np.loadtxt(get_resource_path("jj-nar-dna-pmf-100Mg.dat"))
x0 = d[:,1] + dxParam
@@ -51,26 +52,6 @@ def integrate_potential(potfn,x,y,*parms):
u = u + potfn(r,*parms) # * x/r
return u
-
-# def integrated_potential(potfn,x,numBp,*parms):
-# u = np.zeros(np.shape(x))
-# for h in range(-numBp,numBp+1):
-# r = np.sqrt(x**2 + (3.4*h)**2)
-# r[r<1] = 1
-# u = u + potfn(r,*parms) # * x/r
-# return u
-
-def fitFun(x,*parms):
- ## 1-turn iteracting with 4 turns (more is not needed)
- y = np.arange(-20,21)*3.4
- return 10 * integrate_potential(parametric_potential,x,y,*parms)
-
-def fitFun5(x,*parms):
- ## 1-turn iteracting with 4 turns (more is not needed)
- y = np.arange(-20,21)*(5*3.4)
- return 5 * 5 * integrate_potential(parametric_potential,x,y,*parms)
-
-
xinterp = np.linspace(np.min(x0),np.max(x0),1000) # interpolate potentialb
yinterp = interp1d(x0,y0)(xinterp)
@@ -83,49 +64,52 @@ def fit_potential(bp1,bp2):
return (10.0/bp1) * integrate_potential(parametric_potential,x,y,*parms)
popt, pcov = opt.curve_fit(fitFun, xinterp, yinterp, p0=y0/10**2 ) # find fit to interpolated potential
- return lambda x: parametric_potential(x,*popt)
-
+ return popt
+ # return lambda x: parametric_potential(x,*popt)
-def nbPot(x,bps1,bps2):
+def _round_bp(bp):
+ return 10**(np.around(np.log10(bp)*100)/100.0)
+
+_pot_dict = {}
+_pot_dict_full = {}
+def nbPot_full(x,bps1,bps2):
larger = np.max([bps1,bps2])
smaller = np.min([bps1,bps2])
- if larger >= 2:
- largerInt = int(0.5*larger)
- smaller *= larger/(2*largerInt)
- y = np.arange(-largerInt,largerInt+1)*3.4
- u = smaller * integrate_potential(parametric_potential,x,y,*popt)
- else:
- u = smaller * larger * parametric_potential(x,*popt)
- u1 = maxForce(x,u, 100)
+ key = (smaller,larger)
+ if key not in _pot_dict:
+ _pot_dict_full[key] = fit_potential(*key)
+ u = parametric_potential(x,*_pot_dict_full[key])
+
+ u1 = _maxForce(x,u, 100)
# u2 = savgol(u1, int(5.0/(x0[1]-x0[0])), 3)
u2 = u
assert(np.sum(np.isnan(u2)) == 0)
return u2
-_pot_dict = {}
-
def nbPot(x,bps1,bps2):
larger = np.max([bps1,bps2])
smaller = np.min([bps1,bps2])
- key = (smaller,larger)
- if key not in _pot_dict:
- _pot_dict[key] = fit_potential(*key)
- u = _pot_dict[key](x)
+ smaller_shift, larger_shift = [_round_bp(bp) for bp in (smaller,larger)]
- u1 = maxForce(x,u, 100)
- # u2 = savgol(u1, int(5.0/(x0[1]-x0[0])), 3)
+ key = (smaller_shift,larger_shift)
+ if key not in _pot_dict:
+ cache_file = CACHE_DIR / "nbPot-{}-{}.npz".format(*key)
+ try:
+ _pot_dict[key] = np.load(cache_file)['arr_0'].tolist()
+ except:
+ print("Could not find cache file for {}".format("nbPot-{}-{}.npz".format(*key)))
+ _pot_dict[key] = fit_potential(*key)
+ np.savez(cache_file, _pot_dict[key])
+
+ u = parametric_potential(x,*_pot_dict[key])
+ u = u * ( (smaller/smaller_shift)*(larger/larger_shift) )
+
+ u1 = _maxForce(x,u, 100)
+ u2 = savgol(u1, int(5.0/(x0[1]-x0[0])), 3)
u2 = u
assert(np.sum(np.isnan(u2)) == 0)
return u2
-x = np.linspace(0,100,1001)
-
-# np.savetxt("potentials/nb.orig.dat",np.array([x0,y0 ]).T)
-# np.savetxt("potentials/nb.orig-interp.dat",np.array([xinterp,yinterp ]).T)
-# np.savetxt("potentials/nb.fit.dat",np.array([x,fitFun(x,*popt)]).T)
-# np.savetxt("potentials/nb.fit2.dat",np.array([x,nbPot(x,10,40)]).T)
-
-
def _writeNonbondedParameterFiles(self, prefix):
x = np.arange(0, 50, 0.1)
for i,j,t1,t2 in self._particleTypePairIter():
@@ -149,35 +133,21 @@ class nbDnaScheme(NonbondedScheme):
return u
nbDnaScheme = nbDnaScheme()
-if __name__ == "__main__":
- ## run some tests
+def _run():
np.savetxt("jj-filtered.dat", np.array((x0,y0)).T)
+ x = np.arange(0, 50, 0.1)
+ ## run some tests
+ for i in (0.5,1,1.05,2,3.333,5):
+ for j in (1,1.05,1.1,2,3.333, 4,5):
+ if i > j: continue
+
+ # y = (10.0/i)*integrate_potential(nbPot_full, x, np.arange(-20,20)*(3.4*j) , i, j)
+ # np.savetxt("test1-{}-{}.dat".format(i,j), np.array((x,y)).T),
- # y = single_bp_pot = fitFun(x,*popt)
- # np.savetxt("1-bp-fit.dat", np.array((x,y)).T),
-
- # y = fitFun5(x,*popt5)
- # np.savetxt("5-bp-fit.dat", np.array((x,y)).T),
-
-
- # tmp = nbPot(np.linspace(20,45,100), 1,1)
- # import pdb
- # pdb.set_trace()
- y = 10*integrate_potential(nbPot, x, np.arange(-20,20)*3.4 , 1, 1)
- np.savetxt("nb-1-1.dat", np.array((x,y)).T),
-
- y = 10*integrate_potential(nbPot, x, np.arange(-20,20)*(3.4*2) , 1, 2)
- np.savetxt("nb-1-2.dat", np.array((x,y)).T),
-
- y = 10*integrate_potential(nbPot, x, np.arange(-20,20)*(3.4*5) , 1, 5)
- np.savetxt("nb-1-5.dat", np.array((x,y)).T),
-
- y = 5*integrate_potential(nbPot, x, np.arange(-20,20)*(3.4*2) , 2, 2)
- np.savetxt("nb-2-2.dat", np.array((x,y)).T),
-
- y = 2*integrate_potential(nbPot, x, np.arange(-20,20)*(3.4*5) , 5, 5)
- np.savetxt("nb-5-5.dat", np.array((x,y)).T),
+ y = (10.0/i)*integrate_potential(nbPot, x, np.arange(-20,20)*(3.4*j) , i, j)
+ np.savetxt("test2-{}-{}.dat".format(i,j), np.array((x,y)).T),
- # y = 10*5*integrate_potential(parametric_potential, x, np.arange(-20,20)*(3.4*5) , *popt)
- # np.savetxt("scale-5-5.dat", np.array((x,y)).T),
+if __name__ == "__main__":
+ import cProfile
+ cProfile.run("_run()")
--
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