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carboniferous_AtR_solver.py
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carboniferous_AtR_solver.py
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# -*- coding: utf-8 -*-
"""
Created on Sat Jul 18 11:09:29 2015
@author: bdyer
"""
import DiagenesisMesh
import scipy.integrate as integrate
import matplotlib.pyplot as plt
import numpy as np
import matplotlib
from numpy import load,linspace,meshgrid
from matplotlib import animation
from pylab import rcParams
from matplotlib import gridspec
import pickle
from matplotlib import rcParams
import pandas as pd
import time
from matplotlib.colors import LinearSegmentedColormap
cm_data = pickle.load( open( "viridis.pkl", "rb" ) )
viridis = LinearSegmentedColormap.from_list('viridis', np.flipud(cm_data))
ArrowCanyon=pd.read_csv('samples_ArrowCanyon.csv')
Leadville=pd.read_csv('samples_B416.csv')
BattleshipWash=pd.read_csv('samples_BattleshipWash.csv')
#%%
with plt.style.context('ggplot'):
rcParams.update({'figure.autolayout': True})
fig = plt.figure(figsize=(6, 8))
gs = gridspec.GridSpec(1, 1)
AC = plt.subplot(gs[:,:])
#BW = plt.subplot(gs[:,3:])
AC.scatter(ArrowCanyon.d13c,ArrowCanyon.SAMP_HEIGHT,s=10,color=[.7,.7,.7],edgecolor='none')
AC.set_xlabel('$\delta$13C')
AC.set_ylabel('height(m)')
AC.set_ylim([0,120])
AC.set_xlim([-10,6])
BattleshipWash.d44ca=BattleshipWash.d44ca[BattleshipWash.d44ca<-.9]
cmin=round(np.min([ArrowCanyon.d44ca.min(),BattleshipWash.d44ca.min()]),1)
cmax=round(np.max([ArrowCanyon.d44ca.max(),BattleshipWash.d44ca.max()]),1)
AC.scatter(BattleshipWash.d13c,BattleshipWash.SAMP_HEIGHT-240.0,s=10,color=[.7,.7,.7],edgecolor='none')
cmax=-1.0
d44ca=AC.scatter(ArrowCanyon.d13c,ArrowCanyon.SAMP_HEIGHT,c=ArrowCanyon.d44ca,cmap=viridis,vmin=cmin,vmax=cmax,s=25,edgecolor=[.2,.2,.2])
cbar=fig.colorbar(d44ca,ax=AC,label='$\delta$44Ca', orientation='vertical',pad=.05,shrink=.4,ticks=[ round(a, 1) for a in np.linspace(cmin,cmax,7)])
d44ca=AC.scatter(BattleshipWash.d13c,BattleshipWash.SAMP_HEIGHT-240.0,c=BattleshipWash.d44ca,cmap=viridis,s=25,edgecolor=[.2,.2,.2],vmin=cmin,vmax=cmax)
#%%
meshY=3
meshX=104
v=np.zeros([meshY,meshX])
u=np.ones([meshY,meshX])
aveSpeed=np.sqrt(v.mean()**2+u.mean()**2)
#
#modelData=(ArrowCanyon.d13c[ArrowCanyon.SAMP_HEIGHT<103])
#modelData2=(BattleshipWash.d13c[(((BattleshipWash.SAMP_HEIGHT-240)<103) & ((BattleshipWash.SAMP_HEIGHT-240)>0))])
#modelData=list(modelData)+list(modelData2)
#modelHeight=(ArrowCanyon.SAMP_HEIGHT[ArrowCanyon.SAMP_HEIGHT<103])
#modelHeight2=(BattleshipWash.SAMP_HEIGHT[(((BattleshipWash.SAMP_HEIGHT-240)<103) & ((BattleshipWash.SAMP_HEIGHT-240)>0))]-240.0)
#modelHeight=list(modelHeight)+list(modelHeight2)
#LVData=Leadville.d13c[Leadville.d13c<0]
#LVHeight=Leadville.SAMP_HEIGHT[Leadville.d13c<0]+7
injectionSites=np.zeros([meshY,meshX])
injectionSites=injectionSites>0
injectionSites[:,0]=True
N=100
K=20
rmse=np.zeros((K,N))
rmse2=np.zeros((K,N))
mag=np.linspace(2.5,8.0,K)
age=500000.0
meshd13c=np.zeros((K,N,meshX))
for j in range(K):
ACmesh=DiagenesisMesh.meshRock(meshX,meshY,u,v,2,2,-1,aveSpeed/(10**mag[j]),injectionSites)
for k in range(N):
ACmesh.inject(int(age/N))
meshd13c[j,k,:]=ACmesh.printBox('rock','d13c')[1,:]
# rmse[j,k]=calcRMSE(ACmesh.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),modelData,modelHeight)
# rmse2[j,k]=calcRMSE(ACmesh.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),LVData,LVHeight)
#with plt.style.context('fivethirtyeight'):
# fig=plt.figure(figsize=(16, 5))
# gs = gridspec.GridSpec(1, 2)
# ac = plt.subplot(gs[0,0])
# lv = plt.subplot(gs[0,1])
# acFig=ac.imshow(rmse,cmap=viridis,interpolation='none',extent=[0,age/(1e6),mag[K-1],mag[0]], aspect='auto'); ac.set_ylabel('Advection to Reaction Ratio (10^N)'); ac.set_xlabel('age of diagenesis (Ma)'); fig.colorbar(acFig, ax=ac, label='rmse', orientation='vertical',pad=.0)
# lvFig=lv.imshow(rmse2,cmap=viridis,interpolation='none',extent=[0,age/(1e6),mag[K-1],mag[0]], aspect='auto'); lv.set_ylabel('Advection to Reaction Ratio (10^N)'); lv.set_xlabel('age of diagenesis (Ma)'); fig.colorbar(lvFig, ax=lv, label='rmse', orientation='vertical',pad=.0)
#np.unravel_index(np.argmin(rmse2),rmse2.shape)
def save_object(obj, filename):
with open(filename, 'wb') as output:
pickle.dump(obj, output, pickle.HIGHEST_PROTOCOL)
#save_object(rmse, 'ACrmse4ma.pkl')
#save_object(rmse2, 'LVrmse4ma.pkl')
save_object(meshd13c, 'MeshSolutions_2.pkl')
#%%
ACmesh=DiagenesisMesh.meshRock(meshX,meshY,u,v,2,2,-1,aveSpeed/(10**mag[6]),injectionSites)
ACmesh.inject(int(600000/ACmesh.dt))
with plt.style.context('ggplot'):
rcParams.update({'figure.autolayout': True})
fig = plt.figure(figsize=(6, 8))
gs = gridspec.GridSpec(1, 1)
AC = plt.subplot(gs[:,:])
#BW = plt.subplot(gs[:,3:])
AC.plot(ACmesh.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),lw=2,alpha=.66)
AC.scatter(ArrowCanyon.d13c,ArrowCanyon.SAMP_HEIGHT,s=10,color=[.7,.7,.7],edgecolor='none')
AC.set_xlabel('$\delta$13C')
AC.set_ylabel('height(m)')
AC.set_ylim([0,120])
AC.set_xlim([-10,6])
BattleshipWash.d44ca=BattleshipWash.d44ca[BattleshipWash.d44ca<-.9]
cmin=round(np.min([ArrowCanyon.d44ca.min(),BattleshipWash.d44ca.min()]),1)
cmax=round(np.max([ArrowCanyon.d44ca.max(),BattleshipWash.d44ca.max()]),1)
AC.scatter(BattleshipWash.d13c,BattleshipWash.SAMP_HEIGHT-240.0,s=10,color=[.7,.7,.7],edgecolor='none')
cmax=-1.0
d44ca=AC.scatter(ArrowCanyon.d13c,ArrowCanyon.SAMP_HEIGHT,c=ArrowCanyon.d44ca,cmap='Spectral',vmin=cmin,vmax=cmax,s=25,edgecolor=[.2,.2,.2])
cbar=fig.colorbar(d44ca,ax=AC,label='$\delta$44Ca', orientation='vertical',pad=.05,shrink=.4,ticks=[ round(a, 1) for a in np.linspace(cmin,cmax,7)])
d44ca=AC.scatter(BattleshipWash.d13c,BattleshipWash.SAMP_HEIGHT-240.0,c=BattleshipWash.d44ca,cmap=viridis,s=25,edgecolor=[.2,.2,.2],vmin=cmin,vmax=cmax)
#%% 10300 injections for arrow canyon, now lets try leadville, AtR = 10**4.63
N=20
rmseLV=np.zeros(20)
mag=np.linspace(4,6,20)
for k in range(N):
meshY=3
meshX=101
v=np.zeros([meshY,meshX])
u=np.ones([meshY,meshX])
aveSpeed=np.sqrt(v.mean()**2+u.mean()**2)
AtR=10**(mag[k])
injectionSites=np.zeros([meshY,meshX])
injectionSites=injectionSites>0
injectionSites[:,0]=True
LVmesh=DiagenesisMesh.meshRock(meshX,meshY,u,v,-1.8,2,-1,aveSpeed/AtR,injectionSites)
N=200
INJECTS=10300
rmse=np.zeros(N)
LVData=Leadville.d13c[Leadville.d13c<0]
LVHeight=Leadville.SAMP_HEIGHT[Leadville.d13c<0]
LVmesh.inject(int(9270/LVmesh.dt))
rmseLV[k]=calcRMSE(LVmesh.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),LVData,LVHeight)
with plt.style.context('fivethirtyeight'):
plt.plot(mag,rmseLV)
#%%
meshY=3
meshX=101
v=np.zeros([meshY,meshX])
u=np.ones([meshY,meshX])
aveSpeed=np.sqrt(v.mean()**2+u.mean()**2)
AtR=10**mag[2] #10^4.63
injectionSites=np.zeros([meshY,meshX])
injectionSites=injectionSites>0
injectionSites[:,0]=True
LVmesh=DiagenesisMesh.meshRock(meshX,meshY,u,v,-1.8,2,-1,aveSpeed/AtR,injectionSites)
INJECTS=10300
LVData=Leadville.d13c[Leadville.d13c<0]
LVHeight=Leadville.SAMP_HEIGHT[Leadville.d13c<0]
LVmesh.inject(10300)
#rmseLV[k]=calcRMSE(LVmesh.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),LVData,LVHeight)
#%%
meshY=3
meshX=101
v=np.zeros([meshY,meshX])
u=np.ones([meshY,meshX])
aveSpeed=np.sqrt(v.mean()**2+u.mean()**2)
AtR=10**mag[19] #10^4.63
injectionSites=np.zeros([meshY,meshX])
injectionSites=injectionSites>0
injectionSites[:,0]=True
LVmesh2=DiagenesisMesh.meshRock(meshX,meshY,u,v,2,2,-1,aveSpeed/AtR,injectionSites)
LVData=Leadville.d13c[Leadville.d13c<0]
LVHeight=Leadville.SAMP_HEIGHT[Leadville.d13c<0]
LVmesh2.inject(int(600000)/LVmesh2.dt)
#rmseLV[k]=calcRMSE(LVmesh.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),LVData,LVHeight)
with plt.style.context('ggplot'):
rcParams.update({'figure.autolayout': True})
fig = plt.figure(figsize=(6, 8))
gs = gridspec.GridSpec(1, 1)
LdV = plt.subplot(gs[:,:])
LdV.plot(LVmesh2.printBox('rock','d13c')[1,1:],np.linspace(meshX-1,0,meshX-1),lw=2,alpha=.66)
LdV.scatter(LVData,LVHeight,s=10,color=[.7,.7,.7],edgecolor='none')
LdV.set_xlabel('$\delta$13C')
LdV.set_ylabel('height(m)')
LdV.set_ylim([0,100])
LdV.set_xlim([-10,6])
#%%
def calcRMSE(modelData,modelHeight,sampData,sampHeights):
highResModel=scipy.interpolate.interp1d(modelHeight,modelData)
rmse=np.sqrt((np.sum((highResModel(sampHeights)-sampData)**2))/len(sampData))
return rmse
#%%
import DiagenesisMesh
import scipy.integrate as integrate
import matplotlib.pyplot as plt
import numpy as np
import matplotlib
from numpy import load,linspace,meshgrid
from matplotlib import animation
from pylab import rcParams
from matplotlib import gridspec
import pickle
from matplotlib import rcParams
import pandas as pd
import time
from matplotlib.colors import LinearSegmentedColormap
cm_data = pickle.load( open( "viridis.pkl", "rb" ) )
viridis = LinearSegmentedColormap.from_list('viridis', np.flipud(cm_data))
ArrowCanyon=pd.read_csv('samples_ArrowCanyon.csv')
Leadville=pd.read_csv('samples_B416.csv')
BattleshipWash=pd.read_csv('samples_BattleshipWash.csv')
#%%
meshY=3
meshX=104
v=np.zeros([meshY,meshX])*0.0
u=np.ones([meshY,meshX])*.006
aveSpeed=np.sqrt(v.mean()**2+u.mean()**2)
injectionSites=np.zeros([meshY,meshX])
injectionSites=injectionSites>0
injectionSites[:,0]=True
mesh=DiagenesisMesh.meshRock(meshX,meshY,u,v,2,2,-1,1e-6,injectionSites)
#mesh.inject(int(1.1e6/mesh.dt))
#%%
frames=100
def aniStep(step):
mesh.inject(int(1.1e6/mesh.dt/frames))
with plt.style.context('fivethirtyeight'):
rcParams.update({'figure.autolayout': True})
gs = gridspec.GridSpec(2, 2)
AC = plt.subplot(gs[:,0])
#BW = plt.subplot(gs[:,3:])
AC.scatter(ArrowCanyon.d13c,ArrowCanyon.SAMP_HEIGHT,s=10,color=[.7,.7,.7],edgecolor='none')
AC.set_xlabel('$\delta$13C')
AC.set_ylabel('height(m)')
AC.set_ylim([0,120])
AC.set_xlim([-10,6])
BattleshipWash.d44ca=BattleshipWash.d44ca[BattleshipWash.d44ca<-.9]
cmin=round(np.min([ArrowCanyon.d44ca.min(),BattleshipWash.d44ca.min()]),1)
cmax=round(np.max([ArrowCanyon.d44ca.max(),BattleshipWash.d44ca.max()]),1)
specCM=plt.get_cmap('Spectral')
minCa=-1.4
rangeCa=.4
for i in range(meshX-1):
avCa=np.mean(mesh.printBox('rock','d44ca')[1,i:i+2])
AC.plot(mesh.printBox('rock','d13c')[1,i:i+2],np.linspace(meshX-(i-1),meshX-i,2),color=specCM(np.abs(minCa-avCa)/rangeCa))
AC.scatter(BattleshipWash.d13c,BattleshipWash.SAMP_HEIGHT-240.0,s=10,color=[.7,.7,.7],edgecolor='none')
cmax=-1.0
d44ca=AC.scatter(ArrowCanyon.d13c,ArrowCanyon.SAMP_HEIGHT,c=ArrowCanyon.d44ca,cmap='Spectral',vmin=cmin,vmax=cmax,s=25,edgecolor=[.2,.2,.2])
cbar=fig.colorbar(d44ca,ax=AC,label='$\delta$44Ca', orientation='vertical',pad=.05,shrink=.4,ticks=[ round(a, 1) for a in np.linspace(cmin,cmax,7)])
d44ca=AC.scatter(BattleshipWash.d13c,BattleshipWash.SAMP_HEIGHT-240.0,c=BattleshipWash.d44ca,cmap=viridis,s=25,edgecolor=[.2,.2,.2],vmin=cmin,vmax=cmax)
#cbar=fig.colorbar(d44ca,ax=AC,label='$\delta$44Ca', orientation='vertical',pad=.01,shrink=.25,ticks=[ round(a, 1) for a in np.linspace(cmin,cmax,7)])
#fig.savefig('CaData.pdf', format='pdf', dpi=300)
Xplt = plt.subplot(gs[0,1])
Xplt2 = plt.subplot(gs[1,1])
Xplt.plot(mesh.printBox('rock','d13c')[1,:],mesh.printBox('rock','d44ca')[1,:],color=plt.rcParams['axes.color_cycle'][0])
Xplt.plot(ArrowCanyon.d13c,ArrowCanyon.d44ca,markeredgecolor='none',linestyle='none',marker='o',color=plt.rcParams['axes.color_cycle'][1])
Xplt2.plot(mesh.printBox('rock','d18o')[1,:],mesh.printBox('rock','d44ca')[1,:],color=plt.rcParams['axes.color_cycle'][0])
Xplt2.plot(ArrowCanyon.d18o,ArrowCanyon.d44ca,markeredgecolor='none',linestyle='none',marker='o',color=plt.rcParams['axes.color_cycle'][1])
Xplt.set_xlabel('$\delta$13C')
Xplt.set_ylabel('$\delta$44Ca')
Xplt.set_xlim(-8,3.0)
Xplt2.set_xlabel('$\delta$18O')
Xplt2.set_xlim(-8,0.0)
Xplt2.set_ylabel('$\delta$44Ca')
fig = plt.figure(figsize=(12, 8))
ani = animation.FuncAnimation(fig, aniStep, frames=100)
FFwriter = animation.FFMpegWriter()
ani.save('ArrowCanyon_fits.mp4', dpi=300, writer = FFwriter, fps=30, extra_args=['-vcodec', 'libx264'])
#fig.savefig('crossPlotsModelFit.pdf', format='pdf', dpi=300)