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tadded forcechain vis. method (untested), fixed bond bugs - sphere - GPU-based … |
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git clone git://src.adamsgaard.dk/sphere |
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LICENSE |
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--- |
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commit b62c9479b44eeba854093a26b5ad4c19325ae6a8 |
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parent 658c4499b8a4ee10c5ca6fddcb8ca22514cd26e0 |
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Author: Anders Damsgaard <[email protected]> |
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Date: Tue, 12 Mar 2013 05:30:44 +0100 |
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added forcechain vis. method (untested), fixed bond bugs |
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Diffstat: |
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M python/sphere.py | 67 ++++++++++++++++++++++++-----… |
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1 file changed, 53 insertions(+), 14 deletions(-) |
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--- |
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diff --git a/python/sphere.py b/python/sphere.py |
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t@@ -695,6 +695,20 @@ class Spherebin: |
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x_j[2] = x_j[2] + dist_ij * numpy.sin(ang) * numpy.cos(azi) |
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self.x[j] = x_j |
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+ if (self.x[j,0] < self.origo[0]): |
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+ self.x[j,0] += x_i[0] - x_j[0] |
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+ if (self.x[j,1] < self.origo[1]): |
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+ self.x[j,1] += x_i[1] - x_j[1] |
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+ if (self.x[j,2] < self.origo[2]): |
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+ self.x[j,2] += x_i[2] - x_j[2] |
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+ |
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+ if (self.x[j,0] > self.L[0]): |
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+ self.x[j,0] -= abs(x_j[0] - x_i[0]) |
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+ if (self.x[j,1] > self.L[1]): |
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+ self.x[j,1] -= abs(x_j[1] - x_i[1]) |
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+ if (self.x[j,2] > self.L[2]): |
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+ self.x[j,2] -= abs(x_j[2] - x_i[2]) |
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+ |
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self.bond(i,j) # register bond |
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# Check that the spacing is correct |
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t@@ -706,6 +720,7 @@ class Spherebin: |
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print(x_ij_length); print(dist_ij) |
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raise Exception("Error, something went wrong in createBondPair") |
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+ |
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def random2bonds(self, ratio=0.3, spacing=-0.1): |
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""" Bond an amount of particles in two-particle clusters |
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@param ratio: The amount of particles to bond, values in ]0.0;1.0] (fl… |
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t@@ -716,14 +731,12 @@ class Spherebin: |
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specified, due to the random selection algorithm. |
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""" |
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- bondparticles = numpy.unique(numpy.random.random_integers(0, high=self… |
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+ bondparticles = numpy.unique(numpy.random.random_integers(0, high=self… |
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if (bondparticles.size % 2 > 0): |
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bondparticles = bondparticles[:-1].copy() |
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bondparticles = bondparticles.reshape(int(bondparticles.size/2), 2).co… |
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- print(bondparticles.size) |
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- print(bondparticles.shape) |
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- for n in numpy.arange(self.nb0): |
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+ for n in numpy.arange(bondparticles.shape[0]): |
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self.createBondPair(bondparticles[n,0], bondparticles[n,1], spacin… |
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t@@ -1028,15 +1041,18 @@ class Spherebin: |
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return numpy.sum(self.ev_dot) |
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elif method == 'bondpot': |
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- R_bar = self.lambda_bar * numpy.min(self.radius[self.bonds[:,0]], … |
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- A = numpy.pi * R_bar**2 |
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- I = 0.25 * numpy.pi * R_bar**4 |
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- J = I*2.0 |
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- bondpot_fn = numpy.sum(0.5 * A * self.k_n * numpy.abs(self.bonds_d… |
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- bondpot_ft = numpy.sum(0.5 * A * self.k_t * numpy.linalg.norm(self… |
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- bondpot_tn = numpy.sum(0.5 * J * self.k_t * numpy.abs(self.bonds_o… |
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- bondpot_tt = numpy.sum(0.5 * I * self.k_n * numpy.linalg.norm(self… |
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- return bondpot_fn + bondpot_ft + bondpot_tn + bondpot_tt |
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+ if (self.nb0 > 0): |
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+ R_bar = self.lambda_bar * numpy.min(self.radius[self.bonds[:,0… |
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+ A = numpy.pi * R_bar**2 |
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+ I = 0.25 * numpy.pi * R_bar**4 |
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+ J = I*2.0 |
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+ bondpot_fn = numpy.sum(0.5 * A * self.k_n * numpy.abs(self.bon… |
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+ bondpot_ft = numpy.sum(0.5 * A * self.k_t * numpy.linalg.norm(… |
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+ bondpot_tn = numpy.sum(0.5 * J * self.k_t * numpy.abs(self.bon… |
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+ bondpot_tt = numpy.sum(0.5 * I * self.k_n * numpy.linalg.norm(… |
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+ return bondpot_fn + bondpot_ft + bondpot_tn + bondpot_tt |
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+ else : |
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+ return 0.0 |
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def voidRatio(self): |
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'Returns the current void ratio' |
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t@@ -1185,7 +1201,7 @@ class Spherebin: |
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def shearstrain(self): |
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- 'Calculates and returns the shear strain (gamma) value of the experime… |
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+ 'Calculates and returns the current shear strain (gamma) value of the … |
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# Current height |
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w_x0 = self.w_x[0] |
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t@@ -1196,6 +1212,29 @@ class Spherebin: |
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# Return shear strain |
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return xdisp/w_x0 |
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+ def forcechains(self, lc=200.0, uc=650.0, outformat='png', disp='2d'): |
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+ ''' Visualizes the force chains in the system from the magnitude of the |
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+ normal contact forces, and produces an image of them. |
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+ @param lc: Lower cutoff of contact forces. Contacts below are not |
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+ visualized (float) |
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+ @param uc: Upper cutoff of contact forces. Contacts above are |
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+ visualized with this value (float) |
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+ @param outformat: Format of output image. Possible values are |
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+ 'interactive', 'png', 'epslatex', 'epslatex-color' |
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+ @param disp: Display forcechains in '2d' or '3d' |
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+ Warning: Will segfault if no contacts are found. |
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+ ''' |
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+ |
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+ self.writebin() |
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+ |
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+ nd = '' |
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+ if (disp == '2d'): |
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+ nd = '-2d ' |
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+ |
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+ subprocess.call("cd .. && ./forcechains " + nd + "-f " + outformat + "… |
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+ subprocess.call("gnuplot tmp.gp && rm tmp.bin && rm tmp.gp", shell=Tru… |
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+ |
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+ |
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def thinsection_x1x3(self, |
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x2 = 'center', |
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graphicsformat = 'png', |
