Sourcery Starbot ⭐ refactored leshaker/python_integration #1
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@@ -3,7 +3,7 @@ | |
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| from helper_funs import * | ||
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| def parseSym(model_dict): | ||
| ''' | ||
| parse model variables and parameters to symbolic variables | ||
| and calculate derivatives | ||
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@@ -16,14 +16,14 @@ def parseSym(model_dict): | |
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| # get model name | ||
| model_name = cleanModelName(model_dict) | ||
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| # define x names | ||
| ode_species = list(model_dict['odes']) | ||
| ode_alg_species = model_dict['vars'] | ||
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| # read algebraic equations | ||
| if 'alg_eqs' in model_dict: | ||
| alg_eqs_species = list(model_dict['alg_eqs']) | ||
| # define rhs of alg. eqs | ||
| alg_eqs = [model_dict['alg_eqs'][species] for species in alg_eqs_species] | ||
| else: | ||
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@@ -32,7 +32,7 @@ def parseSym(model_dict): | |
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| # define p names | ||
| parameters = model_dict['pars'] | ||
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| # define t name | ||
| t_name = 't' | ||
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@@ -105,27 +105,23 @@ def writeInitSundials(model_dict,xs,ps,fs,xs_alg,gs,atol=1e-6,rtol=1e-6,hmin=0.0 | |
| if not os.path.exists('includes'): | ||
| os.mkdir('./includes') | ||
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| fname_def = f'{model_name}_define.c' | ||
| with open(f'./includes/{fname_def}', 'w') as fid: | ||
| define_str = "#define NPARS %d\t\t/* number of parameters */\n" % (len(ps)) | ||
| define_str = define_str+"#define NEQ %d\t\t/* number of equations */\n" % len(fs) | ||
| fid.write(define_str) | ||
| fname_init = f'{model_name}_initialize.c' | ||
| with open(f'./includes/{fname_init}', 'w') as fid: | ||
| if (type(atol)!=list): | ||
| atol = [atol for _ in range(len(fs))] | ||
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| init_str = "hmin = RCONST(%e);\t\t/* minimal stepsize */\n" % hmin | ||
| init_str = init_str + "hmax = RCONST(%e);\t\t/* maximal stepsize */\n" % hmax | ||
| init_str = init_str + "mxsteps = RCONST(%e);\t\t/* maximal number of steps */\n" % mxsteps | ||
| init_str = init_str + "reltol = RCONST(%e);\t\t/* scalar relative tolerance */\n" % rtol | ||
| for i in range(len(fs)): | ||
| init_str = init_str + "Ith(abstol,%d) = RCONST(%e);\t\t/* vector absolute tolerance components */\n" % (i+1, atol[i]) | ||
| fid.write(init_str) | ||
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| return 1 | ||
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@@ -134,10 +130,7 @@ def writeOdeSundials(model_dict,xs,ps,fs,xs_alg,gs,checknegative): | |
| write ODEs to c-file for sundials | ||
| ''' | ||
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| checknegative_c = "TRUE" if checknegative else "FALSE" | ||
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This removes the following comments ( why? ): |
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| # get model name | ||
| model_name = cleanModelName(model_dict) | ||
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@@ -146,82 +139,83 @@ def writeOdeSundials(model_dict,xs,ps,fs,xs_alg,gs,checknegative): | |
| gs_c = convToCstr(gs) | ||
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| alg_dict = dict(zip(xs_alg,gs_c)) | ||
| fname_ode = f'{model_name}_ode_f.c' | ||
| with open(f'./includes/{fname_ode}', 'w') as fid: | ||
| header = ( | ||
| "static int f(realtype t, N_Vector x, N_Vector xdot, void *user_data)\n" | ||
| + "{\n\n" | ||
| ) | ||
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| header += "\tint i;" | ||
| header += "\tUserData data;\n" | ||
| header += "\tbooleantype check_negative = %s;\n" % (checknegative_c) | ||
| fid.write(header) | ||
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| par_def = ( | ||
| "\t/* Extract needed constants from data */\n" | ||
| + "\tdata = (UserData) user_data;\n" | ||
| ) | ||
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| par_def += "\tdouble p[NPARS];\n" | ||
| par_def += "\tfor (i=0; i<NPARS; i++) p[i] = data->p[i];\n\n" | ||
| fid.write(par_def) | ||
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| for i, p in enumerate(ps): | ||
| tmp_str = '\trealtype %s = p[%d];\n' % (p, i) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # tmp_str = "\tprintf(\"\\n\\n\");\n" | ||
| # fid.write(tmp_str) | ||
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| # write variables definitions | ||
| for i, x in enumerate(xs): | ||
| tmp_str = '\trealtype %s = Ith(x,%d);\n' % (x, i+1) | ||
| fid.write(tmp_str) | ||
| # tmp_str = "\tprintf(\"%%f\\n\", %s);\n" % (x) | ||
| # fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # write alg eqs definitions | ||
| for alg in alg_dict: | ||
| tmp_str = '\t%s = %s;\n' % (alg,alg_dict[alg]) | ||
| fid.write(tmp_str) | ||
| # tmp_str = "\tprintf(\"%%f\\n\", %s);\n" % (alg) | ||
| # fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # tmp_str = "\tprintf(\"\\n\\n\");\n" | ||
| # fid.write(tmp_str) | ||
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| # # check for neg species # FIXME! | ||
| # non_neg_spec = [sp.origins[model.name] for sp in model.sp_obj if not sp.type == 'thermodynamic'] | ||
| # non_neg_spec_cond = ["%s<-1e-5" % (spec) for spec in non_neg_spec] | ||
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| # fid.write("\t%s%s%s" % ("if (check_negative && (", " || ".join(non_neg_spec_cond),")) {\n")) | ||
| # # fid.write("\t\tprintf(\"%s\\n\", \"At least one species turned negative!\");\n") | ||
| # fid.write("\t\treturn(1);\n") | ||
| # fid.write("\t}\n") | ||
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| # write odes | ||
| for i, f in enumerate(fs_c): | ||
| if f not in ['0', '0.0', 0]: | ||
| tmp_str = '\tIth(xdot,%d) = %s;\n' % (i+1, f) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # write variables definitions | ||
| for i, x in enumerate(xs): | ||
| if x in xs_alg: | ||
| tmp_str = '\tIth(x,%d) = %s;\n' % (i+1, x) | ||
| fid.write(tmp_str) | ||
| # tmp_str = "\tprintf(\"%%f\\n\", %s);\n" % (x) | ||
| # fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # write footer | ||
| footer = '\treturn(0);\n}\n' | ||
| fid.write(footer) | ||
| return 1 | ||
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| def writeJacSundials(model_dict,xs,ps,fs,xs_alg,gs,dfdx): | ||
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@@ -235,63 +229,64 @@ def writeJacSundials(model_dict,xs,ps,fs,xs_alg,gs,dfdx): | |
| gs_c = convToCstr(gs) | ||
| alg_dict = dict(zip(xs_alg,gs_c)) | ||
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| fname_jac = f'{model_name}_ode_jac.c' | ||
| with open(f'./includes/{fname_jac}', 'w') as fid: | ||
| header = ( | ||
| "static int Jac(long int N, realtype t, N_Vector x, N_Vector fx, DlsMat J, void *user_data,\nN_Vector tmp1, N_Vector tmp2, N_Vector tmp3)\n" | ||
| + "{\n\n" | ||
| ) | ||
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| header += "\tint i, j;\n" | ||
| header += "\tUserData data;\n" | ||
| fid.write(header) | ||
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| par_def = ( | ||
| "\t/* Extract needed constants from data */\n" | ||
| + "\tdata = (UserData) user_data;\n" | ||
| ) | ||
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| par_def += "\tdouble p[NPARS];\n" | ||
| par_def += "\tfor (i=0; i<NPARS; i++) p[i] = data->p[i];\n\n" | ||
| fid.write(par_def) | ||
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| # write parameter definitions | ||
| for i, p in enumerate(ps): | ||
| tmp_str = '\trealtype %s = p[%d];\n' % (p, i) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| #write variables definitions | ||
| for i, x in enumerate(xs): | ||
| tmp_str = '\trealtype %s = Ith(x,%d);\n' % (x, i+1) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| #write alg eqs | ||
| for alg in alg_dict: | ||
| tmp_str = '\t%s = %s;\n' % (alg,alg_dict[alg]) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # write jacobian | ||
| for i in range(dfdx.shape[0]): | ||
| for j in range(dfdx.shape[1]): | ||
| if dfdx[i, j] != 0: | ||
| # convert formula to c-style | ||
| dfdx_c = convToCstr([dfdx[i,j]]) | ||
| tmp_str = '\tIJth(J,%d,%d) = %s;\n' % (i+1,j+1, dfdx_c[0]) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # write variables definitions | ||
| for i, x in enumerate(xs): | ||
| if x in xs_alg: | ||
| tmp_str = '\tIth(x,%d) = %s;\n' % (i+1, x) | ||
| fid.write(tmp_str) | ||
| fid.write('\n') | ||
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| # write footer | ||
| footer = '\treturn(0);\n}\n' | ||
| fid.write(footer) | ||
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| return 1 | ||
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@@ -452,7 +447,7 @@ def writeModelFiles(model_dict,force=False,atol=1e-6,rtol=1e-6,hmin=0.0,hmax=0.0 | |
| if force or (len(bin_exists) != 1 or bin_exists[0]==False): | ||
| # remove old bin files | ||
| for bin in bin_files: | ||
| rm_cmd = f"rm -rf {os.path.join('./bin/', bin)}" | ||
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| os.system(rm_cmd) | ||
| # parse model | ||
| (xs,ps,fs,xs_alg,gs,dfdx) = parseSym(model_dict) | ||
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@@ -474,9 +469,7 @@ def objectiveFunction(model_dict,initvars,initpars,data,tExp): | |
| model_dict['initvars'] = initvars | ||
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| t,x = integrateSundials(model_dict,tSim=tExp) | ||
| return np.sum((x-data['x'])**2/data['sd']**2) | ||
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| def convertToD2D(model_dict,savepath='./D2D'): | ||
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Function
parseSymrefactored with the following changes:identity-comprehension)