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#include <stan/math/rev/core.hpp>
#include <test/unit/math/rev/mat/util.hpp>
#include <gtest/gtest.h>
#include <algorithm>
#include <sstream>
#include <tuple>
#include <vector>
#include <chrono>

namespace stan {

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#include <stan/math/rev/core.hpp>
#include <test/unit/math/rev/mat/util.hpp>
#include <gtest/gtest.h>
#include <algorithm>
#include <random>
#include <sstream>
#include <tuple>

namespace stan {
  namespace math {

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#include <iostream>
#include "stan/math.hpp"
#include "stan/math/fwd/mat.hpp"

using namespace stan::math;

template<typename T1, typename T2>
std::vector<typename stan::return_type<T1, T2>::type > ode(const double& t,
                   const std::vector<T1>& u,
                   const std::vector<T2>& D,

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        for(int i = 0; i < y.size(); i++) {
          if(i > 0)
            y_var[i - 1].d_ = 0.0;
          y_var[i].d_ = 1.0;

          vector<fvar<double> > dy_dt_var = f_(t, y_var, thetavar, x_, x_int_, msgs_);
          if(i == 0) {
            for(int j = 0; j < y.size(); j++) {
              dy_dt(j) = dy_dt_var[j].val();
            }

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// Build with: clang++ -Wall -I . -isystem lib/eigen_3.3.3 -isystem lib/boost_1.64.0 -isystem lib/cvodes_2.9.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -Wno-unused-function -Wno-uninitialized -DNO_FPRINTF_OUTPUT -pipe test2.cpp  -O3 -o test2 lib/cvodes_2.9.0/lib/libsundials_nvecserial.a lib/cvodes_2.9.0/lib/libsundials_cvodes.a
#include <iostream>
#include "stan/math.hpp"

using namespace stan::math;

// This is a 1D diffusion PDE with a spatially varying diffusion coefficient.
// So if the domain is like this:
// x--o--x--o--x--o--x
// Then diffusion coefficients are defined at the xs and the state is at the o

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#%%

import matplotlib.pyplot as plt
import pystan
import numpy

model_code = """
data {
  int<lower=1> N;
  vector[N] y;

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#%%

import matplotlib.pyplot as plt
import pystan
import numpy

model_code = """
data {
  int<lower=1> N; // Number of single samples
  vector[N] t;

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bbales2@frog:~/smath$ make test/unit/math/mix/mat/prob/categorical_test
make: Warning: Archive 'test/libgtest.a' seems to have been created in deterministic mode. 'test/gtest.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rv test/libgtest.a test/gtest.o
r - test/gtest.o
make: Warning: Archive 'test/libgtest.a' seems to have been created in deterministic mode. 'test/gtest.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
g++ -I . -isystem lib/eigen_3.2.9 -isystem lib/boost_1.62.0 -isystemlib/cvodes_2.9.0/include -Wall -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DNO_FPRINTF_OUTPUT -pipe -fPIC   -c -O3 -DGTEST_USE_OWN_TR1_TUPLE -DGTEST_HAS_PTHREAD=0 -isystem lib/gtest_1.7.0/include -isystem lib/gtest_1.7.0 test/unit/math/mix/mat/prob/categorical_test.cpp -o test/unit/math/mix/mat/prob/categorical_test.o
In file included from ./stan/math/fwd/core.hpp:4:0,
                 from ./stan/math/mix/mat/fun/t

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bbales2@frog:~/stan3$ make test/unit/mcmc/hmc/integrators/impl_leapfrog2
make: Warning: Archive 'test/libgtest.a' seems to have been created in deterministic mode. 'test/gtest.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rv test/libgtest.a test/gtest.o
r - test/gtest.o
make: Warning: Archive 'test/libgtest.a' seems to have been created in deterministic mode. 'test/gtest.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
g++ -I src -isystem lib/stan_math/lib/eigen_3.2.9 -isystem lib/stan_math/lib/boost_1.62.0 -isystem lib/stan_math/lib/cvodes_2.9.0/include -isystem lib/stan_math/ -Wall -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe    -c -O3 -DGTEST_USE_OWN_TR1_TUPLE -DGTEST_HAS_PTHREAD=0 -isystem lib/stan_math/lib/gtest_1.7.0/include -isystem lib/stan_math/lib/gtest_1.7.0 src/test/unit/mcmc/hmc/integrators/impl_leapfrog2_test.cpp -o test/unit/mcmc/

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// Adjusted version of stan-generated cpp code for the calculate_r() function
inline Eigen::Matrix<var, Eigen::Dynamic,1> calculate_r(
                    const Eigen::Matrix<var, Eigen::Dynamic,1>& lambda,
                    const std::vector<std::vector<int> >& lambda_select,
                    const Eigen::Matrix<double, Eigen::Dynamic,Eigen::Dynamic>& M,
                    const std::vector<std::vector<std::vector<int> > >& ht_select,
                    const std::vector<std::vector<std::vector<std::vector<int> > > >& ht_gmap,
                    const std::vector<std::vector<int> >& Ht,
                    const Eigen::Matrix<double, Eigen::Dynamic,Eigen::Dynamic>& Z,
                    const std::vector<int>& Z_type,