descriptors/d2/d2_eam.cpp

@@ -12,7 +12,7 @@ D2_EAM::D2_EAM(Config &c):
 	ef.file_path = c("SETFL")[0];
 	read_setfl();
 
-	if (abs(ef.rcut - c.get<double>("RCUT2B")) > std::numeric_limits<double>::min()) {
+	if (std::abs(ef.rcut - c.get<double>("RCUT2B")) > std::numeric_limits<double>::min()) {
         if (verbose) {
             std::cout << std::endl;
             std::cout << "Config file cutoff and setfl file cutoff differ: "

descriptors/d_base.h

@@ -2,8 +2,7 @@
 #define D_BASE_H
 
 #include "../../CORE/config/config.h"
-#include "../../CORE/typedefs.h"
-#include "../../LIBS/Eigen/Dense"
+#include "../../CORE/core_types.h"
 #include "../../CORE/registry.h"
 
 /** \brief Base class for all descriptor types.

descriptors/dm/dm_eam.cpp

@@ -12,7 +12,7 @@ DM_EAM::DM_EAM(Config &c):
     ef.file_path = c("SETFL")[0];
     read_setfl();
 
-    if (abs(ef.rcut - c.get<double>("RCUTMB")) > std::numeric_limits<double>::min()) {
+    if (std::abs(ef.rcut - c.get<double>("RCUTMB")) > std::numeric_limits<double>::min()) {
         if (verbose) {
             std::cout << "Config file cutoff and setfl file cutoff differ: "
                 << c.get<double>("RCUTMB") << " " << ef.rcut << std::endl;
@@ -193,8 +193,6 @@ void DM_EAM::init_rhoi(rho_type& rhoi)
 {
     rhoi.resize(2);
     rhoi.setZero();
-    //rho.resize(1);
-    //rho[0] = Eigen::Matrix<double,1,2>(1,2);    // [0] - rho, [1] - rho prime aka fp[i]
 }
 void DM_EAM::calc_rho(
 		const double rij,
@@ -210,7 +208,6 @@ void DM_EAM::calc_rho(
     p -= m;
     p = std::min(p,1.0);
     std::vector<double> coeff = rhor_spline[m];
-    // rho[i]
     rho(0) += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
 
 }

ea.h

@@ -3,7 +3,7 @@
 
 #include "../LIBS/Eigen/Dense"
 #include "../CORE/config/config.h"
-#include "../CORE/typedefs.h"
+#include "../CORE/eigen_types.h"
 
 class EA {
     private:

ekm.h

@@ -2,8 +2,8 @@
 #define EKM_H
 
 #include "../LIBS/Eigen/Dense"
-#include "../CORE/typedefs.h"
-#include "../CORE/coretypes.h"
+#include "../CORE/eigen_types.h"
+#include "../CORE/core_types.h"
 
 template <typename K>
 class EKM {

functions/basis_functions/bf_base.h

 #ifndef BASIS_FUNCTIONS_H
 #define BASIS_FUNCTIONS_H
 
-#include "../../../CORE/typedefs.h"
+#include "../../../CORE/core_types.h"
 #include "../function_base.h"
 
 #include <iostream>

functions/function_base.h

@@ -2,7 +2,8 @@
 #define FUNCTION_BASE_h
 
 #include "../../CORE/registry.h"
-#include "../../CORE/typedefs.h"
+#include "../../CORE/core_types.h"
+#include "../../CORE/eigen_types.h"
 #include "../../CORE/config/config.h"
 
 #include <iomanip>

functions/kernels/kern_base.h

 #ifndef KERN_BASE_H
 #define KERN_BASE_H
 
-#include "../../../CORE/typedefs.h"
+#include "../../../CORE/core_types.h"
 #include "../function_base.h"
 
 #include <iostream>

linear_regressor.h

@@ -2,7 +2,8 @@
 #define LINEAR_REGRESSOR_H
 
 #include "../CORE/config/config.h"
-#include "../CORE/typedefs.h"
+#include "../CORE/eigen_types.h"
+#include "../CORE/core_types.h"
 #include "../LIBS/Eigen/Dense"
 #include "ea.h"
 #include <vector>

m_core.h

 #ifndef M_Core_H
 #define M_Core_H
 
-#include "../CORE/typedefs.h"
+#include "../CORE/core_types.h"
+#include "../CORE/eigen_types.h"
 
 class M_Core {
     public: