1 | !> @file surface_output_merge.f90 |
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2 | !------------------------------------------------------------------------------! |
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3 | ! This file is part of the PALM model system. |
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4 | ! |
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5 | ! PALM is free software: you can redistribute it and/or modify it under the |
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6 | ! terms of the GNU General Public License as published by the Free Software |
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7 | ! Foundation, either version 3 of the License, or (at your option) any later |
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8 | ! version. |
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9 | ! |
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10 | ! PALM is distributed in the hope that it will be useful, but WITHOUT ANY |
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11 | ! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR |
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12 | ! A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
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13 | ! |
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14 | ! You should have received a copy of the GNU General Public License along with |
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15 | ! PALM. If not, see <http://www.gnu.org/licenses/>. |
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16 | ! |
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17 | ! Copyright 1997-2018 Leibniz Universitaet Hannover |
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18 | !------------------------------------------------------------------------------! |
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19 | ! |
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20 | ! Current revisions: |
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21 | ! ----------------- |
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22 | ! |
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23 | ! |
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24 | ! Former revisions: |
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25 | ! ----------------- |
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26 | ! $Id: surface_output_to_vtk.f90 3523 2018-11-13 16:09:31Z raasch $ |
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27 | ! Implement interface for posix conform C-systemcalls in order to replace |
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28 | ! non-standard FORTRAN functions ftell and fseek. |
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29 | ! |
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30 | ! 3496 2018-11-06 15:59:50Z suehring |
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31 | ! Use subroutine call for fseek instead of function call. gfortran has some |
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32 | ! problems with this. |
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33 | ! |
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34 | ! 3494 2018-11-06 14:51:27Z suehring |
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35 | ! Initial version |
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36 | ! |
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37 | ! Authors: |
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38 | ! -------- |
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39 | ! @author Matthias Suehring and Klaus Ketelsen |
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40 | ! |
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41 | !------------------------------------------------------------------------------! |
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42 | ! Description: |
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43 | ! ------------ |
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44 | !> Interface to posix systemcalls. The module allows to call the following |
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45 | !> C system calls from FORTRAN: ftell, lseek. |
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46 | !------------------------------------------------------------------------------! |
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47 | MODULE posix_interface |
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48 | |
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49 | INTERFACE |
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50 | INTEGER (C_SIZE_T) FUNCTION C_LSEEK (fd, offset, whence) & |
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51 | BIND(C, NAME='lseek') |
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52 | |
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53 | USE ISO_C_BINDING |
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54 | |
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55 | IMPLICIT NONE |
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56 | |
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57 | INTEGER(KIND=C_INT), VALUE :: fd |
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58 | INTEGER(KIND=C_SIZE_T), VALUE :: offset |
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59 | INTEGER(KIND=C_INT), VALUE :: whence |
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60 | |
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61 | END FUNCTION C_LSEEK |
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62 | |
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63 | END INTERFACE |
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64 | |
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65 | INTERFACE |
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66 | INTEGER (C_SIZE_T) FUNCTION C_FTELL ( fd ) & |
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67 | BIND(C, NAME='ftell') |
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68 | |
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69 | USE ISO_C_BINDING |
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70 | |
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71 | IMPLICIT NONE |
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72 | |
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73 | INTEGER(KIND=C_INT), VALUE :: fd |
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74 | |
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75 | END FUNCTION C_FTELL |
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76 | |
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77 | END INTERFACE |
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78 | |
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79 | PUBLIC posix_lseek, posix_ftell |
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80 | |
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81 | CONTAINS |
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82 | ! |
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83 | !------------------------------------------------------------------------------! |
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84 | ! Description: |
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85 | ! ------------ |
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86 | !> Interface for the C-routine lseek. |
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87 | !------------------------------------------------------------------------------! |
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88 | SUBROUTINE posix_lseek( fid, offset ) |
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89 | |
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90 | USE ISO_C_BINDING |
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91 | |
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92 | IMPLICIT NONE |
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93 | |
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94 | INTEGER,INTENT(IN) :: fid !< file unit |
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95 | INTEGER(KIND=C_SIZE_T),INTENT(IN) :: offset !< file offset from the beginning |
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96 | |
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97 | INTEGER(KIND=C_INT) :: my_fid !< file unit |
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98 | INTEGER(KIND=C_SIZE_T) :: retval !< return value |
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99 | INTEGER(KIND=C_INT) :: whence !< mode, here start from the beginning |
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100 | |
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101 | my_fid = fid |
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102 | whence = 0 |
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103 | |
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104 | retval = C_LSEEK( fid, offset, whence ) |
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105 | |
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106 | END SUBROUTINE posix_lseek |
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107 | ! |
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108 | !------------------------------------------------------------------------------! |
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109 | ! Description: |
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110 | ! ------------ |
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111 | !> Interface for the C-routine ftell. |
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112 | !------------------------------------------------------------------------------! |
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113 | SUBROUTINE posix_ftell( fid, filepos ) |
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114 | |
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115 | USE ISO_C_BINDING |
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116 | |
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117 | IMPLICIT NONE |
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118 | |
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119 | INTEGER,INTENT(IN) :: fid !< file unit |
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120 | INTEGER(KIND=C_SIZE_T), INTENT(INOUT) :: filepos !< file position |
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121 | |
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122 | filepos = C_FTELL( fid ) |
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123 | |
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124 | END SUBROUTINE posix_ftell |
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125 | |
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126 | END MODULE posix_interface |
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127 | ! |
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128 | !------------------------------------------------------------------------------! |
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129 | ! Description: |
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130 | ! ------------ |
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131 | !> This routine combines surface output from PALM-subdomains into one file. |
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132 | !> Output from every processor element is opened and read and output |
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133 | !> from all processor elements are written into one file for each timestep |
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134 | !> according to Paraview's VTK standard. |
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135 | !> Output is distinguished between instantaneous and time-averaged data. |
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136 | !------------------------------------------------------------------------------! |
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137 | PROGRAM surface_output_to_vtk |
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138 | |
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139 | USE, INTRINSIC :: ISO_C_BINDING |
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140 | |
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141 | USE posix_interface, & |
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142 | ONLY: posix_ftell, posix_lseek |
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143 | |
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144 | IMPLICIT NONE |
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145 | |
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146 | CHARACTER(LEN=4) :: char_time !< string indicating simulated time |
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147 | CHARACTER(LEN=4) :: file_suffix = '.bin' !< string which contain the suffix indicating surface data |
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148 | |
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149 | CHARACTER(LEN=10) :: char_dum !< dummy string |
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150 | |
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151 | CHARACTER(LEN=30) :: myid_char !< combined string indicating binary file |
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152 | |
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153 | CHARACTER(LEN=100) :: path !< path to the binary data |
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154 | CHARACTER(LEN=100) :: run !< name of the run |
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155 | CHARACTER(LEN=100) :: variable_name !< name of the processed output variable |
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156 | |
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157 | INTEGER, PARAMETER :: iwp = 4 !< integer precision |
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158 | INTEGER, PARAMETER :: wp = 8 !< float precision |
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159 | INTEGER, PARAMETER :: OFFSET_KIND = C_SIZE_T !< unsigned integer for the C-interface |
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160 | |
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161 | INTEGER(iwp) :: cycle_number !< cycle number |
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162 | INTEGER(iwp) :: f !< running index over all binary files |
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163 | INTEGER(iwp) :: file_id_in = 18 !< file unit for input binaray file |
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164 | INTEGER(iwp) :: file_id_out = 20 !< file unit for output VTK file |
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165 | INTEGER(iwp) :: file_id_out_header = 19 !< file unit for temporary header file |
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166 | INTEGER(iwp) :: length !< length of string on file |
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167 | INTEGER(iwp) :: n !< running index over all points and polygons |
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168 | INTEGER(iwp) :: npoints_total !< total number of points |
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169 | INTEGER(iwp) :: ns_total !< total number of polygons |
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170 | INTEGER(iwp) :: num_pe !< number of processors of the run |
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171 | |
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172 | INTEGER(OFFSET_KIND),DIMENSION(:), ALLOCATABLE :: filepos !< current fileposition in binary file |
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173 | |
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174 | INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: npoints !< number of points/vertices in a binaray file |
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175 | INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ns !< number of surface elements in a binaray file |
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176 | |
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177 | LOGICAL :: convert_average_data = .FALSE. !< namelist parameter to decide whether average or instantaneous data should be converted |
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178 | LOGICAL, DIMENSION(:), ALLOCATABLE :: eof !< flag indicating that end of binary file is reached |
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179 | |
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180 | REAL(wp) :: simulated_time !< output time |
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181 | |
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182 | REAL(wp), DIMENSION(:), ALLOCATABLE :: var !< actual surface data |
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183 | |
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184 | REAL(wp), DIMENSION(:,:), ALLOCATABLE :: points !< point / vertex data |
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185 | REAL(wp), DIMENSION(:,:), ALLOCATABLE :: polygons !< polygon data |
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186 | |
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187 | logical :: flag |
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188 | |
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189 | ! |
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190 | !-- Read namelist. |
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191 | CALL surface_output_parin |
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192 | ! |
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193 | !-- Allocate array which contains the file position in each output file, |
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194 | !-- in order to skip some reading. |
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195 | ALLOCATE( eof( 0:num_pe-1 ) ) |
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196 | ALLOCATE( filepos( 0:num_pe-1 ) ) |
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197 | ALLOCATE( npoints( 0:num_pe-1 ) ) |
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198 | ALLOCATE( ns( 0:num_pe-1 ) ) |
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199 | ! |
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200 | !-- Initialize file position. |
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201 | filepos = 0 |
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202 | ! |
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203 | !-- Open a temporary file which contains all necessary header information for the |
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204 | !-- VTK format. |
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205 | OPEN ( file_id_out_header, FILE = 'HEADER', STATUS = 'REPLACE', & |
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206 | FORM = 'FORMATTED' ) |
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207 | ! |
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208 | !-- READ grid setup, i.e. the number and position of vertices and surface elements |
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209 | !-- and merge all this information into one file. Further, create all the required |
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210 | !-- header information of the VTK file. |
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211 | !-- Note, PARAVIEW expects one VTK file for each variable and each timestep. |
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212 | !-- Hence, header information needs to be duplicated multiple times, which will be |
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213 | !-- be done later in a bash script. |
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214 | !-- Moreover, Paraview expects consecutive vertex and polygon data, which are |
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215 | !-- all distributed over the binaray files. Hence, first read vertex data from |
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216 | !-- binary file, write this to the HEADER file, close the binary file and read |
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217 | !-- data from the next binary file and so on. This requires several openenings |
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218 | !-- and closings of the binary files and temporarily storage of the |
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219 | !-- file-positions. |
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220 | DO f = 0, num_pe - 1 |
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221 | ! |
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222 | !-- Create filename of the treated binary file. |
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223 | CALL surface_output_create_file_string |
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224 | ! |
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225 | !-- Open file with surface output for processor f. |
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226 | OPEN ( file_id_in, FILE = TRIM( path ) // TRIM( run ) // & |
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227 | TRIM( myid_char ), FORM = 'UNFORMATTED' ) |
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228 | ! |
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229 | !-- Read number of vertices / points and surface elements |
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230 | READ ( file_id_in ) npoints(f) |
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231 | READ ( file_id_in ) npoints_total |
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232 | READ ( file_id_in ) ns(f) |
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233 | READ ( file_id_in ) ns_total |
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234 | |
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235 | ! |
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236 | !-- Allocate arrays where all the surfaces and vertices will be stored. |
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237 | ALLOCATE( points(3,1:npoints(f)) ) |
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238 | |
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239 | ! |
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240 | !-- Read polygon data and store them in a temporary file. |
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241 | READ ( file_id_in ) points |
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242 | ! |
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243 | !-- Obtain current file position. Will be stored for next file opening. |
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244 | CALL posix_ftell( file_id_in, filepos(f) ) |
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245 | ! |
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246 | !-- Write header information. Only one time required. |
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247 | IF ( f == 0 ) THEN |
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248 | WRITE( file_id_out_header,'(A)' ) "# vtk DataFile Version 3.0" |
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249 | WRITE( file_id_out_header,'(A,F8.2,A)' ) "legacy vtk File generated by PALM, simulation time = xxx sec" |
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250 | WRITE( file_id_out_header,'(A)') "ASCII" |
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251 | |
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252 | WRITE( file_id_out_header,'(A)') "DATASET POLYDATA" |
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253 | WRITE( file_id_out_header,'(A,I5,A)') "POINTS ", npoints_total, " float" |
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254 | ENDIF |
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255 | ! |
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256 | !-- Write the vertex data into header file. |
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257 | DO n = 1, npoints(f) |
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258 | WRITE( file_id_out_header, '(8F10.1)' ) points(1:3,n) |
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259 | ENDDO |
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260 | ! |
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261 | !-- Deallocate vertex data and close binary file. |
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262 | DEALLOCATE( points ) |
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263 | |
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264 | CLOSE ( file_id_in ) |
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265 | ENDDO |
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266 | ! |
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267 | !-- Now, treat polygon data. |
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268 | DO f = 0, num_pe - 1 |
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269 | ! |
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270 | !-- Create filename of the treated binary file . |
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271 | CALL surface_output_create_file_string |
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272 | ! |
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273 | !-- Open file with surface output for processor f. |
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274 | OPEN ( file_id_in, FILE = TRIM( path ) // TRIM( run ) // & |
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275 | TRIM( myid_char ), FORM = 'UNFORMATTED' ) |
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276 | ! |
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277 | !-- Move to last postion. |
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278 | CALL posix_lseek( file_id_in, filepos(f) ) |
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279 | ! |
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280 | !-- Allocate array for polygon data |
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281 | ALLOCATE( polygons(5,1:ns(f)) ) |
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282 | ! |
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283 | !-- Read polygon data and store them in a temporary file. |
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284 | READ ( file_id_in ) polygons |
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285 | ! |
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286 | !-- Obtain current file position after reading the local polygon data. |
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287 | !-- Will be used for next file opening. |
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288 | CALL posix_ftell( file_id_in, filepos(f) ) |
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289 | ! |
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290 | !-- Write further header information. Only one time required. |
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291 | IF ( f == 0 ) & |
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292 | WRITE ( file_id_out_header, '(A,8I10)') "POLYGONS ", & |
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293 | ns_total, 5 * ns_total |
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294 | ! |
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295 | !-- Write the polygons into the header file. Note, polygon data is of type |
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296 | !-- integer, as it just connects the point-indices which describe the given |
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297 | !-- surface element. |
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298 | DO n = 1, ns(f) |
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299 | WRITE ( file_id_out_header, '(8I10)' ) INT( polygons(1:5,n) ) |
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300 | ENDDO |
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301 | ! |
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302 | !-- Deallocate array for polygon data and close the file. |
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303 | DEALLOCATE( polygons ) |
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304 | |
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305 | CLOSE ( file_id_in ) |
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306 | |
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307 | ENDDO |
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308 | |
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309 | f = 0 |
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310 | CALL surface_output_create_file_string |
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311 | ! |
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312 | !-- Write further header information. Only once required. |
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313 | WRITE ( file_id_out_header, '(A,I10)') "CELL_DATA ", ns_total |
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314 | WRITE ( file_id_out_header, '(A,I10)') "SCALARS cell_scalars float 1 " |
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315 | WRITE ( file_id_out_header, '(A,I10)') "LOOKUP_TABLE default " |
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316 | ! |
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317 | !-- Header creation has now been completed. File can be closed. |
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318 | CLOSE( file_id_out_header ) |
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319 | ! |
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320 | !-- Now, read all the actual data from the surface output. Please note, Paraview |
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321 | !-- VTK format expects 1 file per variable and time step. |
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322 | !-- The output file is only created once and includes the variable and the |
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323 | !-- simulated time. |
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324 | !-- In the binaray files, several variables and timesteps are stored, data for a |
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325 | !-- given variable, however, is distributed over all binary files. Hence, read |
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326 | !-- variable data for a given timestep from the binary file, write this data into |
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327 | !-- the target output file, remember file position in binary file and close it, |
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328 | !-- open nex binary file and read the variable, and so on, until all variables |
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329 | !-- for all timesteps are processed. |
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330 | eof = .FALSE. |
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331 | DO |
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332 | DO f = 0, num_pe - 1 |
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333 | ! |
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334 | !-- Clean up strings- |
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335 | char_time = '' |
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336 | variable_name = '' |
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337 | ! |
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338 | !-- Create filename of the treated binary file. |
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339 | CALL surface_output_create_file_string |
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340 | ! |
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341 | !-- Open binary file with surface output for processor f. |
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342 | OPEN ( file_id_in, FILE = TRIM( path ) // TRIM( run ) // & |
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343 | TRIM( myid_char ), FORM = 'UNFORMATTED' ) |
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344 | ! |
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345 | !-- Move to last postion. |
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346 | ! ndum = fseek( file_id_in, filepos(f), 0 ) |
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347 | CALL posix_lseek( file_id_in, filepos(f) ) |
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348 | ! CALL FSEEK( file_id_in, filepos(f), 0, ndum ) |
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349 | ! |
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350 | !-- Read string length and string indicating the output time step. |
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351 | READ ( file_id_in ) length |
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352 | READ ( file_id_in ) char_time(1:length) |
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353 | ! |
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354 | !-- If string for the output time indicates the end-of-file, set the eof |
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355 | !-- flag and skip the read of the loop. |
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356 | IF ( char_time(1:length) == 'END' ) THEN |
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357 | eof(f) = .TRUE. |
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358 | CLOSE ( file_id_in ) |
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359 | CYCLE |
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360 | ENDIF |
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361 | ! |
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362 | !-- Read output time, and variable name. |
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363 | READ ( file_id_in ) simulated_time |
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364 | READ ( file_id_in ) length |
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365 | READ ( file_id_in ) variable_name(1:length) |
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366 | ! |
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367 | !-- For first loop index, open the target output file. First create the |
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368 | !-- filename string. Further, copy HEADER file with the given filename |
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369 | !-- string. The header information must be given in each VTK file! |
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370 | IF ( f == 0 ) THEN |
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371 | IF ( simulated_time < 10.0_wp ) THEN |
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372 | WRITE( char_dum, '(I1)' ) INT( simulated_time ) |
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373 | ELSEIF ( simulated_time < 100.0_wp ) THEN |
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374 | WRITE( char_dum, '(I2)' ) INT( simulated_time ) |
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375 | ELSEIF ( simulated_time < 1000.0_wp ) THEN |
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376 | WRITE( char_dum, '(I3)' ) INT( simulated_time ) |
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377 | ELSEIF ( simulated_time < 10000.0_wp ) THEN |
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378 | WRITE( char_dum, '(I4)' ) INT( simulated_time ) |
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379 | ELSEIF ( simulated_time < 100000.0_wp ) THEN |
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380 | WRITE( char_dum, '(I5)' ) INT( simulated_time ) |
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381 | ELSEIF ( simulated_time < 1000000.0_wp ) THEN |
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382 | WRITE( char_dum, '(I6)' ) INT( simulated_time ) |
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383 | ELSEIF ( simulated_time < 10000000.0_wp ) THEN |
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384 | WRITE( char_dum, '(I7)' ) INT( simulated_time ) |
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385 | ELSEIF ( simulated_time < 100000000.0_wp ) THEN |
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386 | WRITE( char_dum, '(I8)' ) INT( simulated_time ) |
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387 | ELSEIF ( simulated_time < 1000000000.0_wp ) THEN |
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388 | WRITE( char_dum, '(I9)' ) INT( simulated_time ) |
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389 | ENDIF |
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390 | ! |
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391 | !-- Copy HEADER file |
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392 | CALL system('cp HEADER ' // TRIM( path ) // TRIM( char_dum ) // & |
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393 | 's_' // TRIM( variable_name ) // '.vtk') |
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394 | !-- Open VTK file. |
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395 | OPEN ( file_id_out, FILE = TRIM( path ) // TRIM( char_dum ) // & |
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396 | 's_' // TRIM( variable_name ) // '.vtk', FORM='FORMATTED', & |
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397 | POSITION = 'APPEND' ) |
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398 | ENDIF |
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399 | ! |
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400 | !-- Allocate and read array for variable data. |
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401 | ALLOCATE( var(1:ns(f)) ) |
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402 | |
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403 | READ( file_id_in ) var |
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404 | ! |
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405 | !-- Write variable data into output VTK file. |
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406 | DO n = 1, ns(f) |
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407 | WRITE( file_id_out, * ) var(n) |
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408 | ENDDO |
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409 | ! |
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410 | !-- Remember file position in binary file and close it. |
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411 | CALL posix_ftell( file_id_in, filepos(f) ) |
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412 | |
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413 | CLOSE ( file_id_in ) |
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414 | ! |
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415 | !-- Deallocate temporary array for variable data. |
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416 | DEALLOCATE( var ) |
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417 | |
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418 | ENDDO |
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419 | ! |
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420 | !-- After data for a variable for one time step is read, close the output |
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421 | !-- VTK file and go to next variable or timestep. |
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422 | CLOSE ( file_id_out ) |
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423 | ! |
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424 | !-- If all files reached the end-of-file, exit the loop. |
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425 | IF ( ALL( eof ) ) EXIT |
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426 | |
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427 | ENDDO |
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428 | ! |
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429 | !-- Finally, remove HEADER file |
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430 | CALL system( 'rm HEADER' ) |
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431 | |
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432 | CONTAINS |
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433 | |
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434 | !------------------------------------------------------------------------------! |
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435 | ! Description: |
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436 | ! ------------ |
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437 | !> This subroutine read the namelist file. |
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438 | !------------------------------------------------------------------------------! |
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439 | SUBROUTINE surface_output_parin |
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440 | |
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441 | IMPLICIT NONE |
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442 | |
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443 | INTEGER(iwp) :: file_id_parin = 90 |
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444 | |
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445 | NAMELIST /surface_output/ convert_average_data, cycle_number, num_pe, & |
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446 | path, run |
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447 | |
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448 | ! |
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449 | !-- Open namelist file. |
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450 | OPEN( file_id_parin, FILE='surface_output_parin', & |
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451 | STATUS='OLD', FORM='FORMATTED') |
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452 | ! |
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453 | !-- Read namelist. |
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454 | READ ( file_id_parin, surface_output ) |
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455 | ! |
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456 | !-- Close namelist file. |
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457 | CLOSE( file_id_parin ) |
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458 | |
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459 | END SUBROUTINE surface_output_parin |
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460 | |
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461 | !------------------------------------------------------------------------------! |
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462 | ! Description: |
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463 | ! ------------ |
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464 | !> This subroutine creates the filename string of the treated binary file. |
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465 | !------------------------------------------------------------------------------! |
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466 | SUBROUTINE surface_output_create_file_string |
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467 | |
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468 | IMPLICIT NONE |
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469 | |
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470 | CHARACTER(LEN=3) :: char_av = '' |
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471 | CHARACTER(LEN=4) :: char_cycle = '' |
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472 | |
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473 | ! |
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474 | !-- Create substring for the cycle number. |
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475 | IF ( cycle_number /= 0 ) THEN |
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476 | IF ( cycle_number < 10 ) THEN |
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477 | WRITE( char_cycle, '(I1)') cycle_number |
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478 | char_cycle = '.00' // TRIM( char_cycle ) |
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479 | ELSEIF ( cycle_number < 100 ) THEN |
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480 | WRITE( char_cycle, '(I2)') cycle_number |
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481 | char_cycle = '.0' // TRIM( char_cycle ) |
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482 | ELSEIF ( cycle_number < 1000 ) THEN |
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483 | WRITE( char_cycle, '(I3)') cycle_number |
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484 | char_cycle = '.' // TRIM( char_cycle ) |
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485 | ENDIF |
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486 | ENDIF |
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487 | ! |
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488 | !-- Create substring for averaged data. |
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489 | IF ( convert_average_data ) char_av = '_av' |
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490 | ! |
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491 | !-- Create substring for the processor id and combine all substrings. |
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492 | IF ( f < 10 ) THEN |
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493 | WRITE( char_dum, '(I1)') f |
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494 | myid_char = TRIM( char_av ) // '_surf_00000' // TRIM( char_dum ) // & |
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495 | TRIM( char_cycle ) // file_suffix |
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496 | ELSEIF ( f < 100 ) THEN |
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497 | WRITE( char_dum, '(I2)') f |
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498 | myid_char = TRIM( char_av ) // '_surf_0000' // TRIM( char_dum ) // & |
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499 | TRIM( char_cycle ) // file_suffix |
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500 | ELSEIF ( f < 1000 ) THEN |
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501 | WRITE( char_dum, '(I3)') f |
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502 | myid_char = TRIM( char_av ) // '_surf_000' // TRIM( char_dum ) // & |
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503 | TRIM( char_cycle ) // file_suffix |
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504 | ELSEIF ( f < 10000 ) THEN |
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505 | WRITE( char_dum, '(I4)') f |
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506 | myid_char = TRIM( char_av ) // '_surf_00' // TRIM( char_dum ) // & |
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507 | TRIM( char_cycle ) // file_suffix |
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508 | ELSEIF ( f < 100000 ) THEN |
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509 | WRITE( char_dum, '(I5)') f |
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510 | myid_char = TRIM( char_av ) // '_surf_0' // TRIM( char_dum ) // & |
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511 | TRIM( char_cycle ) // file_suffix |
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512 | ELSEIF ( f < 1000000 ) THEN |
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513 | WRITE( char_dum, '(I6)') f |
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514 | myid_char = TRIM( char_av ) // '_surf_' // TRIM( char_dum ) // & |
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515 | TRIM( char_cycle ) // file_suffix |
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516 | ENDIF |
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517 | |
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518 | END SUBROUTINE surface_output_create_file_string |
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519 | |
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520 | END PROGRAM surface_output_to_vtk |
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521 | |
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522 | |
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523 | |
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