Merge pull request #25 from lreis2415/dev

unified coding style of python scripts

.gitignore

@@ -66,3 +66,9 @@ dist
 # ignore doxygen files
 doc/html
 doc/img/
+#nfs files on linux
+.nfs*
+
+# add nogit directory which contains personal test code
+seims/nogit
+seims/nogit/*

TODO/README.md

@@ -31,5 +31,10 @@
 ~~利用[DownloadProject](https://github.com/Crascit/DownloadProject)在CMake构建工程的时候自动克隆[GoogleTest](https://github.com/google/googletest)，并在项目编译之前自动编译，从而可供UnitTest自动构建、测试。在CMake命令后追加`-DUNITTEST=1`开启单元测试。参考[这篇博客](https://crascit.com/2015/07/25/cmake-gtest/)~~。
 目前，基于gtest/gmock的单元测试框架已经搭建好，后续写模块的过程中应当同步写单元测试代码！
 + 9.增加flood模拟方法。如openLISEM
++ 10.增加泥沙汇流模块，采用水流功率模型计算，目前需将SWAT中的4种模型集成进来：
+    + ~~Simplified Bagnold model (DONE)~~
+    + Kodatie model (for streams with bed material size ranging from silt to gravel)
+    + Molinas and Wu model (for primarily sand size particles)
+    + Yang sand and gravel model (for primarily sand and gravel size particles)
 
 

data/dianbu/data_prepare/management/areal_source_management.txt

@@ -20,6 +20,6 @@
 ##  ORGP: Organic phosphorus concentration  kg/'size'/day
 ##  CAPEX: capital expenditures  RMB/'size'
 ##  OPEX: operation expenses  RMB/'size'/year
-##  INCOME: additional incoime  RMB/'size'/year
+##  INCOME: additional income  RMB/'size'/year
 SUBSCENARIO,NAME,ARSRC,SEQUENCE,SYear,SMonth,SDay,EYear,EMonth,EDay,Q,SED,TN,NO3,NH4,ORGN,TP,SOLP,ORGP,COD,CAPEX,OPEX,INCOME
 10001,traditional,10000,0,-9999,-9999,-9999,-9999,-9999,-9999,0,0,0,0,0,0,0,0,0,0,0,0,0

data/dianbu/data_prepare/management2/BMP_scenarios.txt

@@ -1,6 +1,11 @@
 ID,NAME,BMPID,SUBSCENARIO,DISTRIBUTION,COLLECTION,LOCATION
-0,Base1,12,0,RASTER|MGT_FIELDS,plant_management,ALL
-0,Base1,12,1,RASTER|MGT_FIELDS,plant_management,ALL
+0,Base1,17,1,RASTER|MGT_FIELDS,areal_struct_management,1-2-3
+0,Base1,17,2,RASTER|MGT_FIELDS,areal_struct_management,4-5-6
+0,Base1,17,3,RASTER|MGT_FIELDS,areal_struct_management,7-8-9
+0,Base1,17,4,RASTER|MGT_FIELDS,areal_struct_management,10-11
+0,Base1,17,5,RASTER|MGT_FIELDS,areal_struct_management,12
+0,Base1,12,0,RASTER|LANDUSE,plant_management,ALL
+0,Base1,12,1,RASTER|LANDUSE,plant_management,ALL
 0,Base1,1,10001,ARRAY|point_source_distribution|10000,point_source_management,10001-10002
 0,Base1,1,20001,ARRAY|point_source_distribution|20000,point_source_management,20001-20002-20003-20004-20005-20006-20007-20008-20009-20010-20011-20012-20013-20014-20015-20016-20017-20018-20019-20020-20021-20022-20023-20024-20025-20026-20027-20028
 0,Base1,1,40001,ARRAY|point_source_distribution|40000,point_source_management,40001

data/dianbu/data_prepare/management2/areal_struct_management.txt

@@ -0,0 +1,18 @@
+## This file define areal structural BMPs parameters.
+# SUBSCENARIO: BMP unique ID
+# NAME: BMP Name
+# DESC: BMP Description
+# REFERENCE: Literature reference
+# LANDUSE: Suitable landuse ID, if not sure, please fill in 'ALL', separated by '-', such as '2-4'
+# PARAMETERS: Spatial parameters that the BMP affects, the format MUST be:
+#             NAME1:DESC1:CHANGE1:IMPACT1-NAME2:DESC2:CHANGE2:IMPACT2-...
+#             where, NAME is the parameter's ID, which will be one of the GridFS file in SPATIAL.files
+#                    DESC is the corresponding description
+#                    CHANGE is the change method, which can be VC,RC,AC. VC: replace, RC: multiply, AC: add.
+#                    IMPACT is the impact value.
+SUBSCENARIO,NAME,DESC,REFERENCE,LANDUSE,PARAMETERS
+1,fengjin,fengjin,fengjin,7-16,Interc_max:Maximum Interception Capacity:AC:1-Conductivity:Soil hydraulic conductivity:RC:3.5-USLE_C:Cover management factor:VC:0.0008-USLE_K:Soil erodibility factor:RC:0.64
+2,shengtailincao,shengtailincao,shengtailincao,4-7-16-33,Interc_max:Maximum Interception Capacity:AC:2.5-Depression:Depression storage capacity:RC:2-Conductivity:Soil hydraulic conductivity:RC:5-USLE_C:Cover management factor:VC:0.0012-USLE_K:Soil erodibility factor:RC:0.095-USLE_P:the erosion control practice factor:RC:0.8
+3,jingjilinguo,jingjilinguo,jingjilinguo,4-7-16-33,Interc_max:Maximum Interception Capacity:AC:1.5-Depression:Depression storage capacity:RC:5-Conductivity:Soil hydraulic conductivity:RC:4-USLE_C:Cover management factor:VC:0.0015-USLE_K:Soil erodibility factor:RC:0.65-USLE_P:the erosion control practice factor:RC:0.6
+4,dixiaolingaizao,dixiaolingaizao,dixiaolingaizao,7-16,Interc_max:Maximum Interception Capacity:AC:2.5-Depression:Depression storage capacity:RC:1.5-Conductivity:Soil hydraulic conductivity:RC:3.5-USLE_C:Cover management factor:VC:0.0024-USLE_K:Soil erodibility factor:RC:0.98-USLE_P:the erosion control practice factor:RC:0.8
+5,chaguoyuanpogaiti,chaguoyuanpogaiti,chaguoyuanpogaiti,4-7-16,Interc_max:Maximum Interception Capacity:AC:1-Depression:Depression storage capacity:RC:5-Conductivity:Soil hydraulic conductivity:RC:3-USLE_C:Cover management factor:VC:0.0008-USLE_K:Soil erodibility factor:RC:0.78-USLE_P:the erosion control practice factor:RC:0.3-Slope:Slope:VC:0.001

data/examples/1.preprocess/dianbu2_30m_omp_dgpm.ini

@@ -46,7 +46,8 @@ landuseFile = landuse_30m.tif
 landcoverInitFile = landcover_initial_parameters.txt
 soilSEQNFile = soil_SEQN_30m.tif
 soilSEQNText = soil_properties_lookup.txt
-mgtFieldFile = mgtfield_t100_2.tif
+
+additionalFile = {"MGT_FIELDS": "mgtfield_t100_2.tif"}
 
 [OPTIONAL_PARAMETERS]
 isTauDEMD8 = True

data/examples/1.preprocess/dianbu2_30m_omp_mac.ini

@@ -46,7 +46,8 @@ landuseFile = landuse_30m.tif
 landcoverInitFile = landcover_initial_parameters.txt
 soilSEQNFile = soil_SEQN_30m.tif
 soilSEQNText = soil_properties_lookup.txt
-mgtFieldFile = mgtfield_t100_2.tif
+
+additionalFile = {"MGT_FIELDS": "mgtfield_t100_2.tif"}
 
 [OPTIONAL_PARAMETERS]
 isTauDEMD8 = True

data/examples/1.preprocess/dianbu2_30m_omp_win.ini

@@ -46,7 +46,8 @@ landuseFile = landuse_30m.tif
 landcoverInitFile = landcover_initial_parameters.txt
 soilSEQNFile = soil_SEQN_30m.tif
 soilSEQNText = soil_properties_lookup.txt
-mgtFieldFile = mgtfield_t100_2.tif
+
+additionalFile = {"MGT_FIELDS": "mgtfield_t100_2.tif"}
 
 [OPTIONAL_PARAMETERS]
 isTauDEMD8 = True

data/examples/3.postprocess/post_dianbu2_30m_longterm_omp_zhulj_win.ini

@@ -0,0 +1,22 @@
+### ZHU LJ-Windows-T430
+[PATH]
+MODEL_DIR = C:\z_code\Hydro\SEIMS\data\dianbu\model_dianbu2_30m_demo
+ScenarioID = 0
+
+[MONGODB]
+HOSTNAME = 127.0.0.1
+PORT = 27017
+ClimateDBName = HydroClimate_dianbu2_demo
+BMPScenarioDBName = BMP_Scenario_dianbu2_30m_demo
+SpatialDBName = model_dianbu2_30m_demo
+
+[PARAMETERS]
+PLOT_SUBBASINID = 4
+PLOT_VARIABLES = Q QI QG QS CH_COD CH_TP CH_TN CH_NO3 CH_NH4 CH_ORGN SED GWNO3 PERCO_N_GW SUR_NO3_TOCH SUR_SOLP_TOCH CH_SOLP
+[OPTIONAL_PARAMETERS]
+#UTCTIME
+Time_start = 2013-01-01
+Time_end = 2013-12-31
+Resolution = 300
+[SWITCH]
+LANG_CN = False

data/examples/5.scenarios/dgpm_hosts_SCOOP

@@ -1,5 +1,5 @@
-dgpm-cluster.local 1
-dgpm-compute-1.local 2
-dgpm-compute-2.local 2
-dgpm-compute-3.local 2
+dgpm-cluster.local 1
+dgpm-compute-1.local 2
+dgpm-compute-2.local 2
+dgpm-compute-3.local 2
 dgpm-compute-4.local 2

data/examples/5.scenarios/nsgaii_dianbu2_30m_longterm_omp_dgpm.ini

@@ -1,40 +1,40 @@
-# Linux-cluster 192.168.6.55, logged in with user: zhulj
-
-[PATH]
-MODEL_DIR = /home/zhulj/SEIMS/models
-fieldFile = /home/zhulj/SEIMS/models/dianbu/data_prepare/spatial/mgtfield_t100_2.txt
-pointFile = /home/zhulj/SEIMS/models/dianbu/data_prepare/management2/point_source_distribution.txt
-pointBMPsFile = /home/zhulj/SEIMS/models/dianbu/data_prepare/management2/point_source_management.txt
-
-[NSGAII]
-GenerationsNum = 2
-PopulationSize = 4
-CrossoverRate = 0.75
-MutateRate = 0.05
-
-[MONGODB]
-HOSTNAME = 192.168.6.55
-PORT = 27017
-BMPScenarioDBName = BMP_Scenario_dianbu2_30m_longterm
-
-[SEIMS_Model]
-model_Exe = /home/zhulj/SEIMS/seims_omp_rel_x86-201611/seims_omp
-model_Workdir = /home/zhulj/SEIMS/models/dianbu/model_dianbu2_30m_longterm
-threadsNum = 4
-layeringMethod = 0
-timeStart = 2014-01-01
-timeEnd = 2014-12-31
-
-[BMPs]
-# BMPs
-bmps_farm = 0 1
-# bmps_cattle = 1 2 3 4
-bmps_cattle = 2 3
-# bmps_pig = 1 2 3 4
-bmps_pig = 2 3
-bmps_sewage = 1 2 3 4 5 6 7 8
-# BMPs cost (Index Correspond with BMPs id, e.g.)
-bmps_farm_cost = 208. 166.
-bmps_cattle_cost = 0. 15. 15. 160. 15.
-bmps_pig_cost = 0. 6. 6. 70. 6.
+# Linux-cluster 192.168.6.55, logged in with user: zhulj
+
+[PATH]
+MODEL_DIR = /home/zhulj/SEIMS/models
+fieldFile = /home/zhulj/SEIMS/models/dianbu/data_prepare/spatial/mgtfield_t100_2.txt
+pointFile = /home/zhulj/SEIMS/models/dianbu/data_prepare/management2/point_source_distribution.txt
+pointBMPsFile = /home/zhulj/SEIMS/models/dianbu/data_prepare/management2/point_source_management.txt
+
+[NSGAII]
+GenerationsNum = 2
+PopulationSize = 4
+CrossoverRate = 0.75
+MutateRate = 0.05
+
+[MONGODB]
+HOSTNAME = 192.168.6.55
+PORT = 27017
+BMPScenarioDBName = BMP_Scenario_dianbu2_30m_longterm
+
+[SEIMS_Model]
+model_Exe = /home/zhulj/SEIMS/seims_omp_rel_x86-201611/seims_omp
+model_Workdir = /home/zhulj/SEIMS/models/dianbu/model_dianbu2_30m_longterm
+threadsNum = 4
+layeringMethod = 0
+timeStart = 2014-01-01
+timeEnd = 2014-12-31
+
+[BMPs]
+# BMPs
+bmps_farm = 0 1
+# bmps_cattle = 1 2 3 4
+bmps_cattle = 2 3
+# bmps_pig = 1 2 3 4
+bmps_pig = 2 3
+bmps_sewage = 1 2 3 4 5 6 7 8
+# BMPs calculate_economy (Index Correspond with BMPs id, e.g.)
+bmps_farm_cost = 208. 166.
+bmps_cattle_cost = 0. 15. 15. 160. 15.
+bmps_pig_cost = 0. 6. 6. 70. 6.
 bmps_sewage_cost = 0. 1000. 1000. 1000. 1000. 8000.15 8000.15 8000.15 8000.15

data/examples/5.scenarios/nsgaii_dianbu2_30m_longterm_omp_gaohr_win.ini

@@ -1,43 +1,43 @@
-## GaoHR-Windows
-
-[PATH]
-MODEL_DIR = D:\GaohrWS\GithubPrj\SEIMS\model_data
-fieldFile = D:\GaohrWS\GithubPrj\SEIMS\model_data\dianbu\data_prepare\spatial\mgtfield_t100_2.txt
-pointFile = D:\GaohrWS\GithubPrj\SEIMS\model_data\dianbu\data_prepare\management2\point_source_distribution.txt
-pointBMPsFile = D:\GaohrWS\GithubPrj\SEIMS\model_data\dianbu\data_prepare\management2\point_source_management.txt
-scenariosInfo = D:\SEIMS_model\Model_data\model_dianbu2_30m_longterm\NSGAII_OUTPUT\scenarios_info.txt
-
-[NSGAII]
-GenerationsNum = 2
-PopulationSize = 4
-CrossoverRate = 0.75
-MutateRate = 0.1
-SelectRate = 0.25
-
-[MONGODB]
-HOSTNAME = 192.168.6.55
-PORT = 27017
-BMPScenarioDBName = BMP_Scenario_dianbu2_30m_longterm
-
-[SEIMS_Model]
-model_Exe = D:\SEIMS_model\SEIMS\Release\seims_omp
-model_Workdir = D:\SEIMS_model\Model_data\model_dianbu2_30m_longterm
-threadsNum = 2
-layeringMethod = 0
-timeStart = 2014-01-01
-timeEnd = 2014-12-31
-
-[BMPs]
-# BMPs
-bmps_farm = 0 1
-# bmps_cattle = 1 2 3 4
-bmps_cattle = 2 3
-# bmps_pig = 1 2 3 4
-bmps_pig = 2 3
-bmps_sewage = 1 2 3 4 5 6 7 8
-# BMPs cost (Index Correspond with BMPs id, e.g.)
-bmps_farm_cost = 208000. 166000.
-bmps_cattle_cost = 0. 15. 15. 160. 15.
-bmps_pig_cost = 0. 6. 6. 70. 6.
-bmps_sewage_cost = 0. 2000. 2000. 2000. 2000. 8000.15 8000.15 8000.15 8000.15
-
+## GaoHR-Windows
+
+[PATH]
+MODEL_DIR = D:\GaohrWS\GithubPrj\SEIMS\model_data
+fieldFile = D:\GaohrWS\GithubPrj\SEIMS\model_data\dianbu\data_prepare\spatial\mgtfield_t100_2.txt
+pointFile = D:\GaohrWS\GithubPrj\SEIMS\model_data\dianbu\data_prepare\management2\point_source_distribution.txt
+pointBMPsFile = D:\GaohrWS\GithubPrj\SEIMS\model_data\dianbu\data_prepare\management2\point_source_management.txt
+scenariosInfo = D:\SEIMS_model\Model_data\model_dianbu2_30m_longterm\NSGAII_OUTPUT\scenarios_info.txt
+
+[NSGAII]
+GenerationsNum = 2
+PopulationSize = 4
+CrossoverRate = 0.75
+MutateRate = 0.1
+SelectRate = 0.25
+
+[MONGODB]
+HOSTNAME = 192.168.6.55
+PORT = 27017
+BMPScenarioDBName = BMP_Scenario_dianbu2_30m_longterm
+
+[SEIMS_Model]
+model_Exe = D:\SEIMS_model\SEIMS\Release\seims_omp
+model_Workdir = D:\SEIMS_model\Model_data\model_dianbu2_30m_longterm
+threadsNum = 2
+layeringMethod = 0
+timeStart = 2014-01-01
+timeEnd = 2014-12-31
+
+[BMPs]
+# BMPs
+bmps_farm = 0 1
+# bmps_cattle = 1 2 3 4
+bmps_cattle = 2 3
+# bmps_pig = 1 2 3 4
+bmps_pig = 2 3
+bmps_sewage = 1 2 3 4 5 6 7 8
+# BMPs calculate_economy (Index Correspond with BMPs id, e.g.)
+bmps_farm_cost = 208000. 166000.
+bmps_cattle_cost = 0. 15. 15. 160. 15.
+bmps_pig_cost = 0. 6. 6. 70. 6.
+bmps_sewage_cost = 0. 2000. 2000. 2000. 2000. 8000.15 8000.15 8000.15 8000.15
+